Haemophilus parainfluenzae (DSM 8978, ATCC 33392, NCTC 7857)

Name: Haemophilus parainfluenzae (DSM 8978, ATCC 33392, NCTC 7857)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11707

Type strain

Strain Designation Wound

Culture col. no. DSM 8978 ATCC 33392 NCTC 7857 CCUG 12836 KCTC 15417 2 more

NCBI tax ID(s) 888828 729

Special Collections DSMZ CCUG KCTC CIP

History <- ATCC; ATCC 33392 <- NCTC; NCTC 7857 <- A.B. Rosher; <- CCUG <- R Mutters, Marburg, Germany <- NCTC <- AB Rosher, London, 1949 <- Glesson-White CIP <- 1986, NCTC <- 1949, A.B. Rosher, London, UK: strain Wound <- Glenson-White

Links

Haemophilus parainfluenzae Wound is a microaerophile bacterium that was isolated from septic finger.

microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 40475

KCTC 15417,ATCC 33392,NCTC 7857,CCUG 12836,CIP 102513,DSM 8978

@ref 20215

Last LPSN update 2026-02-09 11:20:38

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Haemophilus

Species Haemophilus parainfluenzae

Full scientific name Haemophilus parainfluenzae Rivers 1922 (Approved Lists 1980)

BacDive ID	Other strains from **Haemophilus parainfluenzae** (78)	Type strain
134897	H. parainfluenzae 732.86, CIP 102711
134899	H. parainfluenzae 722.86, CIP 102713
135145	H. parainfluenzae CIP A61
135602	H. parainfluenzae CIP 57.39
135854	H. parainfluenzae 97-86, CIP 102157
135981	H. parainfluenzae 940.85, CIP 101971
136063	H. parainfluenzae 179-86, CIP 102219
136125	H. parainfluenzae 669-86, CIP 102668
136126	H. parainfluenzae 667.86, CIP 102669
136139	H. parainfluenzae 63.87, CIP 102804
136818	H. parainfluenzae com 56, CIP 104419
137188	H. parainfluenzae CIP 101262, NCTC 10665
137242	H. parainfluenzae HK 22, CIP 103291, NCTC 11607
137770	H. parainfluenzae 525.85, CIP 101717
137795	H. parainfluenzae 1055.85, CIP 102068
137873	H. parainfluenzae 977.85, CIP 102013
137875	H. parainfluenzae 1007-85, CIP 102026
137911	H. parainfluenzae 89-96, CIP 102169
137924	H. parainfluenzae 151-86, CIP 102202
137925	H. parainfluenzae 150-86, CIP 102204
137988	H. parainfluenzae 387-86, CIP 102391
138020	H. parainfluenzae 494-86, CIP 102486
138663	H. parainfluenzae 655.84, CIP 101069
138702	H. parainfluenzae 172-86, CIP 102208
139206	H. parainfluenzae 496-85, CIP 101701
141205	H. parainfluenzae CCUG 182 A
141306	H. parainfluenzae CCUG 794
141601	H. parainfluenzae CCUG 3422
141836	H. parainfluenzae CCUG 7596
141911	H. parainfluenzae CCUG 8259
142570	H. parainfluenzae CCUG 13084
143139	H. parainfluenzae CCUG 17372, MCCM 03013
143420	H. parainfluenzae CCUG 19058, MCCM 03016
143859	H. parainfluenzae CCUG 21610
145371	H. parainfluenzae CCUG 28294
145380	H. parainfluenzae CCUG 28326
146550	H. parainfluenzae CCUG 31417
146991	H. parainfluenzae CCUG 32611
147178	H. parainfluenzae CCUG 33001
147188	H. parainfluenzae CCUG 33021
147516	H. parainfluenzae CCUG 33722
147593	H. parainfluenzae CCUG 33850
147845	H. parainfluenzae CCUG 34360
148229	H. parainfluenzae CCUG 35077
148505	H. parainfluenzae CCUG 35562
148713	H. parainfluenzae CCUG 35841
148838	H. parainfluenzae CCUG 36116, MCCM 02684
148839	H. parainfluenzae CCUG 36129, MCCM 02683, NCTC 10672
148840	H. parainfluenzae CCUG 36131, MCCM 00225
148841	H. parainfluenzae CCUG 36134, MCCM 00540
148842	H. parainfluenzae CCUG 36136, MCCM 02199
148843	H. parainfluenzae CCUG 36137, MCCM 02202
148844	H. parainfluenzae CCUG 36138, MCCM 02203
149016	H. parainfluenzae CCUG 36730
149847	H. parainfluenzae CCUG 38535
150067	H. parainfluenzae CCUG 38942
150070	H. parainfluenzae CCUG 38945
150113	H. parainfluenzae CCUG 39007
150805	H. parainfluenzae CCUG 42394
151628	H. parainfluenzae CCUG 44486
151729	H. parainfluenzae CCUG 44743
151914	H. parainfluenzae CCUG 45191
152322	H. parainfluenzae CCUG 46440
152558	H. parainfluenzae CCUG 47051
152775	H. parainfluenzae CCUG 47595
153403	H. parainfluenzae CCUG 49489
153404	H. parainfluenzae CCUG 49490
153405	H. parainfluenzae CCUG 49491
153998	H. parainfluenzae CCUG 51895
154591	H. parainfluenzae CCUG 54510
154882	H. parainfluenzae CCUG 55527
155561	H. parainfluenzae CCUG 58157
155615	H. parainfluenzae CCUG 58392
155670	H. parainfluenzae CCUG 58848
156096	H. parainfluenzae CCUG 60358
156555	H. parainfluenzae CCUG 62654
156556	H. parainfluenzae CCUG 62655
156672	H. parainfluenzae CCUG 64046

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771
67771	negative
121563	negative	rod-shaped
125439	negative		98.3
125438			93.768
125438	negative		97.082

Colony morphology

@ref	Incubation period
3450	1-2 days
121563

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3450	HAEMOPHILUS MEDIUM (DSMZ Medium 804)	Medium recipe at MediaDive	Name: HAEMOPHILUS MEDIUM (DSMZ Medium 804) Composition: Mueller-Hinton broth 21.0 g/l Yeast extract 5.0 g/l Distilled water
33555	MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and Neisseria		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
121563	CIP Medium 10	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3450	positive	growth	37
33555	positive	growth	37
45838	positive	growth	37
67771	positive	growth	37
121563	positive	growth	25-41
121563	negative	growth	15
121563	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3450	microaerophile
45838	microaerophile
67771	microaerophile
125439	obligate aerobe	98.7

Spore formation

@ref	Spore formation	Confidence
125439		98.9
125438		91.939

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68377	17634 ChEBI	D-glucose	+	builds acid from	from API NH
121563	4853 ChEBI	esculin	-	hydrolysis
121563	606565 ChEBI	hippurate	-	hydrolysis
121563	17632 ChEBI	nitrate	+	reduction
121563	16301 ChEBI	nitrite	-	reduction
68377	27897 ChEBI	tryptophan	-	energy source	from API NH

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121563	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68377	35581 ChEBI	indole		from API NH
121563	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68377	35581 ChEBI	indole	-	from API NH

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121563	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
121563	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
3450	catalase	+	1.11.1.6
121563	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
3450	cytochrome-c oxidase	+	1.9.3.1
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
121563	gamma-glutamyltransferase	-	2.3.2.2
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121563	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121563	ornithine decarboxylase	+	4.1.1.17
121563	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68377	tryptophan deaminase	-	4.1.99.1	from API NH
121563	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@ref

45838

Fatty acid	Percentage	ECL
C16:1 ω7c	37.4	15.819
C16:0	29.7	16
C14:0	18.5	14
C14:0 3OH/C16:1 ISO I	7.4	15.485
C18:2 ω6,9c/C18:0 ANTE	1.5	17.724
C18:1 ω9c	1.1	17.769
C18:1 ω7c /12t/9t	0.9	17.824
C16:1 ω7c DMA	0.8	16.288
C15:0 ISO 3OH	0.7	16.135
C18:0	0.6	18
C14:1 CIS 7 DMA	0.5	14.291
C13:0 ISO 2OH	0.4	13.814
unknown 14.503	0.4	14.503
C16:1 ω9c	0.2	15.774

Metadata FA analysis

@ref

45838

Fatty acid	Percentage	ECL
C16:1 ω7c	39.5	15.819
C16:0	26	16
C14:0	21	14
C14:0 3OH/C16:1 ISO I	9.8	15.485
C18:2 ω6,9c/C18:0 ANTE	1.3	17.724
C18:1 ω9c	1.1	17.769
C13:0 ISO 2OH	0.5	13.814
unknown 14.503	0.5	14.503
C18:0	0.4	18

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121563	-	+	-	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API NH

@ref	PEN	GLU	FRU	MAL	SAC	ODC	URE	LIP	PAL	beta GAL	ProA	GGT	IND
3450	-	+	+	+	+	+	-	-	+	-	-	-	-
3450	+	+	+	+	+	-	-	+	+	-	+	-	not determinedn.d.
3450	+	+	+	+	+	-	+/-	+	+/-	-	-	-	not determinedn.d.
3450	+	+	+	+	+	-	-	+	+	-	-	-	-
3450	+	+	+	+	+	-	-	+	+	-	+	-	-
3450	-	+	-	-	-	-	-	-	+	+	-	-	-
3450	not determinedn.d.	+	+	+	+	+	-	-	+	+	-	+	-
3450	not determinedn.d.	+	+	+	+	+	-	+/-	+	+/-	-	-	-
3450	-	+	+	+	+	+	-	-	+	+	-	-	-
3450	-	+	+	+	+	+	-	-	+	+	-	+	-
3450	+	+	+	+	+	+	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host Body-Site	#Limb	#Hand

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3450	septic finger
45838	Human wound,septic finger	London?	United Kingdom	GBR	Europe
67771	From human wound, septic finger
121563	Animal, Septic finger

Taxonmaps

69479

Global distribution of 16S sequence AY362908 (>99% sequence identity) for Haemophilus parainfluenzae subclade from Microbeatlas

Aquatic Samples	4078
Soil Samples	1672
Animal Samples	121644
Plant Samples	1461
Total Samples	128855

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3450	2	Risk group (German classification) According to TRBA 466
121563	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3119120v1 assembly for Haemophilus parainfluenzae ATCC 33392 DSM 8978	complete	GCA_031191205	888828.235	8116908403	888828	98.93
124043	ASM1612721v1 assembly for Haemophilus parainfluenzae FDAARGOS_1000	complete	GCA_016127215	729.2141	8120161293	729	98.83
66792	45473_E02 assembly for Haemophilus parainfluenzae ATCC 33392 NCTC 7857	contig	GCA_900450845	888828.150	2916268294	888828	78.6
66792	ASM74648v1 assembly for Haemophilus parainfluenzae ATCC 33392	contig	GCA_000746485	888828.6	2600255006	888828	74.12
66792	ASM19140v1 assembly for Haemophilus parainfluenzae ATCC 33392	scaffold	GCA_000191405	888828.3	651324039	888828	73.65

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Haemophilus parainfluenzae strain DSM 8978 16S ribosomal RNA gene, partial sequence	HQ012020	934	888828
20218	Haemophilus parainfluenzae ATCC 33392 16S ribosomal RNA gene, partial sequence	M75081	1483	888828
3450	Haemophilus parainfluenzae ATCC 33392 strain CCUG 12836 16S ribosomal RNA gene, partial sequence	AY362908	1362	888828
124043	Haemophilus parainfluenzae strain CIP 102513 16S ribosomal RNA gene, partial sequence.	EU083530	1505	888828
124043	Haemophilus parainfluenzae CCUG 12836 gene for 16S rRNA, partial sequence.	LC752345	585	888828
124043	Haemophilus parainfluenzae CIP 102513 gene for 16S rRNA, partial sequence.	LC752416	585	888828

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Haemophilus parainfluenzae ATCC 33392
NCBI: GCA_000191405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	no	55.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Haemophilus parainfluenzae strain FDAARGOS_1000 strain Not applicable
PATRIC: 729.2141

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.08	yes
125438	anaerobic	anaerobicⓘ	no	87.34	yes
125438	spore-forming	spore-formingⓘ	no	91.94	no
125438	aerobic	aerobicⓘ	no	87.21	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	93.77	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	Microbiological Studies on the Influence of Essential Oils from Several Origanum Species on Respiratory Pathogens.	Piasecki B, Balazs VL, Kieltyka-Dadasiewicz A, Szabo P, Kocsis B, Horvath G, Ludwiczuk A.	Molecules	10.3390/molecules28073044	2023
	Glycoengineering with neuraminic acid analogs to label lipooligosaccharides and detect native sialyltransferase activity in gram-negative bacteria.	Alvarado-Melendez EI, de Jong H, Hartman JEM, Ong JY, Wosten MMSM, Wennekes T.	Glycobiology	10.1093/glycob/cwae071	2024
	Immortelle (Helichrysum italicum (Roth) G. Don) Essential Oil Showed Antibacterial and Biofilm Inhibitory Activity against Respiratory Tract Pathogens.	Balazs VL, Filep R, Repas F, Kerekes E, Szabo P, Kocsis B, Boszormenyi A, Krisch J, Horvath G.	Molecules	10.3390/molecules27175518	2022
Pathogenicity	Anti-Haemophilus Activity of Selected Essential Oils Detected by TLC-Direct Bioautography and Biofilm Inhibition.	Balazs VL, Horvath B, Kerekes E, Acs K, Kocsis B, Varga A, Boszormenyi A, Nagy DU, Krisch J, Szechenyi A, Horvath G.	Molecules	10.3390/molecules24183301	2019
	Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.	Bako C, Balazs VL, Kerekes E, Kocsis B, Nagy DU, Szabo P, Micalizzi G, Mondello L, Krisch J, Petho D, Horvath G.	BMC Complement Med Ther	10.1186/s12906-023-03966-1	2023
Metabolism	Potent Cas9 Inhibition in Bacterial and Human Cells by AcrIIC4 and AcrIIC5 Anti-CRISPR Proteins.	Lee J, Mir A, Edraki A, Garcia B, Amrani N, Lou HE, Gainetdinov I, Pawluk A, Ibraheim R, Gao XD, Liu P, Davidson AR, Maxwell KL, Sontheimer EJ.	mBio	10.1128/mbio.02321-18	2018
	Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections.	Roth SB, Jalava J, Ruuskanen O, Ruohola A, Nikkari S.	J Clin Microbiol	10.1128/jcm.42.9.4268-4274.2004	2004
Enzymology	Specific and rapid detection by fluorescent in situ hybridization of bacteria in clinical samples obtained from cystic fibrosis patients.	Hogardt M, Trebesius K, Geiger AM, Hornef M, Rosenecker J, Heesemann J.	J Clin Microbiol	10.1128/jcm.38.2.818-825.2000	2000
	Essential genes for Haemophilus parainfluenzae survival and biofilm growth.	de Palma TH, Powers C, McPartland MJ, Mark Welch J, Ramsey M.	mSystems	10.1128/msystems.00674-24	2024
	Anthocyanin-Rich Extract Mitigates the Contribution of the Pathobiont Genus Haemophilus in Mild-to-Moderate Ulcerative Colitis Patients.	Zobrist Y, Doulberis M, Biedermann L, Leventhal GE, Rogler G.	Microorganisms	10.3390/microorganisms12112376	2024
	Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.	Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.	Sci Rep	10.1038/s41598-024-54769-4	2024
Phylogeny	SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia.	Adzdzakiy MM, Sutarno S, Asyifa IZ, Sativa AR, Fiqri ARA, Fibriani A, Ristandi RB, Ningrum RA, Iryanto SB, Prasetyoputri A, Dharmayanthi AB, Saputra S.	J Taibah Univ Med Sci	10.1016/j.jtumed.2023.09.001	2024
	Periodontal disease is associated with increased gut colonization of pathogenic Haemophilus parainfluenzae in patients with Crohn's disease.	Sohn J, Li L, Zhang L, Genco RJ, Falkner KL, Tettelin H, Rowsam AM, Smiraglia DJ, Novak JM, Diaz PI, Sun Y, Kirkwood KL.	Cell Rep	10.1016/j.celrep.2023.112120	2023
Phylogeny	Extent of Oral-Gut Transmission of Bacterial and Fungal Microbiota in Healthy Chinese Adults.	Cheung MK, Tong SLY, Wong MCS, Chan JYK, Ip M, Hui M, Lai CKC, Ng RWY, Ho WCS, Yeung ACM, Chan PKS, Chen Z.	Microbiol Spectr	10.1128/spectrum.02814-22	2023
	Thiazolidin-4-Ones as a Promising Scaffold in the Development of Antibiofilm Agents-A Review.	Trotsko N.	Int J Mol Sci	10.3390/ijms25010325	2023
	Molecular characterization, chemical profile and biological properties of essential oils from Chamaemelum nobile (L.) flowers of Morocco: in vitro and in silico studies.	El-Assri EM, El-Assri Y, El Brahimi R, El Fadili M, Baghouz A, Abuelizz HA, Er-Rahmani S, Lahkimi A, Bouia A.	Front Chem	10.3389/fchem.2025.1539872	2025
Pathogenicity	Influence of Thiazolidine-2,4-Dione Derivatives with Azolidine or Thiosemicarbazone Moieties on Haemophilus spp. Planktonic or Biofilm-Forming Cells.	Trotsko N, Kosikowska U, Andrzejczuk S, Paneth A, Wujec M.	Molecules	10.3390/molecules24061051	2019
	Prevalence of susceptibility patterns of opportunistic bacteria in line with CLSI or EUCAST among Haemophilus parainfluenzae isolated from respiratory microbiota.	Kosikowska U, Andrzejczuk S, Grywalska E, Chwiejczak E, Winiarczyk S, Pietras-Ozga D, Stepien-Pysniak D.	Sci Rep	10.1038/s41598-020-68161-5	2020
	Mechanisms underlying interactions between two abundant oral commensal bacteria.	Perera D, McLean A, Morillo-Lopez V, Cloutier-Leblanc K, Almeida E, Cabana K, Mark Welch J, Ramsey M.	ISME J	10.1038/s41396-021-01141-3	2022
	Rapid high-throughput processing of tissue samples for microbiological diagnosis of periprosthetic joint infections using bead-beating homogenization.	Jazmati N, Liebold C, Offerhaus C, Volkenand A, Grote S, Popsel J, Korber-Irrgang B, Hoppe T, Wisplinghoff H.	J Clin Microbiol	10.1128/jcm.01486-23	2024
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	Exploring the Antibacterial Potency of Cymbopogon Essential Oils: Liposome Encapsulation and Phytochemical Insights.	Elmi A, Abdoul-Latif FM, Pasc A, Risler A, Philippot S, Gil-Ortiz R, Laurain-Mattar D, Spina R.	Antibiotics (Basel)	10.3390/antibiotics14050510	2025
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Genetics	Comparative Genome Analyses Provide Insight into the Antimicrobial Activity of Endophytic Burkholderia.	Jia J, Lu SE.	Microorganisms	10.3390/microorganisms12010100	2024
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Phylogeny	Age and sex-related variations in murine laryngeal microbiota.	An R, Venkatraman A, Binns J, Saric C, Rey FE, Thibeault SL.	PLoS One	10.1371/journal.pone.0300672	2024
	Genomic profiling of cefotaxime-resistant Haemophilus influenzae from Norway and Sweden reveals extensive expansion of virulent multidrug-resistant international clones	Skaare D, Anthonisen I, Zecic N, Jenkins A, Caugant D, Ranheim T, Sundsfjord A, Hegstad K.	Front Microbiol		2025
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Enzymology	Duplex Quantitative PCR Assay for Detection of Haemophilus influenzae That Distinguishes Fucose- and Protein D-Negative Strains.	de Gier C, Pickering JL, Richmond PC, Thornton RB, Kirkham LA.	J Clin Microbiol	10.1128/jcm.00982-16	2016
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Genetics	Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016.	Sommerstein R, Fuhrer U, Lo Priore E, Casanova C, Meinel DM, Seth-Smith HM, Kronenberg A, Anresis, Koch D, Senn L, Widmer AF, Egli A, Marschall J, Swissnoso.	Euro Surveill	10.2807/1560-7917.es.2017.22.49.17-00213	2017
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Enzymology	Selective microbial genomic DNA isolation using restriction endonucleases.	Barnes HE, Liu G, Weston CQ, King P, Pham LK, Waltz S, Helzer KT, Day L, Sphar D, Yamamoto RT, Forsyth RA.	PLoS One	10.1371/journal.pone.0109061	2014
Enzymology	Microbiological evaluation of the new VITEK 2 Neisseria-Haemophilus identification card.	Valenza G, Ruoff C, Vogel U, Frosch M, Abele-Horn M.	J Clin Microbiol	10.1128/jcm.00953-07	2007
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Phylogeny	Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species.	Suttisunhakul V, Pumpuang A, Ekchariyawat P, Wuthiekanun V, Elrod MG, Turner P, Currie BJ, Phetsouvanh R, Dance DA, Limmathurotsakul D, Peacock SJ, Chantratita N.	PLoS One	10.1371/journal.pone.0175294	2017
Metabolism	Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes.	Sun Y, Wang M, Wang Q, Cao B, He X, Li K, Feng L, Wang L.	Appl Environ Microbiol	10.1128/aem.07825-11	2012
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Enzymology	pH gradient and distribution of streptococci, lactobacilli, prevotellae, and fusobacteria in carious dentine.	Kianoush N, Nguyen KA, Browne GV, Simonian M, Hunter N.	Clin Oral Investig	10.1007/s00784-013-1009-0	2014
	The Bioeffects Resulting from Prokaryotic Cells and Yeast Being Exposed to an 18 GHz Electromagnetic Field.	Nguyen TH, Pham VT, Nguyen SH, Baulin V, Croft RJ, Phillips B, Crawford RJ, Ivanova EP.	PLoS One	10.1371/journal.pone.0158135	2016
Phylogeny	Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities.	Kent AD, Smith DJ, Benson BJ, Triplett EW.	Appl Environ Microbiol	10.1128/aem.69.11.6768-6776.2003	2003
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Phylogeny	Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing.	Karger A, Stock R, Ziller M, Elschner MC, Bettin B, Melzer F, Maier T, Kostrzewa M, Scholz HC, Neubauer H, Tomaso H.	BMC Microbiol	10.1186/1471-2180-12-229	2012
	Chemical composition and in vitro evaluation of the antioxidant and antimicrobial activities of Eucalyptus gillii essential oil and extracts.	Ben Hassine D, Abderrabba M, Yvon Y, Lebrihi A, Mathieu F, Couderc F, Bouajila J.	Molecules	10.3390/molecules17089540	2012
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	"Emergence of a CTX-M-15-producing multidrug-resistance Haemophilus parainfluenzae in Southern Spain".	Perez-Vazquez M, Perez-Carrasco V, Aguilera-Franco M, Lara N, Rivero-Rodriguez M, Navarro-Mari JM, Gutierrez-Fernandez J.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-025-05287-2	2025
	A Rare Case of Rapidly Progressive Haemophilus Parainfluenzae Endocarditis With Cerebral Emboli.	Orta Z, Kir MH, Ala Selek S, Benli A, Simsek Yavuz S.	Cureus	10.7759/cureus.85347	2025
	Rising Prevalence of Nontypeable Haemophilus influenzae and Haemophilus parainfluenzae in People With Primary Ciliary Dyskinesia: A Single-center Experience.	Bar-On O, Suryadinata R, Suryadinata R, Tannenbaum EL, Robinson P.	Pediatr Infect Dis J	10.1097/inf.0000000000004901	2025
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Phylogeny	The site-specific subgingival microbiome across periodontal conditions and its relationship with clinical parameters.	Chen K, Ren X, Du R, Lei L, Cheng R, Hu T.	Clin Oral Investig	10.1007/s00784-025-06625-6	2025
	Molecular detection and clinical relevance of Haemophilus spp. in male urethritis: Prevalence and risk factors.	Mar-Herrera O, Llaca-Diaz J, Flores-Arechiga A, Casillas-Vega N.	Actas Urol Esp (Engl Ed)	10.1016/j.acuroe.2025.501790	2025
	Recommendation of antibiotic prophylaxis in orthognathic surgery according to current microbial resistance, a retrospective analysis of 100 operated cases.	Sole P, Tapia P, Mordoh S, Carvajal M, Matus-Miranda G, Ossandon-Zuniga B.	Med Oral Patol Oral Cir Bucal	10.4317/medoral.27519	2025
	Deciphering the Role of VIM, STX8, and MIF in Pneumoconiosis Susceptibility: A Mendelian Randomization Analysis of the Lung-Gut Axis and Multi-Omics Insights from European and East Asian Populations.	Zhang CW, Wan BB, Zhang YK, Xiong T, Li YS, Su XS, Liu G, Wei YY, Sun YY, Zhang JF, Yu X, Shi YW.	Biomed Environ Sci	10.3967/bes2025.028	2025
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Phylogeny	Longitudinal Profiling of the Human Milk Microbiome from Birth to 12 Months Reveals Overall Stability and Selective Taxa-Level Variation.	Xu R, Gridneva Z, Payne MS, Nicol MP, Cheema AS, Geddes DT, Stinson LF.	Microorganisms	10.3390/microorganisms13081830	2025
	Tonsil-induced autoimmune/inflammatory syndrome: Current insights into the pathogenic role of tonsils in immunoglobulin A nephropathy, palmoplantar pustulosis and psoriasis.	Harabuchi Y.	Auris Nasus Larynx	10.1016/j.anl.2025.06.004	2025
	A rare case of Haemophilus parainfluenzae periprosthetic joint infection: A case report with literature review.	Cheong T, Moo IH.	Int J Surg Case Rep	10.1016/j.ijscr.2025.111380	2025
	Gut and oral microbial profile associations to oral cancer.	Nayyar J, Bedu-Ferrari C, Patangia D, Hurley E, Feeley L, Ross RP, Stanton C, Brady P.	J Dent	10.1016/j.jdent.2025.105848	2025
	Dynamic changes of dental plaque and saliva microbiota in OSCC progression.	Zhang M, Zhang H, Hong A, Huang J, Yang L, Long Y, Yu Z.	Clin Oral Investig	10.1007/s00784-025-06391-5	2025
	Exploring the plausible genetic relationship of salivary and tongue microbiome with periodontitis: A mendelian randomization study.	Li J, Wang S, Luo P, Li Z, Gopinath D.	Saudi Dent J	10.1007/s44445-025-00087-y	2025
	Epidemiological Insights into HACEK Bacteria: A Seven-year Retrospective Analysis at a Tertiary Care Center in Istanbul.	Dundar T, Habip Z, Kocoglu ME, Ozekinci T.	Medeni Med J	10.4274/mmj.galenos.2025.69327	2025
	Characteristics of Pathogens of Acute Exacerbation of Chronic Obstructive Pulmonary Disease Hospitalized Patients: A Retrospective Study From 2010 to 2020.	Yu S, Yang T.	Pulm Med	10.1155/pm/4025205	2025
Genetics	Molecular characterization of macrolide resistance in Haemophilus influenzae and Haemophilus parainfluenzae strains (2018-21).	Cadenas-Jimenez I, Saiz-Escobedo L, Carrera-Salinas A, Camprubi-Marquez X, Calvo-Silveria S, Camps-Massa P, Berbel D, Tubau F, Santos S, Dominguez MA, Gonzalez-Diaz A, Ardanuy C, Marti S.	J Antimicrob Chemother	10.1093/jac/dkae214	2024
	Alterations of gut microbiome in chronic rhinosinusitis: insights from a mendelian randomization study.	Wang KS, Tu JH, Wang QX, Zhou SZ, Wu JR, Qiu QH.	Braz J Otorhinolaryngol	10.1016/j.bjorl.2025.101698	2025
	Haemophilus parainfluenzae infective endocarditis complicated by multiorgan septic emboli.	Bowden J, Hunt M, Harhay J, Patel T, Thomas-Gosain N.	BMJ Case Rep	10.1136/bcr-2023-256308	2024
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Genetics	A novel capsular operon and potentially conjugative plasmids in extensively drug-resistant urogenital Haemophilus parainfluenzae.	Saiz-Escobedo L, Ballestero-Tellez M, Rajadell M, Garreta-Esteban M, Gisbert L, Cadenas-Jimenez I, Costa RM, Tubau F, Sanchez-Ramos D, Dominguez MA, Xanthopoulou K, Higgins PG, Ardanuy C, Gonzalez-Diaz A, Marti S.	Front Microbiol	10.3389/fmicb.2025.1659538	2025
Genetics	Antimicrobial efficacy and amino acid substitutions associated with susceptibility to the tellurium compound AS101 against Haemophilus influenzae and Haemophilus parainfluenzae.	Ho CH, Yang TY, Tseng SP, Su PY.	Int Microbiol	10.1007/s10123-024-00558-y	2025
	Intestinal Absorption Characteristics and Reciprocal Interactions of Forsythiae Fructus and Lonicerae Japonicae Flos-Containing Chinese Herbal Formulation with Human Gut Microbiome.	He JY, Xiao FL, Zheng QY, Wang CH, Tang YY, Fu JX, Huang JY, Zhou LD, Zhang QH.	Am J Chin Med	10.1142/s0192415x25500211	2025
	Oral microbial alterations by smoking and metabolic factors in esophageal squamous cell carcinoma.	Jung K, Joo M, Nam K, Cho JH, Cho YS, Nam S, Nam SY.	J Gastrointest Oncol	10.21037/jgo-2025-432	2025
	Association between sphingomyelin levels and gut microbiota abundance in Alzheimer's disease: a two-sample Mendelian randomization study.	Wang L, Ding Y, Tang Y, Yang M, Yang Z, Yang X, Xia J.	BMC Neurol	10.1186/s12883-025-04207-3	2025
	Incidence and Outcomes of Infectious Keratitis After Corneal Collagen Cross-Linking Over 10 Years From a Tertiary Care Center in South India.	Lakshmipathy M, Deepak MH, Agarwal S, Narayanan N, Rajagopal R, Sudhir RR, Anand AR.	Cornea	10.1097/ico.0000000000003732	2024
Transcriptome	deepBreaks identifies and prioritizes genotype-phenotype associations using machine learning.	Baghbanzadeh M, Dawson T, Sayoldin B, Frazer SA, Oakley TH, Crandall KA, Rahnavard A.	Sci Rep	10.1038/s41598-025-25580-6	2025
	Uncommon presentation of Haemophilus parainfluenzae bacteremia: A case study on aortic valve endocarditis.	Dhapa N, Rodriguez H, Visinoni Z, Misra N, Lingam D.	SAGE Open Med Case Rep	10.1177/2050313x241306239	2024
Phylogeny	Isolation and Epidemiology of Respiratory Bacteria From Unusual Sites: Demographic, Seasonal, and Geographic Distribution in a Laboratory-Based Study From a Tertiary Care Hospital in Karachi, Pakistan.	Zehra SR, Khan SM, Mehmood S, Farooqi J, Jabeen K.	Cureus	10.7759/cureus.80213	2025
	Identification of a novel beta-1,4-galactosyltransferase from Haemophilus parainfluenzae for efficient biosynthesis of lacto-N-neotetraose in Escherichia coli.	Liu D, Ying C, Ping Y, Liang S, Yan Q, Jiang Z.	Synth Syst Biotechnol	10.1016/j.synbio.2025.09.006	2026
	Dislocation and two-stage septic complications after buttock augmentation with polyamide filler: A case report.	Diete S, Mille M, Schreiber M.	JPRAS Open	10.1016/j.jpra.2025.08.014	2025
	Detection of CTX-M-15 ESBL in XDR Haemophilus parainfluenzae from a urethral swab.	Camelena F, Merimeche M, Liberge M, Maubaret C, Donay JL, Taha MK, Fouere S, Bercot B.	J Antimicrob Chemother	10.1093/jac/dkad408	2024
	Exploring the role of gut microbiota in rheumatoid arthritis: the effects of diet and drug supplementation.	Genc DE, Ozbek O, Ulgen KO.	BMC Rheumatol	10.1186/s41927-025-00541-8	2025
Enzymology	A multiplex microbial profiling system for the identification of the source of body fluid and skin samples.	Yao H, Wang Y, Wang S, Sun C, Zhou Y, Jiang L, Wang Z, Wang X, Zhang Z, Yang T, Song F, Luo H.	Forensic Sci Int Genet	10.1016/j.fsigen.2024.103124	2024
Phylogeny	Revealing microbial community characteristics in healthy human, cat and canine salivas and looking for species-specific microbes.	Mei S, Cai M, Lei F, Wang X, Yuan X, Lin Y, Zhu B.	Int J Legal Med	10.1007/s00414-024-03277-1	2024
	Application value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid in pathogen detection and diagnostic efficiency of acute exacerbation of bronchiectasis.	He Z, Kong J, Su Q, Lin J.	Am J Transl Res	10.62347/wolq1347	2025
	Culture-Negative Transcatheter Pulmonary Valve Endocarditis.	Odukwe C, Abdelrahman A, Zaidi AN, Love B, El-Hamamsy I, Ghesani M, Hopkins KA.	JACC Case Rep	10.1016/j.jaccas.2025.105324	2025
	Distinct trajectory of gut microbiota driven by a human oral commensal: insights from a murine study.	Lin WT, Lee SP, Li C, Chang CB, Chien HC, Wang JT, Hsieh SC, Wu SF, Tseng YC.	J Oral Microbiol	10.1080/20002297.2025.2569524	2025
	Detection of bla_CTX-M-15 in an integrative and conjugative element in four extensively drug-resistant Haemophilus parainfluenzae strains causing urethritis.	Saiz-Escobedo L, Cadenas-Jimenez I, Olmos R, Carrera-Salinas A, Berbel D, Camara J, Tubau F, Dominguez MA, Ardanuy C, Gonzalez-Diaz A, Marti S.	Int J Antimicrob Agents	10.1016/j.ijantimicag.2023.106991	2023
	[Assessment of species diversity of anaerobic intestinal microbiota in children and adolescents with exogenous constitutional obesity].	Migacheva NB, Skvortsova OV, Lyamin AV, Alekseev DV, Kayumov KA, Antipov VA.	Vopr Pitan	10.33029/0042-8833-2024-93-3-14-22	2024
	Septic Arthritis Caused by Haemophilus parainfluenzae : A Pediatric Case Report and Literature Review.	Fukayama H, Myojin S, Funaki T, Fukuda Y, Nakamura T, Ishiguro A, Ogimi C.	Pediatr Infect Dis J	10.1097/inf.0000000000003979	2023
	Chemical compositions of Eucalyptus sp. Essential oils and the evaluation of their combinations as a promising treatment against ear bacterial infections.	Ameur E, Sarra M, Yosra D, Mariem K, Nabil A, Ibrahim J, Alarjani KM, Lynen F, Larbi KM.	BMC Complement Med Ther	10.1186/s12906-024-04494-2	2024
	It's Never Too Late: A Case of Cystic Fibrosis Diagnosed at the Age of 58.	Di Giorgi F, De Francesco M, Catone A, Lomi M.	Cureus	10.7759/cureus.92472	2025
	Infections Combined With Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disease: A Case Report and Systematic Review of the Literature.	Xiang H, Cai M.	Cureus	10.7759/cureus.71229	2024
	Maternal dietary intervention during lactation impacts the maternal faecal and human milk microbiota.	Sindi AS, Stinson LF, Gridneva Z, Leghi GE, Netting MJ, Wlodek ME, Muhlhausler BS, Rea A, Trevenen ML, Geddes DT, Payne MS.	J Appl Microbiol	10.1093/jambio/lxae024	2024
	Whole-genome sequence of Haemophilus parainfluenzae EL1 isolated from healthy supragingival plaque.	de Palma TH, Loomis E, Perera D, Ramsey M.	Microbiol Resour Announc	10.1128/mra.00476-23	2023
	Focus on studying the effects of different exposure durations on the microbial structures and characteristics of three types of body fluids.	Mei S, Wang X, Lei F, Lan Q, Cai M, Zhu B.	Forensic Sci Int	10.1016/j.forsciint.2024.111949	2024
	7-Year (2015-21) longitudinal surveillance of lefamulin in vitro activity against bacterial pathogens collected worldwide from patients with respiratory tract infections including pneumonia and characterization of resistance mechanisms.	Paukner S, Mendes RE, Arends SJR, Gassner G, Gelone SP, Sader HS.	J Antimicrob Chemother	10.1093/jac/dkad389	2024
Genetics	Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.	Tynior W, Klosek M, Salatino S, Cuber P, Hudy D, Nalecz D, Chan YT, Gustave C, Strzelczyk JK.	Int J Mol Sci	10.3390/ijms252313143	2024
	A human oral commensal-mediated protection against Sjögren's syndrome with maintenance of T cell immune homeostasis and improved oral microbiota.	Tseng YC, Liao KS, Lin WT, Li C, Chang CB, Hsu JW, Chan CP, Chen CM, Wang HP, Chien HC, Wang JT, Hsieh SC, Wu SF.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00654-5	2025
	Application of metagenomic next-generation sequencing in the diagnosis and treatment of acute pneumonia caused by Tropheryma whipplei.	Huo Y, Wu C, Ma D.	BMC Pulm Med	10.1186/s12890-025-03657-2	2025
	Neisseria species on the tonsillar surface predicts favorable clinical outcomes in patients with Immunoglobulin A nephropathy who underwent tonsillectomy.	Sato R, Inoue T, Wakisaka R, Kono M, Yamaki H, Ohara K, Kumai T, Kishibe K, Nakagawa N, Takahara M.	Ren Fail	10.1080/0886022x.2025.2550617	2025
	Pancytopenia Unraveled: Tracing Rare Cardiobacterium hominis Bacteremia Back to the Gut.	Kleynerman A, Day RC, Honkanen I.	Cureus	10.7759/cureus.86358	2025
	An unusual presentation of subacute Haemophilus parainfluenzae endocarditis in a low-risk woman treated by minimally invasive mitral valve repair: a case report.	Qamar Y, Shazly A, Qamar A, Islam H, Yonis H, Sabry H.	Egypt Heart J	10.1186/s43044-024-00482-6	2024
	Metagenomic sequencing for identification of nontuberculous mycobacteria and other pathogens in patients with mixed infection of the lung	Yu J, Lv X, Wang Q, Gao M, Li W.	Front Cell Infect Microbiol		2025
	Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.	Otani K, Nakatsu G, Fujimoto K, Miyaoka D, Sato N, Nadatani Y, Nishida Y, Maruyama H, Ominami M, Fukunaga S, Hosomi S, Tanaka F, Imoto S, Uematsu S, Watanabe T, Fujiwara Y.	J Gastroenterol	10.1007/s00535-025-02298-w	2025
	Exploring Competitive Relationship Between Haemophilus parainfluenzae and Mitis Streptococci via Co-Culture-Based Molecular Diagnosis and Metabolomic Assay.	Choi Y, Jeong J, Han Y, Han M, Yu B, Han K.	Microorganisms	10.3390/microorganisms13020279	2025
	Analysis of microbiological profiles of Indian patients with peri-implantitis and periodontitis.	B Mangalekar S, Sultana M, Mulay A, Vaddalapu H, P Newaskar D, Bacha S, V Manek P, Desai P.	Bioinformation	10.6026/973206300200615	2024
	Methodology and application of multiplex PCR-dipstick DNA chromatography for the detection of eight respiratory bacterial pathogens.	Hu L, Wang X, Li Q.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1558612	2025
	Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.	Ashton PM, Mageiros L, Meiring JE, Chunga-Chirambo A, Khanam F, Dongol S, Banda H, Karkey A, Preciado-Llanes L, Thomaides-Brears H, Gibani M, Rajib NH, Rahman N, Biswas PK, Bhuiyan MAI, Kay S, Auger K, Seret O, Thomson NR, Pollard AJ, Baker S, Basnyat B, Clemens JD, Dolecek C, Dunstan SJ, Dougan G, Heyderman RS, Pitzer VE, Qadri F, Gordon MA, Holt KE, Darton TC, STRATAA Study Group.	Microbiome	10.1186/s40168-025-02125-7	2025
	Oral Microbiome as a Biomarker and Therapeutic Target in Head and Neck Cancer: Current Insights and Future Directions	Ahmad S, Jayamanne D, Bergamin S, Lawless A, Guminski A, Lee A, Yuile A, Wheeler H, Eade T, Back M, Molloy M, Oh B.	Cancers (Basel)		2025
	Baseline Gut Microbiota Was Associated with Long-Term Immune Response at One Year Following Three Doses of BNT162b2.	Zhang LN, Tan JT, Ng HY, Liao YS, Zhang RQ, Chan KH, Hung IF, Lam TT, Cheung KS.	Vaccines (Basel)	10.3390/vaccines12080916	2024
	Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.	Chen J, Xu Q, Zhang L, Zhang D, Wu X.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1594460	2025
	Epidemiology and co-infection patterns of community-acquired pneumonia among children from 2015 to 2023 in Henan Province, China: longitudinal surveillance study.	Li T, Chen S, Shen Y, Li Z, Han S, Yuan Y, Zhang Y, Feng D, Jin Z, Jin Y, Wang F.	Sci Rep	10.1038/s41598-025-14685-7	2025
	Mitral Valve Repair in a 15-Month-Old Child With Kingella kingae Endocarditis.	McGee MD, Coyne SA, Contractor RN, Winburn B.	Cureus	10.7759/cureus.63670	2024
Genetics	Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study.	Yang YH, Yu JJ, Han HY, Chang WM, Wang CW.	J Dent Sci	10.1016/j.jds.2024.05.014	2025
	The Role of the Microbiome in Oropharyngeal Squamous Cell Carcinoma: A Systematic Review.	Lechien JR.	J Pers Med	10.3390/jpm15090399	2025
	Infective Endocarditis Due to Haemophilus parainfluenzae: A Case Report and Review of the Literature.	Rabinovich D, Yazigi M, Yazigi A, Zainah H.	J Brown Hosp Med	10.56305/001c.77739	2023
	Klebsiella pneumoniae detection by a light-controlled one-pot RPA-CRISPR/Cas12a method.	Pan L, Wei L, Luo S, Ren B, Li M, Liang L, Li X, Wei G.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1669860	2025
	Systemic Haemophilus parainfluenzae Infection Manifesting With Endocarditis and Membranoproliferative Glomerulonephritis.	Wajid S, Farrukh L, Rosenberg L, Faiz M, Singh G.	Cureus	10.7759/cureus.41086	2023
Genetics	A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.	Feng M, Chai Y, Li J, Wang Q, Zhang D.	Front Genet	10.3389/fgene.2025.1619911	2025
	Transcatheter Arterial Embolization for Atraumatic Splenic Rupture in TEE-negative Endocarditis: A Case Report.	High DP, Acosta-Rullan JM, Herrera D, Danckers M, Heller D, Zapata D.	Clin Pract Cases Emerg Med	10.5811/cpcem.1399	2024
	Characteristics of Pyomyositis at a Pediatric Hospital in Osaka, Japan.	Higuchi C, Otsuki D, Kobayashi M, Yamanaka A, Tamura D, Okada S, Kawabata H.	Cureus	10.7759/cureus.86325	2025
	Sialadenitis Secondary to Bilateral Hypertrophic Torus Mandibularis.	Basharat R, Bjorling A, Samara G.	Cureus	10.7759/cureus.63484	2024
	The lack of specificity of sodC-based PCR for the detection of Neisseria meningitidis carriage in pharyngeal swabs from adolescents.	Pham-Tran DD, Leong LEX, McMillan M, Lawrence A, Mohammed H, Finn A, Marshall HS.	Microbiol Spectr	10.1128/spectrum.02779-24	2025
Genetics	Meta-omics reveals subgingival plaque reconstruction dynamics.	Zhou F, Wu Y, Ren B, Liu Y, Luo K, Li Q, Huang F, Peng X, Li Y, Su Z, Li J.	J Oral Microbiol	10.1080/20002297.2025.2569528	2025
Phylogeny	Individuality and generality of intratumoral microbiome in the three most prevalent gynecological malignancies: an observational study.	Xiao Q, Chen W-j, Wu F, Zhang X-y, Li X, Wei J, Chen T-t, Liu Z-x.	Microbiol Spectr	10.1128/spectrum.01004-24	2024
Genetics	The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.	Yong Y, Zhou L, Zhang X, Ran X, Guo Y, Gai W, Chen Y.	Sci Rep	10.1038/s41598-025-91520-z	2025
	Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections.	Liang W, Zhang Q, Qian Q, Wang M, Ding Y, Zhou J, Zhu Y, Jin Y, Chen X, Kong H, Song W, Lu X, Wu X, Xu X, Dai S, Sun W.	Ann Clin Microbiol Antimicrob	10.1186/s12941-024-00670-x	2024
Phylogeny	Effects of 0.05% Cetylpyridinium Chloride Mouthwash on Halitosis and Tongue Microbiota in Patients Undergoing Orthodontic Treatment: A Double-Blind Randomized Clinical Trial.	Shiina N, Shimpo Y, Kikuchi K, Sekiya T, Tomonari H.	J Clin Med	10.3390/jcm14134576	2025
	A study of various factors affecting satellitism tests of Haemophilus influenzae and Haemophilus parainfluenzae using Staphylococcus aureus as the source of NAD.	Xi Y, Wang H, Wang S, Wu X, Wang Z.	J Microbiol Methods	10.1016/j.mimet.2022.106417	2022
Pathogenicity	Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease.	Morsy Y, Walberg A, Wawrzyniak P, Hubeli B, Truscello L, Mamie C, Niechcial A, Gueguen E, Manzini R, Gottier C, Lang S, Scharl S, Blumel S, Biedermann L, Rogler G, Turina M, Ramser M, Petrowsky H, Arnold IC, Zeissig S, Zamboni N, Egli A, Niess JH, Hruz P, Knuth A, Fritsch R, Manz MG, Wawrzyniak M, Scharl M.	Gut Microbes	10.1080/19490976.2025.2530157	2025
	Oral microbiota dysbiosis in pediatric patients undergoing treatment for acute lymphoid leukemia a preliminary study.	Souza AV, Barbosa LV, Castro AAC, Carboni EK, Watanabe FM, Rossati R, Costa LMD, Mesa D, Machado-Souza C.	Genet Mol Biol	10.1590/1678-4685-gmb-2023-0359	2025
	Septic Emboli to the Brain Secondary to a Patent Foramen Ovale: A Rare Complication of Internal Jugular Vein Catheter.	Verma N, Gupta N.	Cureus	10.7759/cureus.59419	2024
	Diagnostic and prognostic values of NSCLC patients with or without obstructive pneumonia after sleeve lobectomy.	Huang Y, Zhang L, Zhang W, Lv N, Wang T.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1474998	2024
	Salivaomics: New Frontiers in Studying the Relationship Between Periodontal Disease and Alzheimer's Disease.	Malcangi G, Marinelli G, Inchingolo AD, Trilli I, Ferrante L, Casamassima L, Nardelli P, Inchingolo F, Palermo A, Inchingolo AM, Dipalma G.	Metabolites	10.3390/metabo15060389	2025
	Roles of Gut Microbiota and Associated Metabolites in Clostridioides difficile Infection.	Gao Y, Ma J, Wang K, Ma K, Zhao W, Su J, Ma L.	Pol J Microbiol	10.33073/pjm-2025-017	2025
	Infective Endocarditis With Origin in Orbital Vascular Malformation and Maxillary Sinusitis: A Case Report and Review of Four Patients in the Literature.	Matsuo T, Iwamoto Y, Okamoto H, Iguchi D.	Cureus	10.7759/cureus.74873	2024
	Mediastinitis after endobronchial ultrasound with transbronchial needle aspiration resulting in postpneumonectomy empyema.	Robinson NL, Watkins RD, Tapias LF.	JTCVS Tech	10.1016/j.xjtc.2024.03.012	2024
Phylogeny	Time-dependent microbiome dynamics in orthodontic thermoplastic materials: comparing PETG and TPU.	Gao T, Yun J, Zheng Y, Mu C, Zhao B.	Clin Oral Investig	10.1007/s00784-025-06441-y	2025
Phylogeny	Longitudinal Profiling of the Human Milk Microbiome from Birth to 12 Months Reveals Overall Stability and Selective Taxa-Level Variation	Xu R, Gridneva Z, Payne M, Nicol M, Cheema A, Geddes D, Stinson L.	Microorganisms		2025
Genetics	Active herpesviruses are associated with intensive care unit (ICU) admission in patients pulmonary infection and alter the respiratory microbiome.	Liu Z, Qi CJ, Shi Y, Li T, Fang Y, Zhang Q.	Front Microbiol	10.3389/fmicb.2024.1441476	2024
	Enhanced dominance of nitrate-reducing bacteria using a combination of nitrate and erythritol in in vitro cultured oral biofilm.	Fujii A, Akatsu T, Souno H, Kawano S, Minegishi Y, Ota N.	J Oral Microbiol	10.1080/20002297.2025.2526069	2025
	Evaluation and comparison of microbial colonization on nickel titanium (NiTi) closed coil springs and active tie-backs during orthodontic space closure: An in-vivo study.	George G, Kumar KJ, Anjali K, Jacob SM, Manas G, Nayyar AS.	J Orthod Sci	10.4103/jos.jos_102_24	2025
Genetics	RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data.	Zhou J, Tian Y, Yang M, Hao T, Ma J, Wang S.	PeerJ	10.7717/peerj.19849	2025
	An Unusual Case of Haemophilus parainfluenzae Endocarditis in a Young Patient With Crohn's Disease.	Shah V, Berdichevskiy G, Abello V, Ijaz H, Khalid I, Rahim M, Asif M, Cusnir H.	Cureus	10.7759/cureus.33770	2023
	The association of depression and oral microbiota.	Liu F, Yang Y, Zhang N, Wang S, Wang CX.	Sci Rep	10.1038/s41598-025-26526-8	2025
	Assessment of Sexual Function in Relation to Microbiological Findings in Patients with Chronic Bacterial Prostatitis.	Magri V, Perletti G, Stamatiou K, Trinchieri A.	Diagnostics (Basel)	10.3390/diagnostics15070887	2025
	Application of metagenomic next-generation sequencing in the etiological diagnosis of refractory pneumonia in children.	Wang YN, Wu YT, Cao L, Niu WQ.	Front Microbiol	10.3389/fmicb.2024.1357372	2024
Genetics	Associations of central obesity and habitual food consumption with saliva microbiota and its enzymatic profiles - a pilot study in Finnish children.	Agrawal N, Fontana F, Tarracchini C, Lommi S, Ventura M, Milani C, Viljakainen H.	Front Microbiol	10.3389/fmicb.2023.1323346	2023
	Differences in the gut microbiota between Gurkhas and soldiers of British origin.	Troth TD, McInnes RS, Dunn SJ, Mirza J, Whittaker AH, Goodchild SA, Loman NJ, Harding SV, van Schaik W.	PLoS One	10.1371/journal.pone.0292645	2023
	Evaluation of prosthetic dysfunction in the diagnosis of endocarditis associated to prosthetic pulmonary valve and pulmonary conduit.	Perez AC, Melero LO, Egurbide JFL, Lopez JL, Gonzalez LF, Mata RB, Meabe JA, Mendizabal LA, Goikoetxea Agirre AJ, Blanco Vidal MJ, Curiel JA, Montes Orbe PM.	Int J Cardiol Congenit Heart Dis	10.1016/j.ijcchd.2025.100591	2025
	Functional Abdominal Bloating Is Associated With Gut Microbiota Dysbiosis and Altered Intestinal Barrier Function: Experimental Evidence.	Akkoyunlu DS, Celebi A, Gur B, Kanli A, Ugurtas C, Ozer T, Sarikaya NK, Keskin SE, Cine N, Savli H.	In Vivo	10.21873/invivo.14130	2025
Genetics	Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.	Kumari V S S, Potdar V, Shinde M, Parashar D, Alagarasu K, Cherian S, Lavania M.	J Oral Microbiol	10.1080/20002297.2025.2569523	2025
	Microbiome Shifts in Peri-Implantitis: Longitudinal Characterization of Dysbiosis and Resolution.	Anuntakarun S, Thaweesapphithak S, Krasaesin A, Prommanee S, Arunyanak S, Kungsadalpipob K, Acharya A, Porntaveetus T, Mattheos N.	Int Dent J	10.1016/j.identj.2025.100951	2025
	Haemophilus parainfluenzae Pyogenic Liver Abscess Associated With Cholangiocarcinoma.	Finniss MC, Ibrahim L.	Cureus	10.7759/cureus.22501	2022
	Unusual presentation of distal ICA aneurysm in relation to dental abscess.	Kumar K, Bamezai S, Sharma SB, Zhou S, Spector M, Obi AT.	J Vasc Surg Cases Innov Tech	10.1016/j.jvscit.2022.07.003	2022
	Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4_Hpa.	Hwang S, Pan C, Garcia B, Davidson AR, Moraes TF, Maxwell KL.	J Mol Biol	10.1016/j.jmb.2021.167420	2022
Phylogeny	Exploring the Microbial Landscape of Bone and Joint Infections: An Analysis Using 16S rRNA Metagenome Sequencing.	Maimaiti Z, Liu L.	Infect Drug Resist	10.2147/idr.s482931	2024
	Subdural empyema caused by Aggregatibacter segnis: a rare case report and literature review.	Li Q, Fan X, Wang K, Wu X, Li J, An Y, Wei P, Shi W, Shan Y, Chen S, Zhao G.	BMC Infect Dis	10.1186/s12879-025-11479-0	2025
	Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients	Qin M, Ding W, Qin L, Liang R, Guo Y, Zhao Y, Xu H, Wen Y, Pang Y, Li L.	BMC Microbiol		2025
	Metagenomic next-generation sequencing for detecting lower respiratory tract infections in sputum and bronchoalveolar lavage fluid samples from children.	Shi R, Wang Y, Zhou S, Zhang Y, Zheng S, Zhang D, Du X, Gu W, Xu Y, Zhu C.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1228631	2023
	Pyopneumothorax Caused by Aspergillus terreus and Haemophilus influenzae: A Case Report.	Odeyemi J, Emoto J, Abu-Samra AG.	Cureus	10.7759/cureus.76683	2024
	A Series of Haemophilus parainfluenzae Surgical Infections and Review of the Literature.	Onafowokan OO, Mateo R, Bonatti HJR.	Surg Infect (Larchmt)	10.1089/sur.2020.172	2021
Pathogenicity	Correlation Analysis of Characteristics of Intestinal Microbiota and Cytokine Levels in Patients with Obstructive Sleep Apnea-Hypopnea Syndrome.	Liu KL, Xu SJ, Chen SW, Zhang MJ, Ye N, Li J.	Nat Sci Sleep	10.2147/nss.s471264	2024
	Exploring the Relationship between MicroRNAs, Intratumoral Microbiota, and Breast Cancer Progression in Patients with and without Metastasis.	Laborda-Illanes A, Aranega-Martin L, Sanchez-Alcoholado L, Boutriq S, Plaza-Andrades I, Peralta-Linero J, Garrido Ruiz G, Pajares-Hachero B, Alvarez M, Alba E, Gonzalez-Gonzalez A, Queipo-Ortuno MI.	Int J Mol Sci	10.3390/ijms25137091	2024
	Diagnosing Prosthetic Valve Endocarditis Despite a Negative Work-Up.	Johnson BV, Kumbhakar RG, Corcorran MA, Burke CR, Krieger EV.	JACC Case Rep	10.1016/j.jaccas.2024.102492	2024
	Refractory nontuberculous mycobacterial infection and potential hidden immunodeficiency related to RAG mutation and production of anti-interferon-alpha autoantibodies: a case report.	Liang X, Liang H, Liang S, Ning Y, Luo Z, Chen Q, He Z.	BMC Infect Dis	10.1186/s12879-025-10975-7	2025
	Clinical characteristics of acquired anti-IFN-gamma autoantibodies in patients infected with non-tuberculous mycobacteria: a prospective cohort study.	Liang H, Liang S, Ning Y, Huang X, Ning R, Chen N, Hong L, Liang X, Wu S, Yan P, Wei H, Luo Z, Zeng Q, Qu D, He Z.	BMC Pulm Med	10.1186/s12890-025-03566-4	2025
	Species-level enterosignatures predict clinical phenotypes in chronic hepatitis B and causal triangulation of gut-metabolite-CHB interactions.	Yuan T, Chen J, Yang J, Li L, Lu S, Pu J, Sun Y, Lin W, Lu Y, Zhu Z, Zheng H, Xu J.	Front Microbiol	10.3389/fmicb.2025.1683451	2025
	The Impact of Bacterial-Fungal Interactions on Childhood Caries Pathogenesis.	Huang S, Wang H, Tian J, Qin M, Gao R, Zhao B, Wang J, Wu H, Xu H.	Pathogens	10.3390/pathogens14101033	2025
	Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review.	Del Pilar Angarita-Diaz M, Fong C, Medina D.	Eur J Med Res	10.1186/s40001-024-01908-2	2024
	Serum proteins and faecal microbiota as potential biomarkers in newly diagnosed, treatment-naïve inflammatory bowel disease and irritable bowel syndrome patients.	Matijasic M, Baresic A, Cipcic Paljetak H, Peric M, Panek M, Kunovic A, Ljubas Kelecic D, Vranesic Bender D, Grubelic Ravic K, Rogic D, Antolic M, Horvat I, Kraljevic I, Banic M, Krznaric Z, Verbanac D.	J Mol Med (Berl)	10.1007/s00109-025-02558-5	2025
	Clinical characteristics of SFTPC gene mutations in children: a single-center experience.	Yang T, Zhang F, Zheng G, Yang D, Wu L, Jia X, Zhu G, Tang L.	Ital J Pediatr	10.1186/s13052-025-02101-9	2025
	Microbiota Transplantation as an Adjunct to Standard Periodontal Treatment in Periodontal Disease: A Systematic Review.	Lindo CE, Sebastian J, Kuntjoro KN, Halim VA, Tadjoedin FM, Kuswandani SO, Sulijaya B.	Medicina (Kaunas)	10.3390/medicina60040672	2024
	Exploring Relationships Within the Microbiome of Root Canal Infections and the Influence of Associated Clinical Parameters.	Mominkhan D, Brito LCN, Yakubu AR, Larson E, Martin L, Patel M, Tavares WLF, Ribeiro-Sobrinho A, Teles F.	Int Endod J	10.1111/iej.70011	2025
	Infected Left Atrial Myxoma Presenting Without Bacterial Growth on Blood Cultures: A Case Report.	Kim SA, Pyo W, Jung SH.	J Chest Surg	10.5090/jcs.22.069	2023
	Splinter Hemorrhage.	Grugan BM, Dyer SP.	J Emerg Med	10.1016/j.jemermed.2022.05.021	2022
	Clinical characteristics analysis and prediction model construction for pediatric influenza virus pneumonia complicated by bacterial infection.	Xie X, Wang W, Liu Z, Sun T, Song Y, Wang N, Wang Z, Wang Y.	Transl Pediatr	10.21037/tp-2025-340	2025
	Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.	Bessa LJ, Egas C, Pires C, Proenca L, Mascarenhas P, Pais RJ, Barroso H, Machado V, Botelho J, Alcoforado G, Mendes JJ, Alves R.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1543100	2025
	The Association Between Maternal Diet and the Human Milk Microbiome: A Review of Evidence and Methodological Challenges.	Sindi AS.	Microorganisms	10.3390/microorganisms13102347	2025
	Genome-wide analysis of urogenital and respiratory multidrug-resistant Haemophilus parainfluenzae.	Sierra Y, Gonzalez-Diaz A, Carrera-Salinas A, Berbel D, Vazquez-Sanchez DA, Tubau F, Cubero M, Garmendia J, Camara J, Ayats J, Ardanuy C, Marti S.	J Antimicrob Chemother	10.1093/jac/dkab109	2021
	Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.	Zheng H, Peng P, Wang S, Zhang B, Yang L, Wang Y, Li L, Pang G.	Infect Drug Resist	10.2147/idr.s462358	2025
Genetics	Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.	Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL.	Microbiol Spectr	10.1128/spectrum.04017-23	2024
	Haemophilus influenzae and Moraxella catarrhalis in sputum of severe asthma with inflammasome and neutrophil activation.	Versi A, Ivan FX, Abdel-Aziz MI, Bates S, Riley J, Baribaud F, Kermani NZ, Montuschi P, Dahlen SE, Djukanovic R, Sterk P, Maitland-Van Der Zee AH, Chotirmall SH, Howarth P, Adcock IM, Chung KF, U-BIOPRED consortium.	Allergy	10.1111/all.15776	2023
	The effect of Beta vulgaris on an in vitro oral microbiome of electronic cigarette users.	Staton DV, Tang J, Barbisan M, Nussbaum J, Baker JL.	J Oral Microbiol	10.1080/20002297.2025.2509669	2025
	Large-scale bidirectional Mendelian randomization study identifies new gut microbiome significantly associated with immune thrombocytopenic purpura.	Li J, Li J, Liu Y, Zeng J, Liu Y, Wu Y.	Front Microbiol	10.3389/fmicb.2024.1423951	2024
	Haemophilus parainfluenzae endocarditis in a low-risk woman: a case report.	Gagliardi R, Sensi C, Flaminio G, De Canale E, Vettor R, De Carlo E.	Clin Case Rep	10.1002/ccr3.5066	2021
	Adverse events associated with third-generation cephalosporins: Analysis of the FDA adverse event reporting system database.	Ahmed NJ.	Medicine (Baltimore)	10.1097/md.0000000000045778	2025
	Salivary microbial dysbiosis may predict lung adenocarcinoma: A pilot study.	Roy P, Sarma A, Kataki AC, Rai AK, Chattopadhyay I.	Indian J Pathol Microbiol	10.4103/ijpm.ijpm_1111_20	2022
	Characterization of tongue coating microbiome from patients with colorectal cancer.	Chen Q, Huang X, Zhang H, Jiang X, Zeng X, Li W, Su H, Chen Y, Lin F, Li M, Gu X, Jin H, Wang R, Diao D, Wang W, Li J, Wei S, Zhang W, Liu W, Huang Z, Deng Y, Luo W, Liu Z, Zhang B.	J Oral Microbiol	10.1080/20002297.2024.2344278	2024
	Gut Microbiota in Adults with Chronic Widespread Pain: A Systematic Review.	Leong PY, Shi LH.	Diseases	10.3390/diseases13090299	2025
	Changes in the intestinal microbiota of healthy adults induced by brown yogurt and relationships of bacterial taxa with specific components.	Jiang TM, Liang Y, Liu B, Liu BY, Li X, Zhao JY, Li JT, Liu YP, Chen LJ.	Food Funct	10.1039/d1fo03885k	2022
	Two Japanese Pediatric Patients With Primary Ciliary Dyskinesia Caused by Loss-of-Function Variants in the CCNO gene.	Xu Y, Ueda K, Nishikido T, Matsumoto T, Takeuchi K.	Cureus	10.7759/cureus.58854	2024
	Virulent endocarditis due to Haemophilus parainfluenzae: A systematic review of the literature.	Olagunju A, Martinez J, Kenny D, Gideon P, Mookadam F, Unzek S.	World J Cardiol	10.4330/wjc.v14.i10.546	2022
	Unveiling the Relationship Between Oral Microbiota and Alzheimer's Disease: A Genetic Instrumental Variable Analysis via Mendelian Randomization.	Li Z, Kang Y, Li S, Guo S, Zheng H.	Brain Behav	10.1002/brb3.70753	2025
Genetics	A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.	Kim S, Thapa I, Ali H.	BMC Microbiol	10.1186/s12866-024-03633-6	2024
	Analysis of Pathogenic Bacteria and Drug Resistance Among Girls with Bacterial Vaginitis.	Zhang M, Liu J, Pan YC, Liu HL, Shu J, Wu XM, Yang Y.	Infect Drug Resist	10.2147/idr.s403304	2023
	Intratumoral Microbiota Impacts the First-Line Treatment Efficacy and Survival in Non-Small Cell Lung Cancer Patients Free of Lung Infection.	Zhang M, Zhang Y, Sun Y, Wang S, Liang H, Han Y.	J Healthc Eng	10.1155/2022/5466853	2022
	Esophageal cancer presenting with brain abscess.	Sekimori K, Sato S, Higashizono K, Nagai E, Taki Y, Nishida M, Watanabe M, Miyakoshi A, Oba N.	Int Cancer Conf J	10.1007/s13691-022-00584-5	2023
	The epidemiology and the pathogen distribution of pediatric dacryocystitis in Chinese population 2017-2022.	Sun Z, Li M, Sun H.	Ital J Pediatr	10.1186/s13052-024-01582-4	2024
	Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.	Roongpiboonsopit D, Wairit S, Nithisathienchai C, Pakdee A, Cheibchalard T, Sayasathid J, Wilantho A, Tongsima S, Somboonna N.	PLoS One	10.1371/journal.pone.0333676	2025
	A Case of Gemella morbillorum Causing Multi-valvular Endocarditis.	Panama G, Martinez A, Yavari M, Geunwon Kim A, Abela G.	Cureus	10.7759/cureus.53716	2024
	Oral microbiome and nitric oxide biomarkers in older people with mild cognitive impairment and APOE4 genotype.	L'Heureux JE, Corbett A, Ballard C, Vauzour D, Creese B, Winyard PG, Jones AM, Vanhatalo A.	PNAS Nexus	10.1093/pnasnexus/pgae543	2025
	Description of the Distinctive Changes in the Colonic Microbiome Associated with Irritable Bowel Syndrome, Uncomplicated Diverticulitis, and Tubular Adenoma.	Saavedra-Bravo R, Mendez-Tenorio A, Lopez-Luis MA, Davila-Martinez EA, Vazquez-Avila MA, Garcia-Gutierrez L, Leon-Avila G, Bandala C, Cureno-Diaz MA, Fernandez-Sanchez V, Morales-Gonzalez JA, Lara-Padilla E, Mancilla-Ramirez J, Ibanez-Cervantes G.	Biomedicines	10.3390/biomedicines13102424	2025
	Clinical Experience with Inosine Pranobex in Pediatric Acute Respiratory Infections with Comorbidities: A Case Series from a Specialised Centre.	Kunc P, Fabry J, Istvankova K, Pecova R, Jesenak M.	Pediatr Rep	10.3390/pediatric17060123	2025
	Clinical characteristics and risk factors for right-sided infective endocarditis in Korea: a 12-year retrospective cohort study.	Lee Y, Kim JH, Lee JA, Ahn SM, Han M, Ahn JY, Jeong SJ, Choi JY, Yeom JS, Lee SH, Ku NS.	Sci Rep	10.1038/s41598-024-60638-x	2024
Genetics	Clinical application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia pathogens.	Huang R, Zhang Y, Dong C, Chen J, Zou H, Liu Y, Guo M, Gao H, Ke Q, Wu W.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1661213	2025
	Characteristics of pathogenic microbes in lung microenvironment of lung cancer patients without respiratory infection.	Zhang M, Zhang Y, Han Y, Zhao X, Sun Y.	J BUON		2021
	Association of distinct microbial and metabolic signatures with microscopic colitis.	Chen AS, Kim H, Nzabarushimana E, Shen J, Williams K, Gurung J, McGoldrick J, Burke KE, Yarze JC, Nguyen LH, Staller K, Chung DC, Xavier RJ, Khalili H.	Nat Commun	10.1038/s41467-025-59566-9	2025
	A case of complicated parapneumonic pleural effusion caused by paragonimus infection in a child was successfully treated by intrapleural injection of urokinase: a case report and literature review.	Shi Y, Li Y, Hu Y.	Front Pediatr	10.3389/fped.2025.1557273	2025
	Ultra-rapid and sensitive detection of African swine fever virus using multiple cross displacement amplification combined with nanoparticle-based lateral flow biosensor.	Mao S, Zhang R, Yang X, Huang J, Kang Y, Wang Y, Chen H, Li S.	Front Microbiol	10.3389/fmicb.2024.1403577	2024
	Premature Infant with Haemophilus parainfluenzae Sepsis: Case Report and Literature Review.	Alsuhaibani MA.	J Trop Pediatr	10.1093/tropej/fmz010	2019
	Haemophilus spp., an emerging multidrug-resistant sexually transmitted pathogen.	Ducours M, Puges M, Desclaux A, Barthod L, Peuchant O, Cazanave C.	Med Mal Infect	10.1016/j.medmal.2020.06.003	2020
	Bacterial Isolates from Bronchoalveolar Lavage in Pediatric Patients with Protracted Bacterial Bronchitis or Bronchiectasis: A Retrospective Comparative Study.	Moriki D, Tsouprou M, Prountzos S, Koumpagioti D, Kalogiannis M, Alexopoulou E, Douros K.	J Clin Med	10.3390/jcm14217653	2025
	A Case of Vascular Graft Infection Caused by Haemophilus parainfluenzae.	Okuhama A, Murai Y, Ishikane M, Mezaki K, Isaka E, Matsushiro T, Yamada G, Nomoto H, Yamamoto K, Morioka S, Ohmagari N, Horai T.	Open Forum Infect Dis	10.1093/ofid/ofac187	2022
Phylogeny	16S rDNA PCR for the aetiological diagnosis of culture-negative infective endocarditis.	Anton-Vazquez V, Dworakowski R, Cannata A, Amin-Youssef G, Gunning M, Papachristidis A, MacCarthy P, Baghai M, Deshpande R, Khan H, Byrne J, Fife A.	Infection	10.1007/s15010-021-01690-x	2022
	Haemophilus parainfluenzae-related cellulitis of the penis following tearing of a short frenulum.	Dauendorffer JN, Janier M, Bagot M, Fouere S.	Ann Dermatol Venereol	10.1016/j.annder.2019.08.022	2020
	Infective endocarditis due to Haemophilus sputorum.	Costello VH, Robinson SL, Klusewitz S, Surpris G, Nahid M, Backlund MG.	Access Microbiol	10.1099/acmi.0.000410	2022
	Influence of cigarette smoking on oral microbiota in patients with recurrent aphthous stomatitis.	Wang X, Luo N, Mi Q, Kong W, Zhang W, Li X, Gao Q.	J Investig Med	10.1136/jim-2021-002119	2022
Enzymology	Cefotaxime Versus Ceftriaxone: A Comprehensive Comparative Review.	Sharma B, Chalikwar R, Bhalerao S, Gondane AA, Pawar D, Sharma A.	Cureus	10.7759/cureus.69146	2024
	Identification and Characterization of a Rare Exon 22 Duplication in CFTR in Two Families.	Ahting S, Henn C, Vom Hove M, Strehlow V, Duffek P, Behrendt S, Drukewitz S, Berger J, Graeber SY, Hentschel J.	Int J Mol Sci	10.3390/ijms26104487	2025
	Genetic evidence from Mendelian randomization strengthens the causality between oral microbiome and chronic obstructive pulmonary disease.	Zhou X, Wen F, Qiu H, Li J.	Medicine (Baltimore)	10.1097/md.0000000000043347	2025
	Pyelonephritis and bacteremia caused by Haemophilus parainfluenzae: case-report of an unusual pathogen.	Nevejan L, Goegebuer T, Mast P, Lemmens A.	Acta Clin Belg	10.1080/17843286.2019.1671059	2021
Phylogeny	Comparison of the microbiome of sputum from HIV/AIDS patients using PacBio 16S rRNA sequencing and ddPCR.	Lai Y, Jiang W, Zhu T, Lin J, Yu X.	BMC Infect Dis	10.1186/s12879-025-11500-6	2025
Genetics	The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.	Li W, Zhao M, Wu W, Chen G, Hang Y, Zheng H, Gao Z, Liu J, Zhao Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1494638	2025
Enzymology	Comparison of culture and PCR-DGGE methods to evaluate the airways of cystic fibrosis patients and determination of their antibiotic resistance profile.	Moazami Goudarzi S, Shahpouri Arani Y, Abdi Ali A, Mohammadi P, Ghorbanmehr N, Modaresi M, Ghorban Movahed M, Ghazanfari T.	Iran J Microbiol	10.18502/ijm.v15i6.14135	2023
	Spontaneous Pancreatic Pseudocyst-Superior Mesenteric Vein Fistula.	Goble S, Ayoub A, Boeke S, Matlock R, Malli A.	ACG Case Rep J	10.14309/crj.0000000000001092	2023
Phylogeny	16S rRNA Gene PCR/Sequencing of Heart Valves for Diagnosis of Infective Endocarditis in Routine Clinical Practice.	Hong HL, Flurin L, Greenwood-Quaintance KE, Wolf MJ, Pritt BS, Norgan AP, Patel R.	J Clin Microbiol	10.1128/jcm.00341-23	2023
Transcriptome	Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.	Lin Z, Jiang Y, Liu H, Yang J, Yang B, Zhang K, Tang P, Xiang B, Sun B.	J Transl Med	10.1186/s12967-025-06986-2	2025
Phylogeny	Comparative analysis of bacterial abundance and diversity in tumour tissue of oral squamous cell carcinoma and non-tumour tissue: insights from a systematic review of 16S ribosomal RNA sequencing.	Mohapatra S, Panda S, Mohanty N, Mishra BP.	BMC Oral Health	10.1186/s12903-025-05941-3	2025
	Arginine modulates the pH, microbial composition, and matrix architecture of biofilms from caries-active patients.	Del Rey YC, Rikvold PD, Lund MB, Raittio EJ, Schramm A, Meyer RL, Schlafer S.	Int J Oral Sci	10.1038/s41368-025-00404-5	2025
	Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups.	Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A, Mukherjee S.	Microbiol Spectr	10.1128/spectrum.02368-23	2023
	IgA Vasculitis Associated With Levofloxacin Use in an Adult Female: A Case Report.	Gomez Contreras KA, Alonzo Canul ME, Mena Rodriguez AL, Castillo Baas MG, Vargas Gutierrez DA.	Cureus	10.7759/cureus.71567	2024
	Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children.	Roslund MI, Puhakka R, Nurminen N, Oikarinen S, Siter N, Gronroos M, Cinek O, Kramna L, Jumpponen A, Laitinen OH, Rajaniemi J, Hyoty H, Sinkkonen A, ADELE research group.	Environ Int	10.1016/j.envint.2021.106811	2021
Phylogeny	Cervicovaginal microbial features predict Chlamydia trachomatis spread to the upper genital tract of infected women.	Jeong S, Tollison T, Brochu H, Chou H, Huntress I, Yount KS, Zheng X, Darville T, O'Connell CM, Peng X.	Infect Immun	10.1128/iai.00057-25	2025
Pathogenicity	Emergence of multidrug resistance among Haemophilus parainfluenzae from respiratory and urogenital samples in Barcelona, Spain.	Sierra Y, Gonzalez-Diaz A, Tubau F, Imaz A, Cubero M, Camara J, Ayats J, Marti S, Ardanuy C.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-019-03774-x	2020
	Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus.	Medina-Martinez I, Gil-Gutierrez R, Garcia-Garcia J, de la Hera-Fernandez FJ, Navarrete-Navarrete N, Zamora-Pasadas M, Ortego-Centeno N, Callejas-Rubio JL, Garcia-Garcia F, Galvez-Peralta J, Rodriguez-Nogales A, Correa-Rodriguez M, Rueda-Medina B.	Med Sci (Basel)	10.3390/medsci13030151	2025
	Deciphering gut microbiome patterns from host preferences and microbial interactions in healthy Korean individuals.	Hong S, Lim MY, Chung WH, Shin JH, Nam YD.	BMC Biol	10.1186/s12915-025-02291-y	2025
	Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance.	Chen Q, Qiu Y, Zhang J, Chen S, Han X, Zeng Q, Wang G, Ji X, Dong L.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1660347	2025
Enzymology	Multisystem organ failure secondary to Haemophilus parainfluenzae infective endocarditis on an ICD lead: A case report.	Bridwell RE, Cibrario A, Long B, Cho AM.	Am J Emerg Med	10.1016/j.ajem.2019.05.016	2019
	Comparative activities of sitafloxacin against recent clinical isolates in hospitals across China.	Wu S, Yang Y, Guo Y, Yin D, Zheng Y, Han R, Ding L, Zhu D, Hu F.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-021-04278-3	2021
	Evaluating the Clinical Relevance of Routine Sonication for Periprosthetic Hip or Knee Joint Infection Diagnosis.	Zouitni A, van Oldenrijk J, Bos PK, Croughs PD, Yusuf E, Veltman ES.	Antibiotics (Basel)	10.3390/antibiotics13040366	2024
	Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches.	Ghaffar SA, Tahir H, Muhammad S, Shahid M, Naqqash T, Faisal M, Albekairi TH, Alshammari A, Albekairi NA, Manzoor I.	Front Immunol	10.3389/fimmu.2024.1380732	2024
	Supra- and Subgingival Microbiome in Gingivitis and Impact of Biofilm Control: A Comprehensive Review	Iniesta M, Vasconcelos V, Sanz M, Herrera D.	Antibiotics (Basel)		2024
	Removal of an infected pulmonary artery fibroelastoma disguised as a presentation of pulmonary embolism using a percutaneous suction thrombectomy device.	Jones DH, Lin B, Brabham D, Trinidad B.	J Vasc Surg Cases Innov Tech	10.1016/j.jvscit.2023.101346	2023
	Disturbances in the gut microbiota potentially associated with metabolic syndrome among patients living with HIV-1 and on antiretroviral therapy at Bafoussam Regional Hospital, Cameroon.	Diesse JM, Jadhav S, Tamekou SL, Simo G, Dzoyem JP, Souopgui J, Kuiate JR, Nema V.	Diabetol Metab Syndr	10.1186/s13098-025-01653-4	2025
	Dynamic microbial changes in exacerbation of chronic obstructive pulmonary disease.	Choi YJ, Park HJ, Kim CY, Choi A, Cho JH, Byun MK.	Front Microbiol	10.3389/fmicb.2024.1507090	2024
	Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples.	Raychaudhuri S, Gem H, Chung K, McLean JS, Kerns KA, Hullar MAJ, Elmorr E, Appelbaum JB, Percival MM, Walter RB, Halpern AB, Minot SS, Kim K, Zevin AS, Rashidi A.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00725-7	2025
Genetics	Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.	Cauwenberghs E, De Boeck I, Delanghe L, Van Rillaer T, Demuyser T, Spacova I, Verhulst S, Van Hoorenbeeck K, Lebeer S.	J Cyst Fibros	10.1016/j.jcf.2025.07.011	2025
	Evaluation of sonication for the detection of periprosthetic joint infection in hip revision arthroplasty: a retrospective observational single-center study of 288 episodes.	Kickinger B, Monsen T, Karis E, Widerstrom M, Sundin P, Nilsson KG, Otten V, Crnalic S.	Acta Orthop	10.2340/17453674.2025.43679	2025
	Formulation and Development of Nanofiber-Based Ophthalmic Insert for the Treatment of Bacterial Conjunctivitis.	Farkas E, Abboud H, Nagy N, Hofmeister B, Ostorhazi E, Toth B, Pinke B, Meszaros L, Zelko R, Kazsoki A.	Int J Mol Sci	10.3390/ijms25179228	2024
	Clinical diagnostic value of metagenomic next-generation sequencing in patients with acute infection in emergency department.	Wei L, Luo J, Wu W, Yin J, Sun Z, Xu X, Gong W, Xu J.	Heliyon	10.1016/j.heliyon.2024.e35802	2024
	Haemophilus parainfluenzae endocarditis presenting with symptoms of COVID-19.	Finch LC, Gerdzhikov S, Buttery R.	BMJ Case Rep	10.1136/bcr-2021-245210	2021
Phylogeny	Lung microbiota features of stage III and IV non-small cell lung cancer patients without lung infection.	Zhang M, Zhang Y, Han Y, Zhao X, Sun Y.	Transl Cancer Res	10.21037/tcr-22-92	2022
	Metabolomic and metagenomic analyses reveal distinct microenvironmental signatures between clear aligner-associated and tooth surface dental plaque.	Xie Q, Li D, Ren C, Shen Y, Lin S, Chen W.	BMC Oral Health	10.1186/s12903-025-07231-4	2025
Pathogenicity	Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli.	Xuan H, Umar S, Zhong C, Yu W, Ahmed I, Wheatley JL, Sampath V, Chavez-Bueno S.	BMC Microbiol	10.1186/s12866-024-03598-6	2024
	Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study.	Wang JZ, Yuan D, Yang XH, Sun CH, Hou LL, Zhang Y, Gao YX.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1291980	2023
Pathogenicity	Fecal microbiota signatures of insulin resistance, inflammation, and metabolic syndrome in youth with obesity: a pilot study.	Del Chierico F, Manco M, Gardini S, Guarrasi V, Russo A, Bianchi M, Tortosa V, Quagliariello A, Shashaj B, Fintini D, Putignani L.	Acta Diabetol	10.1007/s00592-020-01669-4	2021
	Linking Microbiota Profiles to Disease Characterization in Common Variable Immunodeficiency: The Case of Granulomatous-Lymphocytic Interstitial Lung Disease.	Cabanero-Navalon MD, Carda-Dieguez M, Moral Moral P, Mira A, Balastegui-Martin H, Salavert-Lleti M, Garcia-Bustos V.	Biomedicines	10.3390/biomedicines12102239	2024
	The Intratumor Bacterial and Fungal Microbiome Is Characterized by HPV, Smoking, and Alcohol Consumption in Head and Neck Squamous Cell Carcinoma.	Chakladar J, John D, Magesh S, Uzelac M, Li WT, Dereschuk K, Apostol L, Brumund KT, Rodriguez JW, Ongkeko WM.	Int J Mol Sci	10.3390/ijms232113250	2022
	Streptococcus cristatus reduces cariogenicity of saliva-derived microcosms under pH-dependent conditions.	Cai Y, Wu L, Brandt BW, Buijs MJ, Wei X, Liu H, Deng D.	J Oral Microbiol	10.1080/20002297.2025.2565450	2025
	Secondary Ross procedure after failed transcatheter aortic valve replacement.	Fukuhara S.	JTCVS Tech	10.1016/j.xjtc.2022.08.003	2022
Genetics	Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing.	Lim TW, Huang S, Jiang Y, Zhang Y, Burrow MF, McGrath C.	J Oral Microbiol	10.1080/20002297.2024.2317059	2024
	The aetiology and incidence of infective endocarditis in people living with rheumatic heart disease in tropical Australia.	Basaglia A, Kang K, Wilcox R, Lau A, McKenna K, Smith S, Chau KWT, Hanson J.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-023-04641-6	2023
Pathogenicity	Clinical characteristics of bacteremia caused by Haemophilus and Aggregatibacter species and antimicrobial susceptibilities of the isolates.	Chien YC, Huang YT, Liao CH, Chien JY, Hsueh PR.	J Microbiol Immunol Infect	10.1016/j.jmii.2020.12.002	2021
Genetics	Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.	Sun N, Zhang J, Guo W, Cao J, Chen Y, Gao D, Xia X.	BMC Microbiol	10.1186/s12866-025-03887-8	2025
	Persistent pleuritic chest pain in a patient with cystic fibrosis.	Louey S, Shanthikumar S, Vandeleur M, Gwee A, Robinson P.	Breathe (Sheff)	10.1183/20734735.0007-2022	2022
	Antibiotherapy in Children with Cystic Fibrosis-An Extensive Review.	Ciuca IM, Dediu M, Popin D, Pop LL, Tamas LA, Pilut CN, Almajan Guta B, Popa ZL.	Children (Basel)	10.3390/children9081258	2022
	A Rare Case of an Exploratory Laparotomy to Treat a Liver Abscess Secondary to Foreign Body Ingestion.	Chavez M, Khasnabish S, Landry I, Saliaj M.	Cureus	10.7759/cureus.25747	2022
Phylogeny	Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.	Kondo T, Kondo S, Nakayama-Imaohji H, Tada A, Tabassum N, Munyeshyaka E, Koyano K, Nakamura S, Kusaka T, Kuwahara T.	Int J Mol Sci	10.3390/ijms262110775	2025
	Anti-interferon-alpha antibodies associate with disease activity and prognosis in anti-MDA5-positive dermatomyositis.	Sun C, Yang H, Zhang Y, Wu S, Zhang X, Jiang W, Peng Q, Wang G, Lu X.	Arthritis Res Ther	10.1186/s13075-025-03600-0	2025
	Assessment of trimethoprim-sulfamethoxazole susceptibility testing methods for fastidious Haemophilus spp.	Sierra Y, Tubau F, Gonzalez-Diaz A, Carrera-Salinas A, Moleres J, Bajanca-Lavado P, Garmendia J, Dominguez MA, Ardanuy C, Marti S.	Clin Microbiol Infect	10.1016/j.cmi.2019.11.022	2020
	Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.	Zhao X, Xu J, Wu D, Chen N, Liu Y.	Biomedicines	10.3390/biomedicines13030708	2025
	Taxonomic Diversity and Clinical Correlations in Periapical Lesions by Next-Generation Sequencing Analysis.	Bronzato JD, Gomes BPFA, Chen T.	Genes (Basel)	10.3390/genes16070775	2025
	Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition.	Sardaro MLS, Grote V, Baik J, Atallah M, Amato KR, Ring M.	Nutrients	10.3390/nu17030458	2025
	Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic.	Dieckow S, Szafranski SP, Grischke J, Qu T, Doll-Nikutta K, Steglich M, Yang I, Haussler S, Stiesch M.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00624-3	2024
	The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis.	Ajrithirong P, Krasaesin A, Sriarj W, Gavila P, Chetruengchai W, Sriwattanapong K, Manaspon C, Samaranayake L, Porntaveetus T.	J Oral Microbiol	10.1080/20002297.2025.2560591	2025
	Lung abscess due to Streptococcus intermedius associated with SARS CoV-2 infection in pregnancy: Unusual presentation and complication of a commensal bacteria during pregnancy.	Bueno COP, Trillos SJG, Rosales DJC, Garcia EAB.	Clin Case Rep	10.1002/ccr3.6763	2023
	Evaluation of the Tooth Surface after Irradiation with Diode Laser Applied for Removal of Dental Microorganisms from Teeth of Patients with Gingivitis, Using X-ray Photoelectron (XPS) and Optical Profilometry (OP).	Wawrzyk-Bochenek I, Lobacz M, Wilczynski S, Rahnama M, Szulc J, Konka A, Wawrzyk A.	J Clin Med	10.3390/jcm11226840	2022
	Community dynamics during de novo colonization of the nascent peri-implant sulcus.	Dutra TP, Robitaille N, Altabtbaei K, Dabdoub SM, Kumar PS.	Int J Oral Sci	10.1038/s41368-025-00367-7	2025
Pathogenicity	The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19.	Martin-Castano B, Diez-Echave P, Garcia-Garcia J, Hidalgo-Garcia L, Ruiz-Malagon AJ, Molina-Tijeras JA, Rodriguez-Sojo MJ, Redruello-Romero A, Martinez-Zaldivar M, Mota E, Cobo F, Diaz-Villamarin X, Alvarez-Estevez M, Garcia F, Morales-Garcia C, Merlos S, Garcia-Flores P, Colmenero-Ruiz M, Hernandez-Quero J, Nunez M, Rodriguez-Cabezas ME, Carazo A, Martin J, Moron R, Rodriguez Nogales A, Galvez J.	Elife	10.7554/elife.95292	2025
	Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China.	Huang W, Wang F, Cai Q, Xu H, Hong D, Wu H, Zhou L, Hu L, Lu Y.	Ann Clin Microbiol Antimicrob	10.1186/s12941-023-00631-w	2023
	The effects of exposure to O₂- and HOCl-nanobubble water on human salivary microbiota.	Sagara K, Kataoka S, Yoshida A, Ansai T.	Sci Rep	10.1038/s41598-023-48441-6	2023
	Evaluation of clinical characteristics and risk factors associated with Chlamydia psittaci infection based on metagenomic next-generation sequencing.	Yuan L, Chen Q, Zhu XY, Lai LM, Zhao R, Liu Y.	BMC Microbiol	10.1186/s12866-024-03236-1	2024
	Oral microbial dysbiosis in patients with oral cavity cancers.	Unlu O, Demirci M, Paksoy T, Eden AB, Tansuker HD, Dalmizrak A, Aktan C, Senel F, Sunter AV, Yigit O, Cakir BO, Kantarci A.	Clin Oral Investig	10.1007/s00784-024-05770-8	2024
	Draft Genome Sequence of a Haemophilus parainfluenzae Strain Isolated from a Patient with Chronic Obstructive Pulmonary Disease.	Fluit AC, Ekkelenkamp MB, Tunney MM, Elborn JS, Rogers MRC, Bayjanov JR.	Microbiol Resour Announc	10.1128/mra.00079-20	2020
	Multi-Omics Insights into Gingivitis from a Clinical Trial: Understanding the Role of Bacterial and Host Factors.	Ramji N, Hu P, Munoz Bodnar A, Braga CP, Snowball J, Swift D, Ye H, Xie S, Trenner R, Klukowska M, Schneiderman E, Biesbrock AR.	Microorganisms	10.3390/microorganisms13102371	2025
	Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.	Zhu M, Wang Q, Yang Y, Liu X, Zhang J, Li G, Liu W, Xiang X, Chen J.	Nutr J	10.1186/s12937-025-01116-6	2025
	Corticosteroid Dosing Level, Incidence and Profile of Bacterial Blood Stream Infections in Hospitalized COVID-19 Patients.	Papic I, Bistrovic P, Cikara T, Busic N, Keres T, Ortner Hadziabdic M, Lucijanic M.	Viruses	10.3390/v16010086	2024
	Microbial dysbiosis in oral cavity determines obesity status in adolescents.	Malik MZ, Nizam R, Jacob S, Al Alqaderi H, Al-Mulla F, Alqaderi H.	Cell Mol Life Sci	10.1007/s00018-025-05889-1	2025
Pathogenicity	Modulation of opportunistic species Corynebacterium diphtheriae, Haemophilus parainfluenzae, Moraxella catarrhalis, Prevotella denticola, Prevotella melaninogenica, Rothia dentocariosa, Staphylococcus aureus and Streptococcus pseudopneumoniae by intranasal administration of Streptococcus salivarius 24SMBc and Streptococcus oralis 89a combination in healthy subjects.	De Grandi R, Bottagisio M, Di Girolamo S, Bidossi A, De Vecchi E, Drago L.	Eur Rev Med Pharmacol Sci	10.26355/eurrev_201903_17351	2019
	Case report: Inhaled nitric oxide rescued a hypoxemia patient caused by dermatomyositis complicated with interstitial pneumonia.	Wu X, Zheng R, Zhao Z.	Front Med (Lausanne)	10.3389/fmed.2024.1371183	2024
	The Vaginal Microbiome of Transgender and Gender Nonbinary Individuals.	Winston McPherson G, Goldstein Z, Salipante SJ, Rongitsch J, Hoffman NG, Dy GW, Penewit K, Greene DN.	Transgend Health	10.1089/trgh.2022.0100	2024
	Impact of toothpaste use on the subgingival microbiome: a pilot randomized clinical trial.	Iniesta M, Vasconcelos V, Laciar F, Matesanz P, Sanz M, Herrera D.	BMC Oral Health	10.1186/s12903-025-06159-z	2025
	Establishment and Performance Evaluation of Multiplex PCR-Dipstick DNA Chromatography for Mycoplasma pneumoniae and Chlamydia pneumoniae Rapid Detection.	Hu L, Wang X, Cao D, Cheng Q, Li Q.	Can J Infect Dis Med Microbiol	10.1155/2023/6654504	2023
	The Effect of Burn Resuscitation Volumes on the Gut Microbiome in a Swine Model.	McIntyre MK, Winkler CJ, Gomez BI, Lapierre JP, Little JS, Dubick MA, Nicholson SE, Burmeister DM.	Shock	10.1097/shk.0000000000001462	2020
	Neonatal pyogenic liver abscess following omphalitis: A case report.	Dongmo Miaffo DOE, Chafaaoui H, Assan BR, Mantho P, Ntankeu PP.	Int J Surg Case Rep	10.1016/j.ijscr.2023.108711	2023
	Red meat consumption in higher healthy eating index diets is associated with brain health critical nutritional adequacy, and fecal microbial diversity.	Dhakal S, Hossain M, Parajuli S.	Sci Rep	10.1038/s41598-025-18907-w	2025
Genetics	Signature of oral microbial dysbiosis in different periodontitis risk levels.	Xu Y, Liu Y, Leng Y, Qian J, Yang Q, Zhu J, Li G, Peng Y.	Appl Microbiol Biotechnol	10.1007/s00253-025-13574-3	2025
	Multi-year comparison of VITEK MS performance for identification of rarely encountered pathogenic Gram-negative organisms (GNOs) in a large integrated Canadian healthcare region.	Church DL, Griener T, Gregson D.	Microbiol Spectr	10.1128/spectrum.02276-24	2024
	Associations Among Plant-Based Diet Quality, Uremic Toxins, and Gut Microbiota Profile in Adults Undergoing Hemodialysis Therapy.	Stanford J, Charlton K, Stefoska-Needham A, Zheng H, Bird L, Borst A, Fuller A, Lambert K.	J Ren Nutr	10.1053/j.jrn.2020.07.008	2021
	Exploring the Diagnostic and Predictive Value of Oral Microbiome in Esophageal Cancer: A Systematic Review and Meta-Analysis.	Chen JC, Hsu MH, Hu SW, Lin YY.	Int J Mol Sci	10.3390/ijms26199457	2025
Genetics	Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children.	Yang A, Chen C, Hu Y, Zheng G, Chen P, Xie Z, Fan H, Sun Y, Wu P, Jiang W, Wang C, Zhang J, Zhang D, Wang J, Hu X, Xia H, Yin G, Guo Y.	Microbiol Spectr	10.1128/spectrum.01488-22	2022
	Microbiome diversity in mosquitoes and sand flies: implications for vector competence.	Ragini G, Mani MK, Sharma R, Bharadwaj N, Subramanian M, Nagarajan SA, Rahi M.	Parasit Vectors	10.1186/s13071-025-06964-z	2025
Phylogeny	A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.	Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix KA.	Arch Microbiol	10.1007/s00203-024-03985-7	2024
	Exploring the Impact of Biotic and Abiotic Surfaces on Protein Binding Modulation and Bacteria Attachment: Integrating Biological and Mathematical Approaches.	Souza JGS, Bertolini M, Liu J, Nagay BE, Martins R, Costa RC, Brunson JC, Shibli J, Figueiredo LC, Dongari-Bagtzoglou A, Feres M, Barao VAR, Bor B.	ACS Nano	10.1021/acsnano.5c06573	2025
Genetics	[Identification of pathogens in the vitreous of patients with infectious uveitis by metagenomic sequencing].	Zhang MX, Peng XY, Hu F, Wei ZY, Lu XX, Liang QF.	Zhonghua Yan Ke Za Zhi	10.3760/cma.j.cn112142-20190711-00371	2020
	Tumor-associated microbiota: Multi-cancer landscape, mechanistic insights and clinical translation (Review).	Yang J, Dong Y, Chen Y, Liang H, Rong S, Liu Z, Lang Q.	Oncol Lett	10.3892/ol.2025.15273	2025
	Calculus pyelonephritis associated with ureterocutaneostomy.	Matsuo T, Mori N, Sakurai A, Furukawa K.	IDCases	10.1016/j.idcr.2019.e00624	2019
	Saliva and Lung Microbiome Associations with Electronic Cigarette Use and Smoking.	Ying KL, Brasky TM, Freudenheim JL, McElroy JP, Nickerson QA, Song MA, Weng DY, Wewers MD, Whiteman NB, Mathe EA, Shields PG.	Cancer Prev Res (Phila)	10.1158/1940-6207.capr-21-0601	2022
	Study of oral microbiota diversity among groups of families originally from different countries.	Altayb HN, Chaieb K, Baothman O, Alzahrani FA, Zamzami MA, Almugadam BS.	Saudi J Biol Sci	10.1016/j.sjbs.2022.103317	2022
	A cross-cohort study identifies potential oral microbial markers for esophageal squamous cell carcinoma.	Yu Y, Xia L, Wang Z, Zhu T, Zhao L, Fan S.	iScience	10.1016/j.isci.2024.111453	2024
Phylogeny	The Effects of Alcohol Drinking on Oral Microbiota in the Chinese Population.	Liao Y, Tong XT, Jia YJ, Liu QY, Wu YX, Xue WQ, He YQ, Wang TM, Zheng XH, Zheng MQ, Jia WH.	Int J Environ Res Public Health	10.3390/ijerph19095729	2022
Phylogeny	Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.	Lee SH, Kim EB, Park SC, Nam SJ, Cho H, Jeon HJ, Lee SP.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1651316	2025
Phylogeny	Altered Gastric Microbiota and Inflammatory Cytokine Responses in Patients with Helicobacter pylori-Negative Gastric Cancer.	Kim HN, Kim MJ, Jacobs JP, Yang HJ.	Nutrients	10.3390/nu14234981	2022
	Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults.	Rashidi A, Gem H, McLean JS, Kerns K, Dean DR, Dey N, Minot S.	Sci Data	10.1038/s41597-024-02916-x	2024
Genetics	Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study.	Blostein F, Bhaumik D, Davis E, Salzman E, Shedden K, Duhaime M, Bakulski KM, McNeil DW, Marazita ML, Foxman B.	Microbiome	10.1186/s40168-022-01442-5	2022
	Asymptomatic bacteriospermia and infertility-what is the connection?	Volz Y, Ebner B, Pfitzinger P, Berg E, Lellig E, Marcon J, Trottmann M, Becker A, Stief CG, Magistro G.	Infection	10.1007/s15010-022-01828-5	2022
	Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.	Darnindro N, Abdullah M, Sukartini N, Rumende CM, Pitarini A, Nursyirwan SA, Fauzi A, Makmun D, Nelwan EJ, Shatri H, Rinaldi I, Tanadi C.	World J Gastroenterol	10.3748/wjg.v31.i7.100051	2025
	The Efficacy of a Diode Laser on Titanium Implants for the Reduction of Microorganisms That Cause Periimplantitis.	Wawrzyk A, Lobacz M, Adamczuk A, Sofinska-Chmiel W, Rahnama M.	Materials (Basel)	10.3390/ma14237215	2021
Genetics	Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates.	Michel C, Argudin MA, Wautier M, Echahidi F, Prevost B, Vandenberg O, Martiny D, Hallin M.	Access Microbiol	10.1099/acmi.0.000649.v3	2024
	Haemophilus Parainfluenzae mural endocarditis with large atrial septal defect and peripheral embolization.	Bae JY, Murugiah K, McLeod GX, Anwer M, Howes CJ.	J Cardiol Cases	10.1016/j.jccase.2021.08.002	2022
Genetics	Ensemble learning for microbiome-based caries diagnosis: multi-group modeling and biological interpretation from salivary and plaque metagenomic data.	Wei F, Wu Z, Li G, Sun X, Shi X, Tan L, Ai T, Qu L, Zheng S.	BMC Oral Health	10.1186/s12903-025-06590-2	2025
Phylogeny	Comparison of the sputum microbiome between patients with stable nontuberculous mycobacterial pulmonary disease and patients requiring treatment.	Song MJ, Kim DH, Kim SY, Kang N, Jhun BW.	BMC Microbiol	10.1186/s12866-024-03308-2	2024
Genetics	A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients.	Gao Q, Li L, Su T, Liu J, Chen L, Yi Y, Huan Y, He J, Song C.	Respir Res	10.1186/s12931-024-02887-y	2024
Phylogeny	Bacterial contamination of medical face mask wearing duration and the optimal wearing time.	Ding G, Li G, Liu M, Sun P, Ren D, Zhao Y, Gao T, Yang G, Fang Y, Li W.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1231248	2023
Pathogenicity	Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.	Jang S, Lee EJ, Park S, Lim H, Ahn B, Huh Y, Koh H, Park YR.	Microbiome	10.1186/s40168-025-02178-8	2025
	Identifying Microbiome Dynamics in Pediatric IBD: More than a Family Matter.	Dovrolis N, Moschoviti A, Fessatou S, Karamanolis G, Kolios G, Gazouli M.	Biomedicines	10.3390/biomedicines11071979	2023
Pathogenicity	In vitro susceptibility of ceftaroline against clinically important Gram-positive cocci, Haemophilus species and Klebsiella pneumoniae in Taiwan: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) in 2012-2018.	Jean SS, Lee WS, Ko WC, Hsueh PR.	J Microbiol Immunol Infect	10.1016/j.jmii.2020.04.017	2021
	Cross-Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment.	Li J, Li J, Ghosh TS, Arendt E, Shanahan F, O'Toole PW.	Adv Sci (Weinh)	10.1002/advs.202308313	2024
	The Relationship Between Insertive Oral and Anal Sex and Select Measures of the Composition of the Urethral Microbiota Among Men Who Have Sex With Men.	Chambers LC, Tapia KA, Srinivasan S, Proll S, Morgan JL, Hoffman NG, Lowens MS, Glick SN, Khosropour CM, Golden MR, Hughes JP, Manhart LE, Fredricks DN.	Sex Transm Dis	10.1097/olq.0000000000001959	2024
	Evaluating the impact of surgery sequence on infection rates in hip or knee arthroplasty: does sequence matter?	Ruangsomboon P, Ruangsomboon O, Tomescu S, Rahman C, Pincus D, Ravi B.	Int Orthop	10.1007/s00264-024-06317-y	2024
	Aortocavitary fistula secondary to vegetative endocarditis in a rabbit.	Martel-Arquette A, Tjostheim SS, Miller J, Carlson J, Mans C.	J Vet Cardiol	10.1016/j.jvc.2018.08.003	2019
	A review of pleural infection in Northumbria Healthcare NHS Foundation Trust.	Aujayeb A, Jackson K, Conroy K.	Clin Med (Lond)	10.7861/clinmed.20-2-s71	2020
Genetics	Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study.	Zheng YR, Chen XH, Chen Q, Cao H.	Ital J Pediatr	10.1186/s13052-024-01749-z	2024
	Dietary patterns drive loss of fiber-foraging species in the celiac disease patients gut microbiota compared to first-degree relatives.	Roque A, Zanker J, Brigido S, Tomaz MB, Goncalves A, Barbeiro S, Benitez-Paez A, Pereira SG.	Gut Pathog	10.1186/s13099-024-00643-7	2024
	Analyses of single-cell RNA sequencing uncover the role of intratumoral Helicobacter pylori in shaping tumor progression and immunity in gastric cancer.	Xu J, Yang J, Sun Q, Chang J, Wang F.	Cancer Immunol Immunother	10.1007/s00262-025-04048-6	2025
Phylogeny	Tracheal and cloacal bacterial diversity of red listed Eastern Imperial Eagle (Aquila heliaca).	Murtskhvaladze M, Ninua L, Budagashvili N, Tevdoradze E, Gurgenidze Z, Kotorashvili A, Kotaria N, Gavashelishvili A, Javakhishvili Z.	Front Microbiol	10.3389/fmicb.2025.1477032	2025
	FMT reduces systemic inflammatory response in severe acute pancreatitis by increasing the abundance of intestinal Bifidobacteria and fecal bacteria.	Mao Y, Huang Y, Zhang W, Liang H, Liu F, Luo Q, Xu C, Qin Y, Liu J, Tang S, Liu H, Ge X.	Biomol Biomed	10.17305/bb.2024.11445	2025
	Chronic Osteomyelitis Caused by Haemophilus parainfluenzae: A Case Report.	Ramachandran V, Haruno LS, Browne TS, Woc-Colburn LE, Rosenfeld SB, Shenava VR.	JBJS Case Connect	10.2106/jbjs.cc.17.00144	2018
	A comparison of oral microbiome composition between highly trained competitive athletes and untrained controls	Simpson A, Rosier B, Tamarit J, Henriquez F, Mira A, Easton C, Burleigh M.	Sci Rep		2025
	Microbiological Indoor and Outdoor Air Quality in Chicken Fattening Houses.	Almatawah QA, Al-Khalaifah HS, Aldameer AS, Ali AK, Benhaji AH, Varghese JS.	J Environ Public Health	10.1155/2023/3512328	2023
	Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents.	Molli VLP, Kissa J, Baraniya D, Gharibi A, Chen T, Al-Hebshi NN, Albandar JM.	Front Oral Health	10.3389/froh.2023.1288499	2023
	Bacterial findings in patients referred to hospital for the treatment of acute tonsillitis with or without peritonsillar phlegmon.	Andersen C, Greve T, Reinholdt KB, Kjaerulff AMG, Udholm N, Khalid V, Madzak A, Duez C, Munch H, Pauli S, Danstrup CS, Petersen NK, Klug TE.	BMC Infect Dis	10.1186/s12879-023-08420-8	2023
Genetics	Comparative diagnostic performance of metagenomic and two targeted sequencing methods in lower respiratory infection.	Yi L, Tan L, Long Q, Lyu X, Zeng H, Peng Y, Gu D, Liu H, Ge H, Yu Y, Li Z, Hu M.	Sci Rep	10.1038/s41598-025-11834-w	2025
Phylogeny	ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.	Wang M, Fontaine S, Jiang H, Li G.	Bioinformatics	10.1093/bioinformatics/btae661	2024
	Comparison of the Oral Microbiota Structure among People from the Same Ethnic Group Living in Different Environments.	Ma G, Qiao Y, Shi H, Zhou J, Li Y.	Biomed Res Int	10.1155/2022/6544497	2022
	Distinctive salivary oral microbiome in patients with burning mouth syndrome depending on pain intensity compared to healthy subjects.	Ju HM, Ahn YW, Ok SM, Jeong SH, Na HS, Chung J.	J Dent Sci	10.1016/j.jds.2024.05.022	2025
	Mycobacterium nebraskense Isolated from Patients in Connecticut and Oregon, USA.	Metersky ML, Losier AJ, Fraulino DA, Warnock TA, Varley CD, Le AM, Winthrop KL, McArdle JR, Shakir SM, Khare R.	Emerg Infect Dis	10.3201/eid3103.240608	2025
	Idiopathic hemodynamically unstable polymicrobial purulent pericarditis: a rare case presentation.	Ased S, Payne AN, Yang C.	J Am Coll Emerg Physicians Open	10.1002/emp2.12202	2020
	Comparative analysis of the clinical characteristic and lung microbiota in adult and elderly patients with pulmonary tuberculosis	Wu S, Wang S, Wu Z, Chen M, Chen X, Lei D, Peng C.	Sci Rep		2025
	Human Salivary Microbiota Diversity According to Ethnicity, Sex, TRPV1 Variants and Sensitivity to Capsaicin.	Vinerbi E, Morini G, Picozzi C, Tofanelli S.	Int J Mol Sci	10.3390/ijms252111585	2024
	Haemophilus Parainfluenzae Septic Arthritis Following Primary All-Inside Meniscus Repair: A Case Report and Review of the Literature.	Baron JE, Shamrock AG, Volkmar AJ, Westermann RW.	Iowa Orthop J		2020
Phylogeny	Alterations of salivary microbial community associated with oropharyngeal and hypopharyngeal squamous cell carcinoma patients.	Panda M, Rai AK, Rahman T, Das A, Das R, Sarma A, Kataki AC, Chattopadhyay I.	Arch Microbiol	10.1007/s00203-019-01790-1	2020
	Screening of heat-killed lactic acid bacteria based on inhibitory activity against oral bacteria and effects of oral administration of heat-killed Ligilactobacillus salivarius CP3365 on periodontal health in healthy participants: a double-blinded, randomized, placebo-controlled trial.	Sakata S, Sakamaki Y, Yuki M, Sugaya T, Hirota T.	J Oral Microbiol	10.1080/20002297.2023.2250649	2023
	Cefpodoxime proxetil as a therapeutic option in switching therapy for infective endocarditis in children: case reports and literature review.	Krajcar N, Maric LS, Saric D, Milic N, Tesovic G.	J Chemother	10.1080/1120009x.2019.1603797	2019
	Tracheobronchitis Due to Invasive Aspergillus fumigatus in a Male With HIV With Minimal Imaging Findings.	He CA, Smith RA, Wang S, Arabian S, Hasan M.	Cureus	10.7759/cureus.18806	2021
	Profiling of the tumor-associated microbiome in patients with hepatocellular carcinoma.	Schulz C, Vilchez-Vargas R, Ocal E, Koch N, Puhr-Westerheide D, Burnell LF, Hirner-Eppeneder H, Benckert J, Pech M, Reimer P, Verslype C, Kuhl C, Tran A, Ricke J, Malfertheiner P, Alunni-Fabbroni M.	Gut Pathog	10.1186/s13099-025-00727-y	2025
Enzymology	Maintenance of the aseptic working field during endodontic treatment.	Rorslett Hardersen L, Enersen M, Kristoffersen AK, Orstavik D, Sunde PT.	Acta Odontol Scand	10.1080/00016357.2019.1606935	2019
	Radiological features and surgical management of lung abscess directly extending into the chest wall: A case report.	Kuroki S, Inomata M, Matsuo A, Kawano F, Ayabe T, Maeda R.	Int J Surg Case Rep	10.1016/j.ijscr.2023.108887	2023
Phylogeny	Oral Microbiota Development in the First 60 Months: A Longitudinal Study.	Yama K, Morishima S, Tsutsumi K, Jo R, Aita Y, Inokuchi T, Okuda T, Watai D, Ohara K, Maruyama M, Chikazawa T, Iwamoto T, Kakizawa Y, Oniki T.	J Dent Res	10.1177/00220345241272011	2024
	Esketamine prevents postoperative sleep disturbance in patients with preoperative sleep disorders: a role for oral microbiota.	Li XY, Qiu D, Du N, Hashimoto K, Wang XM, Yang JJ.	Transl Psychiatry	10.1038/s41398-025-03705-9	2025
	Haemophilus parainfluenzae endocarditis with multiple cerebral emboli in a pregnant woman with coronavirus.	De Castro A, Abu-Hishmeh M, El Husseini I, Paul L.	IDCases	10.1016/j.idcr.2019.e00593	2019
	Hemophagocytic lymphohistiocytosis associated to Haemophilus parainfluenzae endocarditis- a case report.	Costescu Strachinaru DI, Chaumont M, Gobin D, Sattar L, Strachinaru M, Karakike E, Roman A, Konopnicki D.	Acta Clin Belg	10.1080/17843286.2017.1341691	2018
	Haemophilus parainfluenza bacteremia post-ERCP and cholecystectomy in a pediatric patient: A case report.	Popov J, Strikwerda A, Gubbay J, Pai N.	J Assoc Med Microbiol Infect Dis Can	10.3138/jammi.2018-0027	2019
	Antimicrobial activity of ceftaroline and comparator agents tested against organisms isolated from patients with community-acquired bacterial pneumonia in Europe, Asia, and Latin America.	Sader HS, Flamm RK, Streit JM, Carvalhaes CG, Mendes RE.	Int J Infect Dis	10.1016/j.ijid.2018.10.004	2018
Genetics	Effect of implant abutment surface treatments on bacterial biofilm composition and structure.	Anitua E, Murias-Freijo A, Tierno R, Tejero R, Hamdan Alkhraisat M.	J Oral Microbiol	10.1080/20002297.2025.2459922	2025
	Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia Caused by Chlamydia psittaci.	Tang J, Tan W, Luo L, Xu H, Li N.	Microbiol Spectr	10.1128/spectrum.02384-21	2022
Genetics	Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft.	Fu X, Zhang M, Yuan Y, Chen Y, Ou Z, Hashim Z, Hashim JH, Zhang X, Zhao Z, Norback D, Sun Y.	Metabolites	10.3390/metabo13030343	2023
Enzymology	Clinical and microbiological findings of septic arthritis caused by Haemophilus parainfluenzae.	Cobo F, Jimenez G, Rodriguez-Granger J, Sampedro A, Aliaga-Martinez L, Navarro-Mari JM.	Med Mal Infect	10.1016/j.medmal.2017.08.002	2017
Genetics	Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia.	Zhao M, Shi Y, Zhang C, Lu M, Shen M, Xie L, Wang L, Lu A.	Microbiol Spectr	10.1128/spectrum.01087-24	2025
	The Effects of Drug Addiction and Detoxification on the Human Oral Microbiota.	Zhang J, Liu W, Shi L, Liu X, Wang M, Li W, Yu D, Wang Y, Zhang J, Yun K, Yan J.	Microbiol Spectr	10.1128/spectrum.03961-22	2023
	Endocarditis by Streptococcus pasteurianus.	Pereira C, Nogueira F, Cunha Marques J, Ferreira JP, Almeida JS.	Cureus	10.7759/cureus.34529	2023
	Development of disk diffusion susceptibility test methods for Aerococcus spp. and updates to Clinical and Laboratory Standards Institute MIC breakpoints.	Maynard R, Manuel C, Simpkins S, Haro M, Ledeboer N, Simner PJ, Fisher M, Humphries R.	J Clin Microbiol	10.1128/jcm.00115-25	2025
Pathogenicity	Responsiveness to pulmonary rehabilitation in COPD is associated with changes in microbiota.	Melo-Dias S, Cabral M, Furtado A, Souto-Miranda S, Mendes MA, Cravo J, Almeida CR, Marques A, Sousa A.	Respir Res	10.1186/s12931-023-02339-z	2023
	[Respiratory pathogen spectrum in pulmonary exacerbation of bronchiectasis in adults and its association with disease severity].	Gao YH, Guan WJ, Zhu YN, Chen RC, Zhang GJ.	Zhonghua Jie He He Hu Xi Za Zhi	10.3760/cma.j.issn.1001-0939.2019.04.002	2019
	A Lymphocyte Subset-Based Prediction Model for Refractory Community-Acquired Pneumonia in Immunocompetent Patients.	Zhang J, Hu X, Aili A, Pan L, Xue X, Chen X.	Diagnostics (Basel)	10.3390/diagnostics15131627	2025
Phylogeny	Intragastric bacterial infection and endoscopic findings in Helicobacter pylori-negative patients.	Kawai T, Kawai Y, Akimito Y, Hamada M, Iwata E, Niikura R, Nagata N, Yanagisawa K, Fukuzawa M, Itoi T, Sugimoto M.	J Clin Biochem Nutr	10.3164/jcbn.24-56	2024
	Lower respiratory tract microbiome is associated with checkpoint inhibitor pneumonitis in lung cancer patients.	Zhang D, Fan J, Liu X, Gao X, Zhou Q, Zhao J, Xu Y, Zhong W, Oh IJ, Chen M, Wang M.	Transl Lung Cancer Res	10.21037/tlcr-24-853	2024
Phylogeny	Cariogenic and oral health taxa in the oral cavity among children and adults: A scoping review.	Bhaumik D, Manikandan D, Foxman B.	Arch Oral Biol	10.1016/j.archoralbio.2021.105204	2021
	Microbiological isolates and associated complications of dacryocystitis and canaliculitis in a prominent tertiary ophthalmic teaching hospital in northern China.	Tian X, Sun H, Huang Y, Sui W, Zhang D, Sun Y, Jin J, He Y, Lu X.	BMC Ophthalmol	10.1186/s12886-024-03323-x	2024
	Influence of Non-invasive Ventilation in an Adult Patient With Acute Epiglottitis: A Case Report.	Bamadhaf W, AlRahma A, Ali K, Hamoud K.	Cureus	10.7759/cureus.30595	2022
	Oral Microbiota Alterations in Subjects with SARS-CoV-2 Displaying Prevalence of the Opportunistic Fungal Pathogen Candida albicans.	Alfaifi AA, Holm JB, Wang TW, Lim J, Meiller TF, Rock P, Sultan AS, Jabra-Rizk MA.	Microorganisms	10.3390/microorganisms12071356	2024
Pathogenicity	Substitutions in PBP3 confer resistance to both ampicillin and extended-spectrum cephalosporins in Haemophilus parainfluenzae as revealed by site-directed mutagenesis and gene recombinants.	Wienholtz NH, Barut A, Norskov-Lauritsen N.	J Antimicrob Chemother	10.1093/jac/dkx157	2017
Phylogeny	Concordance between culture, Molecular Culture and Illumina 16S rRNA gene amplicon sequencing of bone and ulcer bed biopsies in people with diabetic foot osteomyelitis.	Gramberg MCTT, Knippers C, Lagrand RS, van Hattem JM, de Goffau MC, Budding Budding AE, Davids M, Matamoros S, Nieuwdorp M, de Groot V, Heijer MD, Sabelis LWE, Peters EJG.	BMC Infect Dis	10.1186/s12879-023-08472-w	2023
	Perinatal factors influencing the earliest establishment of the infant microbiome.	Linehan K, Healy K, Hurley E, O'Shea CA, Ryan CA, Ross RP, Stanton C, Dempsey EM.	Microbiome Res Rep	10.20517/mrr.2024.92	2025
Metabolism	Brain Abscess Causes Brain Damage With Long-Lasting Focal Cerebral Hypoactivity that Correlates With Abscess Size: A Cross-Sectional 18 F-Fluoro-Deoxyglucose Positron Emission Tomography Study.	Muller EG, Dahlberg D, Hassel B, Revheim ME, Connelly JP.	Neurosurgery	10.1227/neu.0000000000003268	2024
Phylogeny	The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment.	Sanchez-Orozco NY, Rosier BT, Ruiz-Gutierrez A, Marquez-Sandoval F, Artacho A, Carrera-Quintanar L, Mira A.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00622-5	2025
	Rice body formation due to Haemophilus parainfluenza-associated chronic arthropathy.	Bhat P, Khurana S, Fanaroff R, Adams SM, Rabinowitz RP.	IDCases	10.1016/j.idcr.2020.e01030	2021
	Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit.	Song Y, Kim MS, Chung J, Na HS.	Diagnostics (Basel)	10.3390/diagnostics13101784	2023
	Endovascular Embolization of Pulmonary Sequestration Presenting With Hemoptysis: A Promising Alternative to Surgery.	Roman S, Millet C, Mekheal N, Mekheal E, Manickam R.	Cureus	10.7759/cureus.17399	2021
Genetics	Genetic Organization of Acquired Antimicrobial Resistance Genes and Detection of Resistance-Mediating Mutations in a Gallibacterium anatis Isolate from a Calf Suffering from a Respiratory Tract Infection.	Schink AK, Hanke D, Semmler T, Roschanski N, Schwarz S.	Antibiotics (Basel)	10.3390/antibiotics12020294	2023
	Fecal shedding of SARS-CoV-2 in infants born to SARS-CoV-2 positive mothers: a pilot study.	Blaufus DKP, Kalanetra KM, Pesavento R, Garlapati P, Baikie BC, Kuhn-Riordon KM, Underwood MA, Taft DH.	PeerJ	10.7717/peerj.17956	2024
Metabolism	Variability in nitrate-reducing oral bacteria and nitric oxide metabolites in biological fluids following dietary nitrate administration: An assessment of the critical difference.	Liddle L, Burleigh MC, Monaghan C, Muggeridge DJ, Sculthorpe N, Pedlar CR, Butcher J, Henriquez FL, Easton C.	Nitric Oxide	10.1016/j.niox.2018.12.003	2019
	Performance of the LifeScale automated rapid phenotypic antimicrobial susceptibility testing on Gram-negative rods directly from positive blood cultures.	Snyder JW, Chaudhry N, Hoffmann W.	J Clin Microbiol	10.1128/jcm.00922-24	2024
	Oral microbiota signatures in obesity with or without acanthosis nigricans in a Chinese cohort	Tang Y, Li Q, Ren Z, Wu N, Zhu H, Zhang T, Yi W, Ju W, Liu Y, Hu J.	J Med Microbiol		2025
Transcriptome	Global transcriptional response of oral squamous cell carcinoma cell lines to health-associated oral bacteria - an in vitro study.	Baraniya D, Chitrala KN, Al-Hebshi NN.	J Oral Microbiol	10.1080/20002297.2022.2073866	2022
Genetics	Linking periodontitis with 20 cancers, emphasis on oropharyngeal cancer: a Mendelian randomization analysis.	Xiong J, Liu H, Li C, Li Y, Feng J.	Sci Rep	10.1038/s41598-024-63447-4	2024
Phylogeny	Salivary microbiota reflecting changes in subgingival microbiota.	Jung J-S, Kook J-K, Park S-N, Lim YK, Choi GH, Kim S, Ji S.	Microbiol Spectr	10.1128/spectrum.01030-24	2024
	Features of the oral microbiome in Japanese elderly people with 20 or more teeth and a non-severe periodontal condition during periodontal maintenance treatment: A cross-sectional study.	Toyama N, Ekuni D, Yokoi A, Fukuhara D, Islam MM, Sawada N, Nakashima Y, Nakahara M, Sumita I, Morita M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.957890	2022
	Microbial variations in sputum cultures among hospitalized patients with community-acquired pneumonia: differences in sputum microbiota between asthma and COPD patients.	Uzer F, Karaboga B, Calis AG, Kaplan N, Gedik RB, Durmus AA, Inanc UB, Akgun M.	J Bras Pneumol	10.36416/1806-3756/e20230329	2024
	Gut microbiota differences in five-year-old children that were born preterm with a history of necrotizing enterocolitis: A pilot trial.	Magnusson A, Jabbari Shiadeh SM, Ardalan M, Swolin-Eide D, Elfvin A.	iScience	10.1016/j.isci.2024.110325	2024
	High-Throughput Sequencing Analysis of the Changes in the Salivary Microbiota of Hungarian Young and Adult Subpopulation by an Anthocyanin Chewing Gum and Toothbrush Change.	Skopko B, Paholcsek M, Szilagyi-Racz A, Fauszt P, David P, Stundl L, Varadi J, Kovacs R, Bagyi K, Remenyik J.	Dent J (Basel)	10.3390/dj11020044	2023
	Esophageal cancer and precancerous lesions: focus on resident bacteria and fungi.	Yuan L, Zhang Y, Wen C, Liu S, Zhang Q, Yin W, Jia Q, Chen M, Luo G, Deng M, Lv M, Xiao W.	Microbiol Spectr	10.1128/spectrum.03137-24	2025
	AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation.	Sun W, Cheng Z, Wang J, Yang J, Li X, Wang J, Chen M, Yang X, Sheng G, Lou J, Wang Y.	Proc Natl Acad Sci U S A	10.1073/pnas.2303675120	2023
Phylogeny	Dynamics of the gut microbiome in subjects challenged with Shigella sonnei 53G in a controlled human infection model.	Liechty Z, Baldwin A, Isidean S, Suvarnapunya A, Frenck R, Porter C, Goodson M.	mSphere	10.1128/msphere.00906-24	2025
Pathogenicity	Molecular Characterization of Fluoroquinolone-Resistant Haemophilus parainfluenzae Clinical Isolates in Spain.	Lopez-Hernandez I, Machuca J, Diaz de Alba P, Sarvise C, Gomez F, Rodriguez-Martinez JM, Pascual A.	Microb Drug Resist	10.1089/mdr.2016.0186	2017
Phylogeny	Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing.	Huang H, Yao T, Wu W, Zhai C, Guan T, Song Y, Sun Y, Xiao C, Liang P, Chen L.	Int J Legal Med	10.1007/s00414-018-1986-2	2019
Enzymology	Role of oral and gut microbiomes in enterosalivary nitrate metabolism and their effects on systemic disease.	Yang Z, Du C, Chang Z, Yang Y, Hu L.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1612223	2025
	Pathogen Detection and Diagnostic Scenarios in Chronic Prostatitis.	Magri V, Perletti G, Stamatiou K.	Diagnostics (Basel)	10.3390/diagnostics15060762	2025
Genetics	A severe asthma phenotype of excessive airway Haemophilus influenzae relative abundance associated with sputum neutrophilia.	Versi A, Azim A, Ivan FX, Abdel-Aziz MI, Bates S, Riley J, Uddin M, Zounemat Kermani N, Maitland-Van Der Zee AH, Dahlen SE, Djukanovic R, Chotirmall SH, Howarth P, Adcock IM, Chung KF, U-BIOPRED study group.	Clin Transl Med	10.1002/ctm2.70007	2024
	Experience in the diagnosis and treatment of pneumonia caused by infection with Tropheryma whipplei: A case series.	Fang Z, Liu Q, Tang W, Yu H, Zou M, Zhang H, Xue H, Lin S, Pei Y, Ai J, Chen J.	Heliyon	10.1016/j.heliyon.2023.e17132	2023
	A rare chest tumor in a 7-year old girl with a neurodegenerative disease.	Benhaim-Mattout E, Cano A, Di Meglio C, Bosdure E, Chabrol B, Dubus JC.	Respir Med Case Rep	10.1016/j.rmcr.2022.101648	2022
	Distribution characteristics of aerosol microorganisms in bronchoscopy room and the risk assessment of nosocomial infection.	Zhu W, Xu Y, Chen T, Shi M.	Front Public Health	10.3389/fpubh.2025.1556364	2025
	Microbial Profiles in Oral Lichen Planus: Comparisons with Healthy Controls and Erosive vs. Non-Erosive Subtypes.	Ju HM, Ahn YW, Ok SM, Jeong SH, Na HS, Chung J.	Diagnostics (Basel)	10.3390/diagnostics14080828	2024
	Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.	Guo Y, Yuan W, Lyu N, Pan Y, Cao X, Wang Y, Han Y, Zhu B.	Microorganisms	10.3390/microorganisms11030546	2023
	Haemophilus parainfluenzae urethritis through orogenital transmission.	Saxena A, Dawar R, Bora U.	Indian J Sex Transm Dis AIDS	10.4103/ijstd.ijstd_45_17	2018
	Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status.	Chang C, Wang H, Zhang L, Hao J, Wang X, Wang Y, Qi F, Lou J, Zhao J, Dong J.	Infect Drug Resist	10.2147/idr.s419892	2023
Pathogenicity	Monitoring sputum culture in resected esophageal cancer patients with preoperative treatment.	Kosumi K, Baba Y, Yamashita K, Ishimoto T, Nakamura K, Ohuchi M, Kiyozumi Y, Izumi D, Tokunaga R, Harada K, Shigaki H, Kurashige J, Iwatsuki M, Sakamoto Y, Yoshida N, Watanabe M, Baba H.	Dis Esophagus	10.1093/dote/dox092	2017
Metabolism	Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults.	Hammond TC, Green SJ, Jacobs Y, Chlipala GE, Xing X, Heil S, Chen A, Aware C, Flemister A, Stromberg A, Balchandani P, Lin AL.	Front Aging Neurosci	10.3389/fnagi.2023.1227203	2023
Pathogenicity	Fluoroquinolone, Macrolide, and Ketolide Resistance in Haemophilus parainfluenzae from South Africa.	Abotsi RE, Govinden U, Moodley K, Essack S.	Microb Drug Resist	10.1089/mdr.2016.0045	2017
	Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome.	Fitzgerald RS, Sanderson IR, Claesson MJ.	Microb Ecol	10.1007/s00248-021-01697-9	2021
	Crystal structure of the anti-CRISPR, AcrIIC4.	Kim GE, Lee SY, Park HH.	Protein Sci	10.1002/pro.4214	2021
	A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients.	Park SY, Goldman JD, Levine DJ, Haidar G.	Open Forum Infect Dis	10.1093/ofid/ofaf001	2025
	Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.	Wang JC, Bergeron M, Andersen H, Tikhtman R, Haslam D, Hunter T, Herr AB, de Alarcon A.	Laryngoscope	10.1002/lary.27356	2019
	Gut Microbiota and Fecal Microbiota Transplantation in Patients with Food Allergies: A Systematic Review.	Jensen C, Antonsen MF, Lied GA.	Microorganisms	10.3390/microorganisms10101904	2022
	Painless penile periurethral polymicrobial abscess causing urinary retention.	Tariq A, Stewart AG, Teloken PE, Dunglison NT, Martin BF, Roberts MJ.	Urol Case Rep	10.1016/j.eucr.2022.102037	2022
	Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.	Ren Y, Hao L, Liu J, Wang P, Ding Q, Chen C, Song Y.	mSystems	10.1128/msystems.01146-22	2023
	Changes in virus-related exacerbations of chronic respiratory diseases before and after the relaxation of COVID-19 infection control measures: a single-centre retrospective study in Japan.	Sasada T, Kishi R, Shirakawa C, Hirabayashi R, Sato Y, Nagata K, Nakagawa A, Tomii K, Ariyoshi K, Tachikawa R.	Ther Adv Infect Dis	10.1177/20499361251379981	2025
Metabolism	Biliary Microbiota and Bile Acid Composition in Cholelithiasis.	Petrov VA, Fernandez-Peralbo MA, Derks R, Knyazeva EM, Merzlikin NV, Sazonov AE, Mayboroda OA, Saltykova IV.	Biomed Res Int	10.1155/2020/1242364	2020
	Cardiobacterium hominis endocarditis associated with cerebral, renal, and splenic infarctions: A case report and review of the literature.	Kitagawa I, Ono R, Tobe S, Nagatsuka M.	IDCases	10.1016/j.idcr.2022.e01655	2023
	Aetiologies of Ear Infections Among Patients Who Visited King Fahad Hospital in Al-Baha, Saudi Arabia.	Alfahemi H, Alghamdi M, Fadlalla MA, Halwani M, Elbadry RM, Alghamdi MK, Alghamdi FS, Alghamdi AM, Sallam TA.	Cureus	10.7759/cureus.67885	2024
	What Is New and What Is Next for SAPHO Syndrome Management: A Narrative Review.	Ferraioli M, Levani J, De Luca R, Matucci-Cerinic C, Gattorno M, Guiducci S, Bellando Randone S, Chimenti MS.	J Clin Med	10.3390/jcm14041366	2025
Genetics	Diagnostic Value of Metagenomic Next-Generation Sequencing for Pulmonary Infection in Intensive Care Unit and Non-Intensive Care Unit Patients.	Zhou JJ, Ding WC, Liu YC, Gao YL, Xu L, Geng RL, Ye Y, Chai YF.	Front Cell Infect Microbiol	10.3389/fcimb.2022.929856	2022
	Genetic Adaptation and Acquisition of Macrolide Resistance in Haemophilus spp. during Persistent Respiratory Tract Colonization in Chronic Obstructive Pulmonary Disease (COPD) Patients Receiving Long-Term Azithromycin Treatment.	Carrera-Salinas A, Gonzalez-Diaz A, Ehrlich RL, Berbel D, Tubau F, Pomares X, Garmendia J, Dominguez MA, Ardanuy C, Huertas D, Marin A, Monton C, Mell JC, Santos S, Marti S.	Microbiol Spectr	10.1128/spectrum.03860-22	2023
	Effect of argon plasma pre-treatment of healing abutments on peri-implant microbiome and soft tissue integration: a proof-of-concept randomized study.	Canullo L, Rakic M, Corvino E, Burton M, Krumbeck JA, Chittoor Prem A, Ravida A, Ignjatovic N, Sculean A, Menini M, Pesce P.	BMC Oral Health	10.1186/s12903-023-02729-1	2023
	Probing the oral-brain connection: oral microbiome patterns in a large community cohort with anxiety, depression, and trauma symptoms, and periodontal outcomes.	Malan-Muller S, Vidal R, O'Shea E, Montero E, Figuero E, Zorrilla I, de Diego-Adelino J, Cano M, Garcia-Portilla MP, Gonzalez-Pinto A, Leza JC.	Transl Psychiatry	10.1038/s41398-024-03122-4	2024
	Differences in the microbiota of oral rinse, lesion, and normal site samples from patients with mucosal abnormalities on the tongue.	Shitozawa Y, Haro K, Ogawa M, Miyawaki A, Saito M, Fukuda K.	Sci Rep	10.1038/s41598-022-21031-8	2022
	Machine learning prediction of obesity-associated gut microbiota: identifying Bifidobacterium pseudocatenulatum as a potential therapeutic target.	Wu H, Li Y, Jiang Y, Li X, Wang S, Zhao C, Yang X, Chang B, Yang J, Qiao J.	Front Microbiol	10.3389/fmicb.2024.1488656	2024
Genetics	Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries.	Blostein F, Zou T, Bhaumik D, Salzman E, Bakulski KM, Shaffer JR, Marazita ML, Foxman B.	J Dent Res	10.1177/00220345231175356	2023
Genetics	Novel potential biomarkers for predicting childhood caries via metagenomic analysis.	Zhang H, Zheng X, Huang Y, Zou Y, Zhang T, Repo MA, Yin M, You Y, Jie Z, Xu WA.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1522970	2025
Pathogenicity	Molecular characterization of a clinical Haemophilus parainfluenzae isolate with cefotaxime resistance and decreased susceptibility to fluoroquinolones.	Faccone D, Lopez-Ruitti P, Vazquez M, Guerriero L, Lucero C, Gagetti P, Ceriana P, Corso A.	Infect Genet Evol	10.1016/j.meegid.2016.08.003	2016
	Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life.	Rosenboom I, Pust MM, Pirr S, Bakker A, Willers M, Davenport CF, Wiehlmann L, Viemann D, Tummler B.	ISME Commun	10.1038/s43705-023-00285-x	2023
	The Relationship between the Oral Microbiota and Metabolic Syndrome.	Prince Y, Davison GM, Davids SFG, Erasmus RT, Kengne AP, Graham LM, Raghubeer S, Matsha TE.	Biomedicines	10.3390/biomedicines11010003	2022
Pathogenicity	Salivary Microbial Dysbiosis Is Associated With Peri-Implantitis: A Case-Control Study in a Brazilian Population.	Pallos D, Sousa V, Feres M, Retamal-Valdes B, Chen T, Curtis M, Boaventura RM, Tanaka MH, Salomao GVDS, Zanella L, Tozetto-Mendoza TR, Schwab G, Franco LAM, Sabino EC, Braz-Silva PH, Shibli JA.	Front Cell Infect Microbiol	10.3389/fcimb.2021.696432	2021
	Conventional tobacco products harbor unique and heterogenous microbiomes.	Chattopadhyay S, Ramachandran P, Malayil L, Mongodin EF, Sapkota AR.	Environ Res	10.1016/j.envres.2022.115205	2023
	Insights into Haemophilus macrolide resistance: A comprehensive systematic review and meta-analysis.	Ahmad I, Kubaev A, Zwamel AH, R R, Baldaniya L, Kaur J, Rani B, Beig M.	PLoS Negl Trop Dis	10.1371/journal.pntd.0012878	2025
	Clostridium scindens promotes gallstone formation by inducing intrahepatic neutrophil extracellular traps through CXCL1 produced by colonic epithelial cells.	Yao W, He Y, Xie Z, Wang Q, Chen Y, Yu J, Liu X, Xue DX, Liyi W, Hao C.	Microb Cell	10.15698/mic2025.03.844	2025
Enzymology	Haemophilus Species Isolated in Urethral Exudates as a Possible Causative Agent in Acute Urethritis: A Study of 38 Cases.	Magdaleno-Tapial J, Valenzuela-Onate C, Giacaman-von der Weth MM, Ferrer-Guillen B, Martinez-Domenech A, Garcia-Legaz Martinez M, Ortiz-Salvador JM, Subiabre-Ferrer D, Hernandez-Bel P.	Actas Dermosifiliogr	10.1016/j.ad.2018.09.003	2019
	The tongue microbiome of young patients with chronic kidney disease and their healthy mothers.	Hoefer KC, Weber LT, Barbe AG, Graf I, Thom S, Nowag A, Scholz CJ, Wisplinghoff H, Noack MJ, Jazmati N.	Clin Oral Investig	10.1007/s00784-024-05492-x	2024
Pathogenicity	Systematic analyses uncover robust salivary microbial signatures and host-microbiome perturbations in oral squamous cell carcinoma.	Han Z, Hu Y, Lin X, Cheng H, Dong B, Liu X, Wu B, Xu ZZ.	mSystems	10.1128/msystems.01247-24	2025
	Differences Between Vietnamese Living in Germany and German Periodontitis Patients in Periodontal Conditions and Subgingival Microbiota.	Reichert S, Switala H, Schulz S.	Int Dent J	10.1016/j.identj.2024.09.021	2025
Enzymology	High frequency of Haemophilus influenzae associated with respiratory tract infections among Malaysian Hajj pilgrims.	Nik Zuraina NMN, Sarimah A, Suharni M, Hasan H, Suraiya S.	J Infect Public Health	10.1016/j.jiph.2018.07.010	2018
	The dual role of gut microbiota in pancreatic cancer: new insights into onset and treatment.	Cheng H, Guo H, Wen C, Sun G, Tang F, Li Y.	Ther Adv Med Oncol	10.1177/17588359251324882	2025
	Marjolin's ulcer in an ischial pressure sore presented with necrotizing soft tissue infection: A case report.	Huang CY, Hsieh ZY, Chang KC, Chang DH.	Medicine (Baltimore)	10.1097/md.0000000000033450	2023
Transcriptome	The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study.	Zakis DR, Brandt BW, van der Waal SV, Keijser BJF, Crielaard W, van der Plas DWK, Volgenant CMC, Zaura E.	J Oral Microbiol	10.1080/20002297.2024.2369350	2024
	Enhancing pathogens detection in suspected geriatric bloodstream infections using Nanopore-targeted sequencing.	Zhao M, Ouyang Y, Mei J, Liu H.	Microbiol Spectr	10.1128/spectrum.01554-24	2025
Genetics	Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.	Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N.	Nat Commun	10.1038/s41467-024-52097-9	2024
	An aggressive form of Haemophilus parainfluenzae infective endocarditis presenting with limb weakness.	McCann N, Barakat MF, Schafer F.	BMJ Case Rep	10.1136/bcr-2017-223775	2018
	Causal relationship between 412 gut microbiota, 1,400 blood metabolites, and diabetic nephropathy: a randomized Mendelian study.	Cao BN, Zhang CY, Wang Z, Wang YX.	Front Endocrinol (Lausanne)	10.3389/fendo.2024.1450428	2024
	Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer.	Hou MF, Ou-Yang F, Li CL, Chen FM, Chuang CH, Kan JY, Wu CC, Shih SL, Shiau JP, Kao LC, Kao CN, Lee YC, Moi SH, Yeh YT, Cheng CJ, Chiang CP.	Exp Mol Med	10.1038/s12276-021-00686-9	2021
	Tongue microbiome in children with autism spectrum disorder.	Abdulhaq A, Halboub E, Homeida HE, Kumar Basode V, Ghzwani AH, Zain KA, Baraniya D, Chen T, Al-Hebshi NN.	J Oral Microbiol	10.1080/20002297.2021.1936434	2021
	Comparison of the BioFire Joint Infection Panel to 16S Ribosomal RNA Gene-Based Targeted Metagenomic Sequencing for Testing Synovial Fluid from Patients with Knee Arthroplasty Failure.	Azad MA, Wolf MJ, Strasburg AP, Daniels ML, Starkey JC, Donadio AD, Abdel MP, Greenwood-Quaintance KE, Patel R.	J Clin Microbiol	10.1128/jcm.01126-22	2022
	The Difference of Gut Microbiota and Their Correlations With Urinary Organic Acids Between Autistic Children With and Without Atopic Dermatitis.	Hong RP, Hou YY, Xu XJ, Lang JD, Jin YF, Zeng XF, Zhang X, Tian G, You X.	Front Cell Infect Microbiol	10.3389/fcimb.2022.886196	2022
	Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.	Wang M, Liu YB, Tong WM, Leung WK, He LL, Xu X, Xu D, Zhou Q.	J Clin Periodontol	10.1111/jcpe.14147	2025
Genetics	Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.	Chavarria X, Park HS, Oh S, Kang D, Choi JH, Kim M, Cho YH, Yi MH, Kim JY.	Microb Genom	10.1099/mgen.0.001365	2025
	Bacterial content of the human pancreatic duct: An observational study.	Demir E, Yilmaz BS, Jager C, Rothe K, Schorn S, Pergolini I, Goss R, Safak O, Wilhelm D, Martignoni ME, Novotny AR, Friess H, Ceyhan GO, Demir IE.	Heliyon	10.1016/j.heliyon.2022.e11771	2022
	Evaluation of the Crosstalk Between the Host Mycobiome and Bacteriome in Patients with Chronic Pancreatitis.	Sarkar P, Chintaluri S, Sarkar S, Unnisa M, Jakkampudi A, Mulukutla AP, Kumari S, Reddy DN, Talukdar R.	Indian J Microbiol	10.1007/s12088-024-01207-8	2024
	The Role of the Western Diet and Oral Microbiota in Parkinson's Disease.	Zapala B, Stefura T, Milewicz T, Wator J, Piwowar M, Wojcik-Pedziwiatr M, Doregowska M, Dudek A, Jania Z, Rudzinska-Bar M.	Nutrients	10.3390/nu14020355	2022
Phylogeny	Alterations in subgingival microbiome and advanced glycation end-products levels in periodontitis with and without type 1 diabetes mellitus: a cross-sectional study.	Chen J, Wang H, Bu S, Cheng X, Hu X, Shen M, Zhuang H.	BMC Oral Health	10.1186/s12903-024-05089-6	2024
	Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 region sequences.	Larios Serrato V, Meza B, Gonzalez-Torres C, Gaytan-Cervantes J, Gonzalez Ibarra J, Santacruz Tinoco CE, Anguiano Hernandez YM, Martinez Miguel B, Cazarez Cortazar A, Sarquiz Martinez B, Alvarado Yaah JE, Mendoza Perez AR, Palma Herrera JJ, Garcia Soto LM, Chavez Rojas AI, Bravo Mateos G, Samano Marquez G, Grajales Muniz C, Torres J.	mSystems	10.1128/msystems.01062-22	2023
	Methodological establishment and diagnostic value of a multiplex fluorescent PCR assay for the detection of three fastidious respiratory pathogens.	Shi J, Zhu Y, Chen S, Shan X, Bo L, Shen K, Chen K.	PLoS One	10.1371/journal.pone.0328651	2025
	The role of non-Helicobacter pylori bacteria in the pathogenesis of gastroduodenal diseases.	Waskito LA, Rezkitha YAA, Vilaichone RK, Sugihartono T, Mustika S, Dewa Nyoman Wibawa I, Yamaoka Y, Miftahussurur M.	Gut Pathog	10.1186/s13099-022-00494-0	2022
	The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study.	Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL, Wallen GR.	Ann Hematol	10.1007/s00277-019-03599-w	2019
Pathogenicity	Inhibitory effect of 1,2,4-triazole-ciprofloxacin hybrids on Haemophilus parainfluenzae and Haemophilus influenzae biofilm formation in vitro under stationary conditions.	Kosikowska U, Andrzejczuk S, Plech T, Malm A.	Res Microbiol	10.1016/j.resmic.2016.05.009	2016
	Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype.	Yuan H, Wu X, Wang X, Zhou JY, Park S.	Int J Mol Sci	10.3390/ijms25042183	2024
Phylogeny	Exclusively Breastfed Infant Microbiota Develops over Time and Is Associated with Human Milk Oligosaccharide Intakes.	Cheema AS, Trevenen ML, Turlach BA, Furst AJ, Roman AS, Bode L, Gridneva Z, Lai CT, Stinson LF, Payne MS, Geddes DT.	Int J Mol Sci	10.3390/ijms23052804	2022
	Assessment and clinical utility of metagenomic next-generation sequencing for suspected lower respiratory tract infections.	Chen H, Huang Q, Wu W, Wang Z, Wang W, Liu Y, Ruan F, He C, Li J, Liu J, Wu G.	Eur J Med Res	10.1186/s40001-024-01806-7	2024
	Characterisation of human milk bacterial DNA profiles in a small cohort of Australian women in relation to infant and maternal factors.	Sindi AS, Cheema AS, Trevenen ML, Geddes DT, Payne MS, Stinson LF.	PLoS One	10.1371/journal.pone.0280960	2023
	A 34-Year-Old Male Intravenous Drug User with a Third Episode of Tricuspid Valve Endocarditis Treated with Repeat Valve Surgery.	Cannon JW, Hayanga JWA, Drvar TB, Ellison M, Cook C, Salman M, Roberts H, Badhwar V, Hayanga HK.	Am J Case Rep	10.12659/ajcr.927385	2021
	Pitfalls in chest CT findings of COVID-19 patients infected during hospitalisation.	Shirota G, Sato Y, Itoh D, Gonoi W, Hayashi TY, Sugita Y, Makita K.	Clin Imaging	10.1016/j.clinimag.2021.03.017	2021
	Prevalence of Slam-dependent hemophilins in Gram-negative bacteria.	Shin HE, Pan C, Curran DM, Bateman TJ, Chong DHY, Ng D, Shah M, Moraes TF.	J Bacteriol	10.1128/jb.00027-24	2024
	Cardiobacterium hominis infective endocarditis: A literature review.	Ono R, Kitagawa I, Kobayashi Y.	Am Heart J Plus	10.1016/j.ahjo.2022.100248	2023
	Transmission of maternal oral pathobionts to the infant gut predisposes offspring to exacerbated enteritis.	Haraguchi M, Kim Y, Watanabe N, Yamazaki K, Newman KL, Gillilland MG, Guo Y, Watanabe D, Bergin IL, Suzuki T, Motooka D, Sugihara K, Kitamoto S, Nagao-Kitamoto H, Kamada N.	Cell Rep	10.1016/j.celrep.2025.115974	2025
	Contribution of PBP3 Substitutions and TEM-1, TEM-15, and ROB-1 Beta-Lactamases to Cefotaxime Resistance in Haemophilus influenzae and Haemophilus parainfluenzae.	Sondergaard A, Norskov-Lauritsen N.	Microb Drug Resist	10.1089/mdr.2015.0189	2016
	Correlation analysis of intestinal flora and immune function in patients with primary hepatocellular carcinoma.	Zhang S, Hou L, Sun Q.	J Gastrointest Oncol	10.21037/jgo-22-427	2022
Phylogeny	SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.	Gong YN, Tsao KC, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR.	Emerg Microbes Infect	10.1080/22221751.2020.1782271	2020
	Oral microbiomes of patients with infective endocarditis (IE): a comparative pilot study of IE patients, patients at risk for IE and healthy controls.	Mougeot JC, Beckman M, Paster BJ, Lockhart PB, Bahrani Mougeot F.	J Oral Microbiol	10.1080/20002297.2022.2144614	2023
Phylogeny	Characteristics of tongue coating microbiota in diabetic and non-diabetic kidney patients receiving hemodialysis.	Luo Q, Chu S, Wu Y, Jin L, Liu R, Xu Y, Yu Y, Jin Y, Houndekon LOEP, Hu H, Zou Y, Huang H, Chen H.	BMC Oral Health	10.1186/s12903-025-05455-y	2025
	Effects of Mint Oils on the Human Oral Microbiome: A Pilot Study.	Abdelrahman SM, El Samak M, El-Baz LMF, Hanora AMS, Satyal P, Dosoky NS.	Microorganisms	10.3390/microorganisms12081538	2024
Enzymology	TEM-1-encoding small plasmids impose dissimilar fitness costs on Haemophilus influenzae and Haemophilus parainfluenzae.	Sondergaard A, Lund M, Norskov-Lauritsen N.	Microbiology (Reading)	10.1099/mic.0.000183	2015
	Role of Human Microbiome in Development and Management of Head and Neck Squamous Cell Carcinoma.	Palkovsky M, Modrackova N, Neuzil-Bunesova V, Liberko M, Hlodakova A, Soumarova R.	Cancers (Basel)	10.3390/cancers17132238	2025
	Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria.	Mazzamurro F, Touchon M, Charpentier X, Rocha EPC.	Mol Biol Evol	10.1093/molbev/msaf192	2025
	Analysis of the Clinical Status and Treatment of Facial Cellulitis of Odontogenic Origin in Pediatric Patients.	Slotwinska-Pawlaczyk A, Orzechowska-Wylegala B, Latusek K, Roszkowska AM.	Int J Environ Res Public Health	10.3390/ijerph20064874	2023
	A rare case of Haemophilus parainfluenzae septic knee following prolotherapy injections.	Bourget-Murray J, Frederick AL, Gibson E, French SJ.	J Clin Orthop Trauma	10.1016/j.jcot.2019.01.009	2019
	The Main Bacterial Communities Identified in the Sites Affected by Periimplantitis: A Systematic Review.	Iusan SAL, Lucaciu OP, Petrescu NB, Mirica IC, Toc DA, Albu S, Costache C.	Microorganisms	10.3390/microorganisms10061232	2022
Genetics	Oral microbiome variations related to ageing: possible implications beyond oral health.	Kazarina A, Kuzmicka J, Bortkevica S, Zayakin P, Kimsis J, Igumnova V, Sadovska D, Freimane L, Kivrane A, Namina A, Capligina V, Poksane A, Ranka R.	Arch Microbiol	10.1007/s00203-023-03464-5	2023
	Gut Microbiome and Plasma Metabolomic Analysis in Patients with Myelodysplastic Syndrome.	Jiang H, Zhao X, Zang M, Fu R, Shao Z, Liu C.	Oxid Med Cell Longev	10.1155/2022/1482811	2022
	Aging characteristics of colorectal cancer based on gut microbiota.	Wu Y, Zhuang J, Zhang Q, Zhao X, Chen G, Han S, Hu B, Wu W, Han S.	Cancer Med	10.1002/cam4.6414	2023
Genetics	Genome Characterisation of Invasive Haemophilus influenzae in Pregnancy: The Noticeable Placental Tissue Tropism Is Distributed across the Species Rather Than Linked with Capsulation or Particular Clones.	Norskov-Lauritsen N, Mohey R, Hansen DS, Duus L, Khalil MR, Wilfred SJ, Nielsen SY.	Pathogens	10.3390/pathogens12111345	2023
Phylogeny	Salivary Microbiome Profile of Diabetes and Periodontitis in a Chinese Population.	Lu C, Zhao Q, Deng J, Chen K, Jiang X, Ma F, Ma S, Li Z.	Front Cell Infect Microbiol	10.3389/fcimb.2022.933833	2022
	A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods.	Anukam KC, Agbakoba NR.	Niger J Clin Pract	10.4103/njcp.njcp_32_17	2017
	HACEK endocarditis: state-of-the-art.	Revest M, Egmann G, Cattoir V, Tattevin P.	Expert Rev Anti Infect Ther	10.1586/14787210.2016.1164032	2016
Phylogeny	Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection.	Bi Y, Wang Y, Li W, Chen Y, Qin J, Zheng H.	BMC Microbiol	10.1186/s12866-024-03709-3	2025
	Efficacy and safety of epidermal cell regeneration for postoperative non-healing wounds: a randomized, partially blinded, parallel-controlled trial	Li X, Wu H, Yang H, Wang P, Cao X, Wang P, Chen Y, Zhou Y, Li S, Hu Z, Zhu J.	Stem Cell Res Ther		2025
Phylogeny	Potential Roles of the Free Salivary Microbiome Dysbiosis in Periodontal Diseases.	Diao J, Yuan C, Tong P, Ma Z, Sun X, Zheng S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.711282	2021
Phylogeny	Comparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis.	Chen X, Zhang H, Feng J, Zhang L, Zheng M, Luo H, Zhuo H, Xu N, Zhang X, Chen C, Qu P, Li Y.	Microbiol Spectr	10.1128/spectrum.04772-22	2023
	Respiratory microbiome and metabolome features associate disease severity and the need for doxycycline treatment in children with macrolide-resistant Mycoplasma pneumoniae-mediated pneumonia	Liao W, Li S, Hsing E, Hsiao S, Chang I, Chen Y, Chen Y, Pan Y, Hsieh Y.	Front Cell Infect Microbiol		2025
	Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages.	Shridhar SV, Beghini F, Alexander M, Singh A, Juarez RM, Brito IL, Christakis NA.	Cell Rep	10.1016/j.celrep.2024.114442	2024
	HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.	Brar NK, Dhariwal A, Shekhar S, Junges R, Hakansson AP, Petersen FC.	Front Microbiol	10.3389/fmicb.2024.1406190	2024
Genetics	Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients.	Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T.	Front Cell Infect Microbiol	10.3389/fcimb.2021.708827	2021
	An Archetypical Model for Engrafting Bacteroides fragilis into Conventional Mice Following Reproducible Antibiotic Conditioning of the Gut Microbiota.	Eribo OA, Naidoo CC, Theron G, Walzl G, du Plessis N, Chegou NN.	Microorganisms	10.3390/microorganisms11020451	2023
	Human MPox (Monkeypox) Virus Membranous Keratoconjunctivitis With Transient Corneal Hypoesthesia and Late Symblepharon Formation: A Novel Case and Clinical Implications.	Uner OE, Hubbard DC, Torres-Quinones C, Pegany R, Huang L, Ponsetto MK, Fletcher M, Sikka MK, Nanji A, Redd TK, Stutzman RD, Chamberlain W, Kim DH.	Cornea	10.1097/ico.0000000000003231	2023
	Differences in oral microbiota associated with type 2 diabetes mellitus between the Dai and Han populations.	Tang L, Ding K, Li M, Chao X, Sun T, Guo Y, Peng X, Jia W, Chen T, Xie G, Feng L.	J Oral Microbiol	10.1080/20002297.2024.2442420	2025
	Differences in the landscape of colonized microorganisms in different oral potentially malignant disorders and squamous cell carcinoma: a multi-group comparative study.	Zhou X, Cai X, Tang Q, Zhang J, Bai J, Jing F, Gao L, Zhang H, Li T.	BMC Microbiol	10.1186/s12866-024-03458-3	2024
	Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.	Junca H, Steube A, Mrowietz S, Stallhofer J, Vital M, Dos Anjos Borges LG, Pieper DH, Stallmach A.	ISME Commun	10.1093/ismeco/ycae167	2025
Phylogeny	Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference.	Lei Y, Li M, Zhang H, Deng Y, Dong X, Chen P, Li Y, Zhang S, Li C, Wang S, Tao R.	mSphere	10.1128/msphere.00672-24	2025
	Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation.	Linkowska K, Bogiel T, Lamperska K, Marszalek A, Starzynski J, Szylberg L, Szwed-Kowalska A, Pawlowska M, Grzybowski T.	Sci Rep	10.1038/s41598-023-34220-w	2023
	Unveiling microbial dynamics in lung adenocarcinoma and adjacent nontumor tissues: insights from nicotine exposure and diverse clinical stages via nanopore sequencing technology.	Yang K, Wang S, Ding Z, Zhang K, Zhu W, Wang H, Pan M, Li X, Wang H, Yu Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1397989	2024
	The Role of Gastrointestinal Dysbiosis and Fecal Transplantation in Various Neurocognitive Disorders.	Castro-Vidal ZA, Mathew F, Ibrahim AA, Shubhangi F, Cherian RR, Choi HK, Begum A, Ravula HK, Giri H.	Cureus	10.7759/cureus.72451	2024
	Saliva as a non-invasive specimen for COPD assessment.	Melo-Dias S, Valente C, Andrade L, Marques A, Sousa A.	Respir Res	10.1186/s12931-022-01935-9	2022
	Infective Endocarditis and Intravenous Drug Users: Never Was and Never Will Be Taken Lightly.	Kansara T, Majmundar MM, Lenik J, Vista M, Chaudhari S.	Cureus	10.7759/cureus.12812	2021
	Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities.	Aljabr W, Dandachi I, Abbas B, Karkashan A, Al-Amari A, AlShahrani D.	Microbiol Spectr	10.1128/spectrum.04166-23	2024
	Haemophilus parainfluenzae aortic prosthetic valve endocarditis (PVE) successfully treated with oral levofloxacin.	Cunha BA, Brahmbhatt K, Raza M.	Heart Lung	10.1016/j.hrtlng.2015.04.006	2015
	Exploring the potential role of microbiota and metabolites in acute exacerbation of chronic obstructive pulmonary disease.	Shi Y, Yang J, Tian T, Li S, Xie Y.	Front Microbiol	10.3389/fmicb.2024.1487393	2024
	Haemophilus parainfluenzae Endocarditis Associated With Maxillary Sinusitis and Complicated by Cerebral Emboli in a Young Man.	Duzenli AE, Dwyer J, Carey J.	J Investig Med High Impact Case Rep	10.1177/2324709617704003	2017
Phylogeny	Oral microbiota in preschoolers with rampant caries: a matched case-control study.	Wu Y, Li G, Lyu CH, Zhou N, Wong HM.	Appl Microbiol Biotechnol	10.1007/s00253-024-13362-5	2024
	Chronic and Severe Non-Lichenoid Oral Ulcers Induced by Nivolumab - Diagnostic and Therapeutic Challenge: A Case Report.	Cardona AF, Ruiz-Patino A, Ricaurte L, Zatarain-Barron ZL, Barron F, Arrieta O.	Case Rep Oncol	10.1159/000505968	2020
	Inhibitory mechanism of CRISPR-Cas9 by AcrIIC4.	Li X, Liao F, Gao J, Song G, Zhang C, Ji N, Wang X, Wen J, He J, Wei Y, Zhang H, Li Z, Yu G, Yin H.	Nucleic Acids Res	10.1093/nar/gkad669	2023
	Hematogenous septic arthritis of a non-prosthetic shoulder caused by Capnocytophaga canimorsus: A case report and review of the literature.	Vanwielendaele M, Cherif MY, Hing M, Colman M, Ferchichi MA, Raoul JF, Maillart E, Badot V, Clevenbergh P.	IDCases	10.1016/j.idcr.2023.e01717	2023
Phylogeny	Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease.	Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H, Sawalha AH.	Clin Immunol	10.1016/j.clim.2016.06.002	2016
	Importance of experience in transoesophageal echocardiographic evaluation of vegetation size in patients with infective endocarditis: a reliability study.	Schmidt L, Ostergaard L, Grund FF, Schmidt L, Linde JJ, Kober L, Fosbol EL.	Eur Heart J Imaging Methods Pract	10.1093/ehjimp/qyae024	2024
	Machine-learning assisted discovery unveils novel interplay between gut microbiota and host metabolic disturbance in diabetic kidney disease.	Wu IW, Liao YC, Tsai TH, Lin CH, Shen ZQ, Chan YH, Tu CW, Chou YJ, Lo CJ, Yeh CH, Chen CY, Pan HC, Hsu HJ, Lee CC, Cheng ML, Sheu WH, Lai CC, Sytwu HK, Tsai TF.	Gut Microbes	10.1080/19490976.2025.2473506	2025
	E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis.	Hickman E, Roca C, Zorn BT, Rebuli ME, Robinette C, Wolfgang MC, Jaspers I.	Nicotine Tob Res	10.1093/ntr/ntae176	2024
Genetics	mBodyMap: a curated database for microbes across human body and their associations with health and diseases.	Jin H, Hu G, Sun C, Duan Y, Zhang Z, Liu Z, Zhao XM, Chen WH.	Nucleic Acids Res	10.1093/nar/gkab973	2022
Enzymology	Isolation of Haemophilus influenzae and Haemophilus parainfluenzae in urethral exudates from men with acute urethritis: a descriptive study of 52 cases.	Deza G, Martin-Ezquerra G, Gomez J, Villar-Garcia J, Supervia A, Pujol RM.	Sex Transm Infect	10.1136/sextrans-2015-052135	2016
	Case Report: Metagenomic next-generation sequencing applied in diagnosing psittacosis caused by Chlamydia psittaci infection.	Xu W, Wang Q, Li L, Zhu B, Cai Q, Yi X, Fang R, Wang Q.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1249225	2023
	Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.	Koohi-Moghadam M, Watt RM, Leung WK.	J Med Microbiol	10.1099/jmm.0.001898	2024
	Why humans should not eat broom straws: Pericarditis and endocarditis.	Novotny WE, Keel CP.	Ann Pediatr Cardiol	10.4103/apc.apc_194_19	2020
	Fatal BK polyomavirus-associated pneumonia: report of two cases with literature review.	Wang Y, Fang Y, Yan Z, Xia R, Zeng W, Deng W, Xu J, Feng X, Peng J, Miao Y.	BMC Infect Dis	10.1186/s12879-023-08577-2	2023
	Evaluation of the BioFire® FilmArray® Pneumonia plus Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method.	Szymankiewicz MT, Szczepanska A, Stefaniuk E.	Pol J Microbiol	10.33073/pjm-2023-035	2023
	Importance of early diagnosis and surgical treatment of calcified amorphous tumor-related native valve endocarditis caused by Escherichia coli: a case report.	Koito S, Unoki Y, Yoshida K, Takemoto S, Uchida T, Matono T.	BMC Infect Dis	10.1186/s12879-022-07220-w	2022
Genetics	Mendelian randomization analyses support causal relationships between gut microbiome and longevity.	Chen S, Chen W, Wang X, Liu S.	J Transl Med	10.1186/s12967-024-05823-2	2024
	A Rare Case of Osteomyelitis Caused by Haemophilus Parainfluenzae.	Cobo F, Jimenez G, Rodriguez-Granger J, Sampedro A, Aliaga-Martinez L.	J Bone Jt Infect	10.7150/jbji.17387	2017
Pathogenicity	The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs.	Palmnas-Bedard MSA, Costabile G, Vetrani C, Aberg S, Hjalmarsson Y, Dicksved J, Riccardi G, Landberg R.	Am J Clin Nutr	10.1093/ajcn/nqac217	2022
	Ischemic Stroke and Septic Shock After Subacute Endocarditis Caused by Haemophilus parainfluenzae: Case Report.	Menegueti MG, Machado-Viana J, Gaspar GG, Nicolini EA, Basile-Filho A, Auxiliadora-Martins M.	J Clin Med Res	10.14740/jocmr2703w	2017
	Tropheryma whipplei detection by metagenomic next-generation sequencing in bronchoalveolar lavage fluid: A cross-sectional study.	Lin M, Wang K, Qiu L, Liang Y, Tu C, Chen M, Wang Z, Wu J, Huang Y, Tan C, Chen Q, Zheng X, Liu J.	Front Cell Infect Microbiol	10.3389/fcimb.2022.961297	2022
Phylogeny	Investigation of a novel biofilm model close to the original oral microbiome.	Li P, Zhang Y, Chen D, Lin H.	Appl Microbiol Biotechnol	10.1007/s00253-024-13149-8	2024
Phylogeny	Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population.	Jia YJ, Liao Y, He YQ, Zheng MQ, Tong XT, Xue WQ, Zhang JB, Yuan LL, Zhang WL, Jia WH.	Front Cell Infect Microbiol	10.3389/fcimb.2021.658203	2021
	The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis.	Cai S, Yang Y, Pan J, Miao Q, Jin W, Ma Y, Zhou C, Gao X, Wang C, Hu B.	Ann Transl Med	10.21037/atm-21-2488	2021
	Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing.	Men Z, Chen Z, Gu X, Wang Y, Zhang X, Fang F, Shen M, Huang S, Wu S, Zhou L, Bai Z.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-024-04980-y	2025
	De novo thrombotic microangiopathy following simultaneous pancreas and kidney transplantation managed with eculizumab.	Shochet L, Kanellis J, Simpson I, Ta J, Mulley W.	Nephrology (Carlton)	10.1111/nep.12936	2017
Phylogeny	Salivary microbiome and MRP-8/14 levels in children with gingivitis, healthy children, and their mothers.	Blufstein A, Pejcic N, Spettel K, Hausmann B, Seki D, Ertekin T, Hinrichs-Priller J, Altner S, Nehr M, Bekes K, Makristathis A, Andrukhov O.	J Periodontol	10.1002/jper.23-0632	2024
	Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data.	Chopra A, Franco-Duarte R, Rajagopal A, Choowong P, Soares P, Rito T, Eberhard J, Jayasinghe TN.	Sci Rep	10.1038/s41598-023-50891-x	2024
	mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.	Zeng Y, Li J, Wei C, Zhao H, Wang T.	Genome Biol	10.1186/s13059-022-02657-3	2022
Genetics	Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.	Pol S, Kallonen T, Maklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J, Turner P.	mBio	10.1128/mbio.00784-24	2024
	Changes in the Composition of Unstimulated and Stimulated Saliva Due to Chewing Sour Cherry Gum and a Toothbrush Change.	Skopko BE, Homoki JR, Fazekas ME, Paholcsek M, Fauszt P, David P, Stundl L, Molnar PB, Forgacs IN, Varadi J, Bagyi KA, Remenyik J.	Cells	10.3390/cells13030251	2024
	Lung Microbial and Host Genomic Signatures as Predictors of Prognosis in Early-Stage Adenocarcinoma.	Tsay JJ, Darawshy F, Wang C, Kwok B, Wong KK, Wu BG, Sulaiman I, Zhou H, Isaacs B, Kugler MC, Sanchez E, Bain A, Li Y, Schluger R, Lukovnikova A, Collazo D, Kyeremateng Y, Pillai R, Chang M, Li Q, Vanguri RS, Becker AS, Moore WH, Thurston G, Gordon T, Moreira AL, Goparaju CM, Sterman DH, Tsirigos A, Li H, Segal LN, Pass HI.	Cancer Epidemiol Biomarkers Prev	10.1158/1055-9965.epi-24-0661	2024
	A Rapid Detection of Haemophilus influenzae Using Multiple Cross Displacement Amplification Linked With Nanoparticle-Based Lateral Flow Biosensor.	Cao Q, Liang S, Wang L, Cao J, Liu M, Li S, Cao X, Guo Y.	Front Cell Infect Microbiol	10.3389/fcimb.2021.721547	2021
Enzymology	A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach.	Barberio B, Facchin S, Patuzzi I, Ford AC, Massimi D, Valle G, Sattin E, Simionati B, Bertazzo E, Zingone F, Savarino EV.	Gut Microbes	10.1080/19490976.2022.2028366	2022
	Metagenomic Next-Generation Sequencing for Diagnostically Challenging Mucormycosis in Patients with Hematological Malignancies.	Zhang M, Lu W, Xie D, Wang J, Xiao X, Pu Y, Meng J, Lyu H, Zhao M.	Infect Drug Resist	10.2147/idr.s393201	2022
Phylogeny	Microbial Signatures in COVID-19: Distinguishing Mild and Severe Disease via Gut Microbiota.	Galeeva JS, Fedorov DE, Starikova EV, Manolov AI, Pavlenko AV, Selezneva OV, Klimina KM, Veselovsky VA, Morozov MD, Yanushevich OO, Krikheli NI, Levchenko OV, Andreev DN, Sokolov FS, Fomenko AK, Devkota MK, Andreev NG, Zaborovskiy AV, Bely PA, Tsaregorodtsev SV, Evdokimov VV, Maev IV, Govorun VM, Ilina EN.	Biomedicines	10.3390/biomedicines12050996	2024
	Clinical and Microbiological Efficacy of Pyrophosphate Containing Toothpaste: A Double-Blinded Placebo-Controlled Randomized Clinical Trial.	Hong I, Lee HG, Keum HL, Kim MJ, Jung UW, Kim K, Kim SY, Park T, Kim HJ, Kim JJ, Sul WJ, An S, Cha JK.	Microorganisms	10.3390/microorganisms8111806	2020
	Compassionate use of contezolid in a toddler with severe community-acquired pneumonia induced by staphylococcus aureus: a case report and follow-up.	Liu HY, Bi XF, Wang YJ, Xie FJ, Zhang H, Zhu YC, Zhang Y, Wang ZH, Wu D, Meng H, Lin YL, Liu LQ, Qiu SX, Gao Y, Kang K, Gao Y.	Front Pediatr	10.3389/fped.2024.1321447	2024
	Prevalence of Resistance to beta-Lactam Antibiotics and bla Genes Among Commensal Haemophilus parainfluenzae Isolates from Respiratory Microbiota in Poland.	Andrzejczuk S, Kosikowska U, Chwiejczak E, Stepien-Pysniak D, Malm A.	Microorganisms	10.3390/microorganisms7100427	2019
Genetics	Causal relationship between Helicobacter pylori infection and IgA nephropathy: a bidirectional two-sample mendelian randomization study.	Jing S, Lin L, Li J, Pan J, Qiao X.	Ren Fail	10.1080/0886022x.2024.2371055	2024
	Case report of multiple mesenteric mycotic aneurysms after perforated appendicitis.	Cuijpers ACM, de Boer SW, van der Leij C, Coolsen MME.	Int J Surg Case Rep	10.1016/j.ijscr.2021.01.064	2021
	Haemophilus parainfluenzae Mural Endocarditis: Case Report and Review of the Literature.	Giurgea LT, Lahey T.	Case Rep Infect Dis	10.1155/2016/3639517	2016
	Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach.	Mann AE, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Kelly C, DOMHaIN Study Team, Coker MO, Richards VP.	Microbiol Spectr	10.1128/spectrum.00871-23	2023
Phylogeny	The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects.	Regueira-Iglesias A, Suarez-Rodriguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C, Tomas I.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1405699	2024
	Functional metagenomics highlights varied infection states with dynamics of pathogens and antibiotic resistance in lower respiratory tract infections.	Shamim U, Yadav A, Maurya R, Devi P, Kumari P, Kanika, Khare K, Tarai B, Pandey R.	Heliyon	10.1016/j.heliyon.2024.e38380	2024
	Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.	Weng L, Cui Y, Jian W, Zhang Y, Pang L, Cao Y, Zhou Y, Liu W, Lin H, Tao Y.	Microbiol Spectr	10.1128/spectrum.02518-24	2025
	Atypical presentation of right-sided native valve infective endocarditis.	Doyle D, Lang R, Larios OE.	J Assoc Med Microbiol Infect Dis Can	10.3138/jammi-2020-0033	2021
	Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries.	Wolff D, Frese C, Schoilew K, Dalpke A, Wolff B, Boutin S.	PLoS One	10.1371/journal.pone.0219714	2019
Enzymology	[Epiglottitis with an abscess caused by Haemophilus parainfluenzae].	Juul ML, Johansen HK, Homoe P.	Ugeskr Laeger		2014
Pathogenicity	Bone marrow mesenchymal stem cells ameliorate lung injury through anti-inflammatory and antibacterial effect in COPD mice.	Liu HM, Liu YT, Zhang J, Ma LJ.	J Huazhong Univ Sci Technolog Med Sci	10.1007/s11596-017-1763-3	2017
Metabolism	Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders.	Kang DW, Ilhan ZE, Isern NG, Hoyt DW, Howsmon DP, Shaffer M, Lozupone CA, Hahn J, Adams JB, Krajmalnik-Brown R.	Anaerobe	10.1016/j.anaerobe.2017.12.007	2018
	Molecular Epidemiology and Antibiotic Resistance Analysis of Non-Typeable Haemophilus influenzae (NTHi) in Guangzhou: A Representative City of Southern China.	Wen S, Mai Y, Chen X, Xiao K, Lin Y, Xu Z, Yang L.	Antibiotics (Basel)	10.3390/antibiotics12040656	2023
Phylogeny	Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area.	Gantuya B, El-Serag HB, Matsumoto T, Ajami NJ, Oyuntsetseg K, Azzaya D, Uchida T, Yamaoka Y.	Cancers (Basel)	10.3390/cancers11040504	2019
	The Oral Microbial Ecosystem in Age-Related Xerostomia: A Critical Review.	Pei XM, Zhou LX, Tsang MW, Tai WC, Wong SC.	Int J Mol Sci	10.3390/ijms252312815	2024
	A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe: Implications for Future Studies.	Zhou DT, Mudhluli TE, Hall LJ, Manasa J, Munyati S.	Pediatric Health Med Ther	10.2147/phmt.s414766	2023
	The impact of neutrophil count on the results of metagenomic next-generation sequencing in immunocompromised febrile children.	Wang D, Chen H, Zhao C, Song H, Zhang J, Zhao F, Liang J, Xu W, Tang Y, Xu X.	Heliyon	10.1016/j.heliyon.2024.e32816	2024
	Diagnostic Significance of Metagenomic Next-Generation Sequencing for Community-Acquired Pneumonia in Southern China.	Liu H, Zhang Y, Chen G, Sun S, Wang J, Chen F, Liu C, Zhuang Q.	Front Med (Lausanne)	10.3389/fmed.2022.807174	2022
	Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.	Hu W, Chen ZM, Li XX, Lu L, Yang GH, Lei ZX, You LJ, Cui XB, Lu SC, Zhai ZY, Zeng ZY, Chen Y, Huang SL, Gong W.	Theranostics	10.7150/thno.66464	2022
	Gemella haemolysans inhibits the growth of the periodontal pathogen Porphyromonas gingivalis.	Miyoshi T, Oge S, Nakata S, Ueno Y, Ukita H, Kousaka R, Miura Y, Yoshinari N, Yoshida A.	Sci Rep	10.1038/s41598-021-91267-3	2021
	Acute septic arthritis of the acromioclavicular joint caused by Haemophilus parainfluenzae: a rare causative origin.	Hong MJ, Kim YD, Ham HD.	Clin Rheumatol	10.1007/s10067-014-2554-x	2015
	Salivary dysbiosis in Sjögren's syndrome and a commensal-mediated immunomodulatory effect of salivary gland epithelial cells.	Tseng YC, Yang HY, Lin WT, Chang CB, Chien HC, Wang HP, Chen CM, Wang JT, Li C, Wu SF, Hsieh SC.	NPJ Biofilms Microbiomes	10.1038/s41522-021-00192-w	2021
	Distinguishing the dominant species of pathogen in ethmoidal sinusitis by sequencing DNA dataset analysis.	Zhang J, He S, Li Y, Lv M, Wei H, Qu B, Zheng Y, Hu C.	Exp Ther Med	10.3892/etm.2018.6726	2018
	Identification and Validation of Signature Genes and Potential Therapy Targets of Inflammatory Bowel Disease and Periodontitis.	Xiong Z, Fang Y, Lu S, Sun Q, Huang J.	J Inflamm Res	10.2147/jir.s426004	2023
	Periodontal and Peri-Implant Microbiome Dysbiosis Is Associated With Alterations in the Microbial Community Structure and Local Stability.	Zhang Y, Li Y, Yang Y, Wang Y, Cao X, Jin Y, Xu Y, Li SC, Zhou Q.	Front Microbiol	10.3389/fmicb.2021.785191	2021
	Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer.	Sun H, Zhao X, Zhou Y, Wang J, Ma R, Ren X, Wang H, Zou L.	Biomed Res Int	10.1155/2020/4712498	2020
	Nasal colonization by potential bacterial pathogens in healthy kindergarten children of Nepal: a prevalence study.	Paudel G, Amatya N, Saud B, Wagle S, Shrestha V, Adhikari B.	Germs	10.18683/germs.2022.1309	2022
	The Effect of Probiotics on Health in Pregnancy and Infants: A Randomized, Double-Blind, Placebo-Controlled Trial.	Binda S, Chow-Shi-Yee M, El Salti S, Auclair-Ouellet N, Oula ML, Carton T, Leuillet S, Tomassi D, Hemmings R, Kadoch IJ.	Nutrients	10.3390/nu17111825	2025
	Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing.	Kumar A, Skrahina V, Atta J, Boettcher V, Hanig N, Rolfs A, Oprea G, Ameziane N.	Front Genet	10.3389/fgene.2023.1081424	2023
Phylogeny	Changes in the pharyngeal and nasal microbiota in pediatric patients with adenotonsillar hypertrophy.	Del Chierico F, Piazzesi A, Fiscarelli EV, Ristori MV, Pirona I, Russo A, Citera N, Macari G, Santarsiero S, Bianco F, Antenucci V, Damiani V, Mercuri L, De Vincentis GC, Putignani L.	Microbiol Spectr	10.1128/spectrum.00728-24	2024
Phylogeny	Necessity of 16S rRNA gene sequencing for identifying Haemophilus parainfluenzae-like strains associated with opportunistic urinary tract infections.	Chow SK, Clarridge JE.	J Med Microbiol	10.1099/jmm.0.071803-0	2014
Pathogenicity	Osteopontin protects from ovalbumin-induced asthma by preserving the microbiome and the intestinal barrier function.	Huang J, Qiao H, Li Q, Zhang Y, Zhang C, Su H, Sun X.	mSystems	10.1128/msystems.00389-25	2025
	Application of metagenomic sequencing of drainage fluid in rapid and accurate diagnosis of postoperative intra-abdominal infection: a diagnostic study.	Zhu R, Hong X, Zhang D, Xiao Y, Xu Q, Wu B, Guo J, Han X, Yang Q, Zhao Y, Wu W.	Int J Surg	10.1097/js9.0000000000000500	2023
	Gluten-free diet affects fecal small non-coding RNA profiles and microbiome composition in celiac disease supporting a host-gut microbiota crosstalk.	Francavilla A, Ferrero G, Pardini B, Tarallo S, Zanatto L, Caviglia GP, Sieri S, Grioni S, Francescato G, Stalla F, Guiotto C, Crocella L, Astegiano M, Bruno M, Calvo PL, Vineis P, Ribaldone DG, Naccarati A.	Gut Microbes	10.1080/19490976.2023.2172955	2023
	Impact the impact of gut microbiota on gastric cancer via immune cells: a comprehensive Mendelian randomization study and mediation analysis.	Wang C, Wang J, Guan W, Fei B.	Discov Oncol	10.1007/s12672-024-01285-6	2024
	Aetiologies and clinical presentation of central nervous system infections in Vietnamese patients: a prospective study.	Gabor JJ, Anh CX, Sy BT, Hoan PQ, Quyen DT, The NT, Kuk S, Kremsner PG, Meyer CG, Song LH, Velavan TP.	Sci Rep	10.1038/s41598-022-23007-0	2022
	Bone and Joint Infections due to Haemophilus parainfluenzae: Case Report and Review of the Literature.	O'Neil CR, Wilson E, Missaghi B.	Can J Infect Dis Med Microbiol	10.1155/2016/4503025	2016
Genetics	Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.	Anitua E, Murias-Freijo A, Tierno R, Tejero R, Alkhraisat MH.	BMC Oral Health	10.1186/s12903-024-04675-y	2024
	Infective endocarditis caused by Abiotrophia defectiva presenting as anterior mitral leaflet perforation mimicking cleft anterior mitral leaflet.	Gupta P, Agstam S, Angrup A, Manoj RK, Kanaujia R, Ray P.	J Family Med Prim Care	10.4103/jfmpc.jfmpc_1004_19	2020
	A case of novel, rapidly-growing Mycolicibacter kumamotonensis infection in a patient with severe pulmonary disease treated in New York City.	Weidmann MD, Wu Y, Wu F, Hapani DD, Green DA, Aaron JG, Berry GJ.	BMC Infect Dis	10.1186/s12879-022-07959-2	2023
	Haemophilus parainfluenzae endocarditis with systemic embolisation following maxillary sinusitis.	Barreto Cortes M, Teixeira V, Fernandes SR, Rego F.	BMJ Case Rep	10.1136/bcr-2016-216473	2016
	Gut Microbiome Alterations in Patients With Carotid Atherosclerosis.	Chen J, Qin Q, Yan S, Yang Y, Yan H, Li T, Wang L, Gao X, Li A, Ding S.	Front Cardiovasc Med	10.3389/fcvm.2021.739093	2021
	Human Adenovirus B7d-Associated Urethritis after Suspected Sexual Transmission, Japan.	Hanaoka N, Ito S, Nojiri N, Konagaya M, Yasuda M, Deguchi T, Fujimoto T.	Emerg Infect Dis	10.3201/eid2610.191538	2020
	Acromioclavicular Septic Arthritis Caused by Veillonella parvula.	Prod'homme M, Pfander G, Pavese P, Cech A, Abouelnaga I, Helfer L.	Case Rep Orthop	10.1155/2019/7106252	2019
	Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection.	Cai S, Yuan J, Li Y, Guo F, Lin Z, Li H, Miao Q, Fang T, Wu Y, Gao X, Li P, Liu J, Hu C, Hu B.	J Thorac Dis	10.21037/jtd-24-400	2024
	Corynebacterium matruchotii: A Confirmed Calcifying Bacterium With a Potentially Important Role in the Supragingival Plaque.	Li Q, Zhou F, Su Z, Li Y, Li J.	Front Microbiol	10.3389/fmicb.2022.940643	2022
Enzymology	Association of bacteria in pancreatic fistula fluid with complications after pancreatic surgery.	Demir E, Abdelhai K, Demir IE, Jager C, Scheufele F, Schorn S, Rothe K, Friess H, Ceyhan GO.	BJS Open	10.1002/bjs5.50272	2020
Pathogenicity	Patterns of pediatric and adolescent female genital inflammation in China: an eight-year retrospective study of 49,175 patients in China	Gao H, Zhang Y, Pan Y, Zhao M, Qi Y, Zhou M, Chan S, Huang S, Song P, Tang K, Sun L, Yuan C.	Front Public Health		2023
	Blastomycosis Presenting With Acute Airway Obstruction From a Retropharyngeal Abscess and Complicated by Severe Hypokalemia During Posaconazole Therapy: A Case Report and Review of Literature.	Hanna JJ, Guastadisegni JM, Kouma MA, Knez EB, Arasaratnam RJ, Storey DF.	Open Forum Infect Dis	10.1093/ofid/ofac414	2022
	ICEHpsaHPS7, a Novel Multiple Drug Resistance Integrative Conjugative Element in Glaesserella parasuis.	An J, Guo G, Yu D, Zhu K, Zhang C, Li Y.	Antimicrob Agents Chemother	10.1128/aac.01716-20	2021
	Examining the Composition of the Oral Microbiota as a Tool to Identify Responders to Dietary Changes.	Vach K, Al-Ahmad A, Anderson A, Woelber JP, Karygianni L, Wittmer A, Hellwig E.	Nutrients	10.3390/nu14245389	2022
Genetics	Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome.	Bhar S, Singh R, Pinna NK, Bose T, Dutta A, Mande SS.	Appl Environ Microbiol	10.1128/aem.00596-22	2022
	Hepatic Steatosis Can Be Partly Generated by the Gut Microbiota-Mitochondria Axis via 2-Oleoyl Glycerol and Reversed by a Combination of Soy Protein, Chia Oil, Curcumin and Nopal.	Sanchez-Tapia M, Tobon-Cornejo S, Noriega LG, Vazquez-Manjarrez N, Coutino-Hernandez D, Granados-Portillo O, Roman-Calleja BM, Ruiz-Margain A, Macias-Rodriguez RU, Tovar AR, Torres N.	Nutrients	10.3390/nu16162594	2024
	Rapid mortality in captive bush dogs (Speothos venaticus) caused by influenza A of avian origin (H5N1) at a wildlife collection in the United Kingdom.	Falchieri M, Reid SM, Dastderji A, Cracknell J, Warren CJ, Mollett BC, Peers-Dent J, Schlachter AD, Mcginn N, Hepple R, Thomas S, Ridout S, Quayle J, Pizzi R, Nunez A, Byrne AMP, James J, Banyard AC.	Emerg Microbes Infect	10.1080/22221751.2024.2361792	2024
Phylogeny	Natal factors influencing newborn's oral microbiome diversity.	Kim YH, Lee TY, Kim HY, Jeong SJ, Han JH, Shin JE, Lee JH, Kang CM.	Sci Rep	10.1038/s41598-024-78609-7	2024
	Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.	Choi JY, Shim B, Park Y, Kang YA.	Korean J Intern Med	10.3904/kjim.2023.097	2023
Enzymology	Rapid urease test (RUT) for evaluation of urease activity in oral bacteria in vitro and in supragingival dental plaque ex vivo.	Dahlen G, Hassan H, Blomqvist S, Carlen A.	BMC Oral Health	10.1186/s12903-018-0541-3	2018
	An Unusual Case of Neisseria flavescens/subflava Group Tricuspid Valve Endocarditis in a Patient With Previously Treated Methicillin-Resistant Staphylococcus aureus Endocarditis.	Solsi A, Findakly D, Mihyawi N, Fath AR.	Cureus	10.7759/cureus.9752	2020
	Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia.	Cui S, Guo R, Chen C, Zhang Y, Meng J, Liu L, Li Y, Kang Z, Li S, Yan Q, Ma Y.	Influenza Other Respir Viruses	10.1111/irv.13362	2024
Genetics	Gut Microbiome Alterations in Patients With Visceral Obesity Based on Quantitative Computed Tomography.	Yan H, Qin Q, Chen J, Yan S, Li T, Gao X, Yang Y, Li A, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.823262	2021
	Capturing the dynamics of microbial interactions through individual-specific networks.	Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B, Van Steen K.	Front Microbiol	10.3389/fmicb.2023.1170391	2023
	High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.	Slager J, Simpson HL, Gacesa R, Chen L, Tan IL, Gelderloos J, Maatman A, Wijmenga C, Zhernakova A, Fu J, Weersma RK, Gonera G, Jonkers IH, Withoff S.	Gut Microbes	10.1080/19490976.2025.2489071	2025
	Early mNGS testing for diagnose and prognostic prediction of early onset pneumonia among in-hospital cardiac arrest patients undergoing extracorporeal cardiopulmonary resuscitation.	Guo RM, Li XX, Zhou YH, Liu YJ, Li J, Fu GW, Zhao H, Zhang X, Zhao YC.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1382273	2024
	Gut Microbiota and Related Electronic Multisensorial System Changes in Subjects With Symptomatic Uncomplicated Diverticular Disease Undergoing Rifaximin Therapy.	De Vincentis A, Santonico M, Del Chierico F, Altomare A, Marigliano B, Laudisio A, Reddel S, Grasso S, Zompanti A, Pennazza G, Putignani L, Guarino MPL, Cicala M, Antonelli Incalzi R.	Front Med (Lausanne)	10.3389/fmed.2021.655474	2021
	Inhibitory effect of topical antibiotics/antiseptics administration on bacterial growth in the open wound of the jawbone surgery: Randomized controlled, preliminary study.	Yanamoto S, Soutome S, Tsuda S, Morishita K, Hayashida S, Harata S, Murata M, Omori K, Rokutanda S, Umeda M.	J Dent Sci	10.1016/j.jds.2020.06.020	2021
	Fast, Simple, and Highly Specific Molecular Detection of Porphyromonas gingivalis Using Isothermal Amplification and Lateral Flow Strip Methods.	Ge D, Wang F, Hu Y, Wang B, Gao X, Chen Z.	Front Cell Infect Microbiol	10.3389/fcimb.2022.895261	2022
	Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness.	Falsey AR, Branche AR, Croft DP, Formica MA, Peasley MR, Walsh EE.	J Infect Dis	10.1093/infdis/jiad221	2024
	Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study.	Ivashkin V, Shifrin O, Maslennikov R, Poluektova E, Korolev A, Kudryavtseva A, Krasnov G, Benuni N, Barbara G.	BMC Gastroenterol	10.1186/s12876-023-02690-x	2023
Phylogeny	Identification of polysaccharide capsules among extensively drug-resistant genitourinary Haemophilus parainfluenzae isolates.	Gonzalez-Diaz A, Tubau F, Pinto M, Sierra Y, Cubero M, Camara J, Ayats J, Bajanca-Lavado P, Ardanuy C, Marti S.	Sci Rep	10.1038/s41598-019-40812-2	2019
	Toxic Streptococcal Infection in Children: Report on Two Cases with Uncharacteristic Course of Scarlet Fever.	Stencel-Gabriel K, Konwant D, Szejnoga-Tulacz K.	Children (Basel)	10.3390/children10030540	2023
	Sex-specific associations between gut microbiota and skeletal muscle mass in a population-based study.	Park CH, Lee EJ, Kim HL, Lee YT, Yoon KJ, Kim HN.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13096	2022
	Leukocyte Esterase and Glucose Reagent Test Can Rule in and Rule out Septic Arthritis.	Kolbeck L, Haertle M, Graulich T, Ettinger M, Suero EM, Krettek C, Omar M.	In Vivo	10.21873/invivo.12420	2021
Pathogenicity	The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids.	Martin MJ, Zain NMM, Hearson G, Rivett DW, Koller G, Wooldridge DJ, Rose G, Gharbia SE, Forbes B, Bruce KD, Harrison TW.	PLoS One	10.1371/journal.pone.0244681	2020
	Six months of different exercise type in sedentary primary schoolchildren: impact on physical fitness and saliva microbiota composition.	Mancini A, Vitucci D, Lasorsa VA, Lupo C, Brustio PR, Capasso M, Orru S, Rainoldi A, Schena F, Buono P.	Front Nutr	10.3389/fnut.2024.1465707	2024
	Inflammatory bowel disease associated with primary sclerosing cholangitis is associated with an altered gut microbiome and bile acid profile.	Leibovitzh H, Nayeri S, Borowski K, Hernandez-Rocha C, Lee SH, Turpin W, Stempak JM, Sandhu I, Milgrom R, Smith MI, Croitoru K, Hirschfield GM, Gulamhusein A, Silverberg MS.	J Crohns Colitis	10.1093/ecco-jcc/jjae096	2024
	HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome.	Mann AE, Aumend C, Crull S, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Rowe M, Blouin T, Soule A, Kelly C, DOMHaIN Study Team, Burne RA, Coker MO, Richards VP.	Microbiome	10.1186/s40168-025-02123-9	2025
Phylogeny	Pyrosequencing Analysis of Subgingival Microbiota in Distinct Periodontal Conditions.	Park OJ, Yi H, Jeon JH, Kang SS, Koo KT, Kum KY, Chun J, Yun CH, Han SH.	J Dent Res	10.1177/0022034515583531	2015
	Thoracoscopic management of a mediastinal abscess caused by extra-esophageal migration of a metal brush bristle.	Ebrahim A, Still S, Schwartz G.	Proc (Bayl Univ Med Cent)	10.1080/08998280.2017.1416240	2018
	Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.	Mouratidis I, Chantzi N, Khan U, Konnaris MA, Chan CSY, Mareboina M, Moeckel C, Georgakopoulos-Soares I.	BMC Genomics	10.1186/s12864-023-09861-w	2023
	Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit.	Li M, Wang J, Yao Z, Liao H, Su S, Yang X, Xie M, Zheng Y.	Front Public Health	10.3389/fpubh.2023.1177069	2023
	Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods.	Kashyap P, Raj KV, Sharma J, Dutt N, Yadav P.	NPJ Syst Biol Appl	10.1038/s41540-025-00491-4	2025
Phylogeny	Haemophilus parainfluenzae urethritis among homosexual men.	Hsu MS, Wu MY, Lin TH, Liao CH.	J Microbiol Immunol Infect	10.1016/j.jmii.2012.11.007	2015
	SMT-738: a novel small-molecule inhibitor of bacterial lipoprotein transport targeting Enterobacteriaceae.	Breidenstein EBM, Khan N, Duffy T, Coward C, Avis T, Abdulle O, Li C-M, Mason CS.	Antimicrob Agents Chemother	10.1128/aac.00695-23	2024
Enzymology	Invasive disease caused by Haemophilus parainfluenzae III in a child with uropathy.	Ariza Jimenez AB, Moreno-Perez D, Nunez Cuadros E, Urda Cardona A.	J Med Microbiol	10.1099/jmm.0.047225-0	2013
Proteome	Probing the salivary proteome for prognostic biomarkers in response to non-surgical periodontal therapy.	Silbereisen A, Bao K, Wolski W, Nanni P, Kunz L, Afacan B, Emingil G, Bostanci N.	J Clin Periodontol	10.1111/jcpe.13990	2025
	A rare cause of culture negative bioprosthetic valve endocarditis: a case report of Aggregatibacter aphrophilus infection.	Wassef N, Sarkar D, Viswanathan G, Hughes GM, Salisbury T, Kuo J, de Silva R.	Eur Heart J Case Rep	10.1093/ehjcr/ytab003	2021
	Role of bronchoscopy for respiratory involvement in granulomatosis with polyangiitis and microscopic polyangiitis.	Villeneuve T, Prevot G, Pugnet G, Plat G, Heluain V, Faguer S, Guibert N.	ERJ Open Res	10.1183/23120541.00141-2023	2023
	Once upon a Time Oral Microbiota: A Cinderella or a Protagonist in Autism Spectrum Disorder?	Mussap M, Beretta P, Esposito E, Fanos V.	Metabolites	10.3390/metabo13121183	2023
	Polymicrobial infective endocarditis caused by Neisseria sicca and Haemophilus parainfluenzae.	Koshkelashvili N, Shah M, Codolosa JN, Climaco A.	IDCases	10.1016/j.idcr.2015.11.002	2016
Enzymology	A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology.	Dione N, Khelaifia S, La Scola B, Lagier JC, Raoult D.	Clin Microbiol Infect	10.1016/j.cmi.2015.10.032	2016
Enzymology	Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis.	Lv LX, Fang DQ, Shi D, Chen DY, Yan R, Zhu YX, Chen YF, Shao L, Guo FF, Wu WR, Li A, Shi HY, Jiang XW, Jiang HY, Xiao YH, Zheng SS, Li LJ.	Environ Microbiol	10.1111/1462-2920.13401	2016
Genetics	Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis.	Watts SC, Judd LM, Carzino R, Ranganathan S, Holt KE.	mSystems	10.1128/msystems.00178-21	2021
Enzymology	Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough.	Hare KM, Marsh RL, Smith-Vaughan HC, Bauert P, Chang AB.	J Med Microbiol	10.1099/jmm.0.000173	2015
	Effect of Lacticaseibacillus rhamnosus IDCC 3201 on irritable bowel syndrome with constipation: a randomized, double-blind, and placebo-controlled trial.	Kwon H, Nam EH, Kim H, Jo H, Bang WY, Lee M, Shin H, Kim D, Kim J, Kim H, Lee J, Jung YH, Yang J, Won DD, Shin M.	Sci Rep	10.1038/s41598-024-72887-x	2024
	Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease.	Zhang L, Liu X, Fan B, Chen J, Chen J, Li Q, Wu X.	Front Med (Lausanne)	10.3389/fmed.2024.1338947	2024
	Dedicator of cytokinesis 8 deficiency and hyperimmunoglobulin E syndrome: A case report.	Wang Z, Zhang Y, Li G, Huang L, Chen J.	Medicine (Baltimore)	10.1097/md.0000000000028807	2022
	Viral Infection and Respiratory Exacerbation in Children: Results from a Local German Pediatric Exacerbation Cohort.	Sallard E, Schult F, Baehren C, Buedding E, Mboma O, Ahmad-Nejad P, Ghebremedhin B, Ehrhardt A, Wirth S, Aydin M.	Viruses	10.3390/v14030491	2022
Metabolism	Title IgA Nephropathy and Oral Bacterial Species Related to Dental Caries and Periodontitis.	Nagasawa Y, Misaki T, Ito S, Naka S, Wato K, Nomura R, Matsumoto-Nakano M, Nakano K.	Int J Mol Sci	10.3390/ijms23020725	2022
	Analysis of bacterial spectrum, activin A, and CD64 in chronic obstructive pulmonary disease patients complicated with pulmonary infections.	Fei ZY, Wang J, Liang J, Zhou X, Guo M.	World J Clin Cases	10.12998/wjcc.v10.i8.2382	2022
Phylogeny	Oral microbial taxa associated with risk for SARS-CoV-2 infection.	Callahan N, Hattar M, Barbour T, Adami GR, Kawar N.	Front Oral Health	10.3389/froh.2022.886341	2022
	Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study.	Diez Lopez C, Kayser M, Vidaki A.	Front Microbiol	10.3389/fmicb.2021.647933	2021
Genetics	Temporal development and potential interactions between the gut microbiome and resistome in early childhood.	Zhao L, Yang X, Liang Y, Zhang Z, Ding Y, Wang Y, Chen B, Wu J, Jin C, Zhao G, Li Z, Zhang L.	Microbiol Spectr	10.1128/spectrum.03177-23	2024
Enzymology	Haemophilus parainfluenzae: report of an unusual cause of neonatal sepsis and a literature review.	Govind B, Veeraraghavan B, Anandan S, Thomas N.	J Infect Dev Ctries	10.3855/jidc.2243	2012
	Antitumor Necrosis Factor-like Ligand 1A Therapy Targets Tissue Inflammation and Fibrosis Pathways and Reduces Gut Pathobionts in Ulcerative Colitis.	Hassan-Zahraee M, Ye Z, Xi L, Baniecki ML, Li X, Hyde CL, Zhang J, Raha N, Karlsson F, Quan J, Ziemek D, Neelakantan S, Lepsy C, Allegretti JR, Romatowski J, Scherl EJ, Klopocka M, Danese S, Chandra DE, Schoenbeck U, Vincent MS, Longman R, Hung KE.	Inflamm Bowel Dis	10.1093/ibd/izab193	2022
	Peritonitis caused by Haemophilus parainfluenzae, Leifsonia aquatica, and Gordonia spp. in a patient undergoing continuous ambulatory peritoneal dialysis.	Gardenier JC, Sawyer RG, Sifri CD, Brayman K, Wispelway B, Bonatti H.	Surg Infect (Larchmt)	10.1089/sur.2011.009	2012
	Gut microbiome profiles to exclude the diagnosis of hepatic encephalopathy in patients with cirrhosis.	Bajaj JS, O'Leary JG, Jakab SS, Fagan A, Sikaroodi M, Gillevet PM.	Gut Microbes	10.1080/19490976.2024.2392880	2024
	Bacteria and viruses and clinical outcomes of asthma-bronchiectasis overlap syndrome: A cohort study.	Zhang XX, He JH, Pan CX, He ZF, Li HM, Lin ZH, Zhang XF, Cen LJ, Zhang RL, Shi MX, Guan WJ.	Clin Transl Allergy	10.1002/clt2.12331	2024
	Efficacy and safety of Bacteroides fragilis BF839 for pediatric autism spectrum disorder: a randomized clinical trial.	Lin CH, Zeng T, Lu CW, Li DY, Liu YY, Li BM, Chen SQ, Deng YH.	Front Nutr	10.3389/fnut.2024.1447059	2024
	Streptococcus Salivarius: A Potential Salivary Biomarker for Orofacial Granulomatosis and Crohn's Disease?	Goel RM, Prosdocimi EM, Amar A, Omar Y, Escudier MP, Sanderson JD, Wade WG, Prescott NJ.	Inflamm Bowel Dis	10.1093/ibd/izz022	2019
Phylogeny	Orientia, Rickettsia, and the microbiome in rodent attached chiggers in North Carolina, USA.	Richardson EA, Garshong R, Chen K, Crossley D, Mclean BS, Wasserberg G, Apperson CS, Roe RM, Ponnusamy L.	PLoS One	10.1371/journal.pone.0311698	2024
	Efficacy and Safety of Ceftaroline Fosamil in Hospitalized Patients with Community-Acquired Pneumonia in China: Subset Analysis of an International Phase 3 Randomized Controlled Trial.	Zhuo C, Huang Y, Liu W, Xu JF, Zhu WY, Stone GG, Yan JL, Mohamed N.	Infect Drug Resist	10.2147/idr.s342558	2022
Genetics	Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'.	Harris TM, Price EP, Sarovich DS, Norskov-Lauritsen N, Beissbarth J, Chang AB, Smith-Vaughan HC.	Microb Genom	10.1099/mgen.0.000303	2020
Metabolism	Haemophilus parainfluenzae has a limited core lipopolysaccharide repertoire with no phase variation.	Young RE, Hood DW.	Glycoconj J	10.1007/s10719-012-9455-5	2013
	Oral dysbiosis initiates periodontal disease in experimental kidney disease.	Randall D, Alsam A, Kieswich J, Joseph S, Aduse-Opoku J, Swann J, Boyde A, Davis G, Mills D, McCafferty K, Curtis M, Yaqoob MM.	Nephrol Dial Transplant	10.1093/ndt/gfae266	2025
Pathogenicity	Design, synthesis and biological evaluation of 4-benzoyl-1-dichlorobenzoylthiosemicarbazides as potent Gram-positive antibacterial agents.	Paneth A, Plech T, Kapron B, Hagel D, Kosikowska U, Kusmierz E, Dzitko K, Paneth P.	J Enzyme Inhib Med Chem	10.3109/14756366.2015.1036050	2016
	Metagenomic Analysis Reveals a Changing Microbiome Associated With the Depth of Invasion of Oral Squamous Cell Carcinoma.	Liu Y, Li Z, Qi Y, Wen X, Zhang L.	Front Microbiol	10.3389/fmicb.2022.795777	2022
	Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.	Lou S, Yang M, Li T, Zhao W, Cevasco H, Yang YT, Gerstein M.	PLoS Comput Biol	10.1371/journal.pcbi.1011222	2023
	Secondary psoas abscess after an open cholecystectomy and a common bile duct exploration.	Alvarado MU, Colindres CA, Pinto LJ, Padilla CG, Reyes CE.	Int J Surg Case Rep	10.1016/j.ijscr.2019.08.026	2019
	Efficacy of a Copper-Calcium-Hydroxide Solution in Reducing Microbial Plaque on Orthodontic Clear Aligners: A Case Report.	Meto A, Colombari B, Castagnoli A, Sarti M, Denti L, Blasi E.	Eur J Dent	10.1055/s-0039-1695653	2019
	Detection of Haemophilus influenzae by loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor assay.	Cao Q, Liang S, Lin F, Cao J, Wang L, Li H, Liu M, Wang Y, Zhao L, Cao X, Guo Y.	BMC Microbiol	10.1186/s12866-022-02547-5	2022
	Gut Microbiota Composition and Metabolic Potential of Long-Living People in China.	Zhang S, Ning R, Zeng B, Deng F, Kong F, Guo W, Zhao J, Li Y.	Front Aging Neurosci	10.3389/fnagi.2022.820108	2022
Pathogenicity	Genital carriage of the genus Haemophilus in pregnancy: species distribution and antibiotic susceptibility.	Cardines R, Daprai L, Giufre M, Torresani E, Garlaschi ML, Cerquetti M.	J Med Microbiol	10.1099/jmm.0.000083	2015
	The diagnosis of microorganism involved in infective endocarditis (IE) by polymerase chain reaction (PCR) and real-time PCR: A systematic review.	Faraji R, Behjati-Ardakani M, Moshtaghioun SM, Kalantar SM, Namayandeh SM, Soltani M, Emami M, Zandi H, Firoozabadi AD, Kazeminasab M, Ahmadi N, Sarebanhassanabadi M.	Kaohsiung J Med Sci	10.1016/j.kjms.2017.09.011	2018
Phylogeny	Comparison of human gut microbiota in control subjects and patients with colorectal carcinoma in adenoma: Terminal restriction fragment length polymorphism and next-generation sequencing analyses.	Kasai C, Sugimoto K, Moritani I, Tanaka J, Oya Y, Inoue H, Tameda M, Shiraki K, Ito M, Takei Y, Takase K.	Oncol Rep	10.3892/or.2015.4398	2016
	Subgingival microbiome is associated with alveolar bone loss measured 5 years later in postmenopausal women.	LaMonte MJ, Andrews CA, Hovey KM, Buck MJ, Li L, McSkimming DI, Banack HR, Rotterman J, Sun Y, Kirkwood KL, Wactawski-Wende J.	J Periodontol	10.1002/jper.20-0445	2021
Phylogeny	16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer.	Nardelli C, Granata I, Nunziato M, Setaro M, Carbone F, Zulli C, Pilone V, Capoluongo ED, De Palma GD, Corcione F, Matarese G, Salvatore F, Sacchetti L.	Int J Mol Sci	10.3390/ijms221910747	2021
	Grade C molar-incisor pattern periodontitis subgingival microbial profile before and after treatment.	Velsko IM, Harrison P, Chalmers N, Barb J, Huang H, Aukhil I, Shaddox L.	J Oral Microbiol	10.1080/20002297.2020.1814674	2020
Phylogeny	The oral microbiome in human immunodeficiency virus (HIV)-positive individuals.	Kistler JO, Arirachakaran P, Poovorawan Y, Dahlen G, Wade WG.	J Med Microbiol	10.1099/jmm.0.000128	2015
Genetics	Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity.	Utter DR, Borisy GG, Eren AM, Cavanaugh CM, Mark Welch JL.	Genome Biol	10.1186/s13059-020-02200-2	2020
	Effects of S-Allylcysteine-Rich Garlic Extract and Dietary Inorganic Nitrate Formula on Blood Pressure and Salivary Nitric Oxide: An Open-Label Clinical Trial Among Hypertensive Subjects.	Houston M, Chen C, D'Adamo CR, Papathanassiu AE, Green SJ.	Cureus	10.7759/cureus.45369	2023
Genetics	Comparison of the oral microbial composition between healthy individuals and periodontitis patients in different oral sampling sites using 16S metagenome profiling.	Kim YT, Jeong J, Mun S, Yun K, Han K, Jeong SN.	J Periodontal Implant Sci	10.5051/jpis.2200680034	2022
	Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis.	Molinero N, Taladrid D, Zorraquin-Pena I, de Celis M, Belda I, Mira A, Bartolome B, Moreno-Arribas MV.	Curr Issues Mol Biol	10.3390/cimb44040103	2022
	Effect of mechanically stimulated saliva on initial human dental biofilm formation.	Inui T, Palmer RJ, Shah N, Li W, Cisar JO, Wu CD.	Sci Rep	10.1038/s41598-019-48211-3	2019
	Low-FODMAP Diet for the Management of Irritable Bowel Syndrome in Remission of IBD.	Wiecek M, Panufnik P, Kaniewska M, Lewandowski K, Rydzewska G.	Nutrients	10.3390/nu14214562	2022
Proteome	Significance of integrated clinical and proteomic characteristics analysis for pathogenesis and management of Crohn's disease with concomitant psoriasis.	Zhang H, He C, Fan X, Song Q, Lin C, Zhou P, Song Y, Li N, Shi Y, Lin Z, Chen Q, Zheng Y, Wang S, Li Z, Zhang W, Liu Q, Qing Q, Sun Y, Huang B, Li M.	EBioMedicine	10.1016/j.ebiom.2025.105981	2025
	Microbiological characteristics of different tongue coatings in adults.	He C, Liao Q, Fu P, Li J, Zhao X, Zhang Q, Gui Q.	BMC Microbiol	10.1186/s12866-022-02626-7	2022
Enzymology	Tigecycline Pharmacokinetic and Pharmacodynamic Profile in Patients with Chronic Obstructive Pulmonary Disease Exacerbation.	Kipourou M, Begou O, Manika K, Ismailos G, Kontou P, Pitsiou G, Gika H, Kioumis I.	Antibiotics (Basel)	10.3390/antibiotics12020307	2023
	Identifying oral microbiome alterations in adult betel quid chewing population of Delhi, India.	Bahuguna M, Hooda S, Mohan L, Gupta RK, Diwan P.	PLoS One	10.1371/journal.pone.0278221	2023
	Impact of active lifestyle on the primary school children saliva microbiota composition.	Mancini A, Cerulli C, Vitucci D, Lasorsa VA, Parente D, Di Credico A, Orru S, Brustio PR, Lupo C, Rainoldi A, Schena F, Capasso M, Buono P.	Front Nutr	10.3389/fnut.2023.1226891	2023
Pathogenicity	Novel mechanisms of resistance to beta-lactam antibiotics in Haemophilus parainfluenzae: beta-lactamase-negative ampicillin resistance and inhibitor-resistant TEM beta-lactamases.	Garcia-Cobos S, Arroyo M, Campos J, Perez-Vazquez M, Aracil B, Cercenado E, Orden B, Lara N, Oteo J.	J Antimicrob Chemother	10.1093/jac/dks525	2013
	The Role of the Microbiome in the Pathogenesis and Treatment of Ulcerative Colitis-A Literature Review.	Swirkosz G, Szczygiel A, Logon K, Wrzesniewska M, Gomulka K.	Biomedicines	10.3390/biomedicines11123144	2023
	In vitro Activity of Lefamulin Against the Common Respiratory Pathogens Isolated From Mainland China During 2017-2019.	Wu S, Zheng Y, Guo Y, Yin D, Zhu D, Hu F.	Front Microbiol	10.3389/fmicb.2020.578824	2020
	Upper respiratory microbial communities of healthy populations are shaped by niche and age.	Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR.	Microbiome	10.1186/s40168-024-01940-8	2024
	An unusual presentation of Merkel cell carcinoma: a case report.	Howell RS, Rice JA, Sticco K, Donovan V, Castellano M, Gillette B, Gorenstein S.	J Surg Case Rep	10.1093/jscr/rjy185	2018
	A score to predict Pseudomonas aeruginosa infection in older patients with community-acquired pneumonia.	Wijit K, Sonthisombat P, Diewsurin J.	BMC Infect Dis	10.1186/s12879-023-08688-w	2023
	Investigating the human jejunal microbiota.	Villmones HC, Svanevik M, Ulvestad E, Stenstad T, Anthonisen IL, Nygaard RM, Dyrhovden R, Kommedal O.	Sci Rep	10.1038/s41598-022-05723-9	2022
	Microbial Biomarkers in Liquid Biopsy for Cancer: An Overview and Future Directions.	Luo F, Wang X, Ye C, Sun H.	Cancer Control	10.1177/10732748241292019	2024
	Comparison of Helicobacter pylori positive and negative gastric cancer via multi-omics analysis.	Shang F, Cao Y, Wan L, Ren Z, Wang X, Huang M, Guo Y.	mBio	10.1128/mbio.01531-23	2023
Enzymology	Association between HACEK bacteraemia and endocarditis.	Sen Yew H, Chambers ST, Roberts SA, Holland DJ, Julian KA, Raymond NJ, Beardsley J, Read KM, Murdoch DR.	J Med Microbiol	10.1099/jmm.0.070060-0	2014
	Exclusive Enteral Nutrition Exerts Anti-Inflammatory Effects through Modulating Microbiota, Bile Acid Metabolism, and Immune Activities.	Xiao F, Gao X, Hu H, Le J, Chen Y, Shu X, Liang Z, Xu Y, Wang Y, Zhang T.	Nutrients	10.3390/nu14214463	2022
	A pangenome approach-based loop-mediated isothermal amplification assay for the specific and early detection of Bordetella pertussis.	Juscamayta-Lopez E, Valdivia F, Soto MP, Nurena B, Horna H.	Sci Rep	10.1038/s41598-023-29773-9	2023
	Synergistic Activity of Remdesivir-Nirmatrelvir Combination on a SARS-CoV-2 In Vitro Model and a Case Report.	Gidari A, Sabbatini S, Schiaroli E, Bastianelli S, Pierucci S, Busti C, Saraca LM, Capogrossi L, Pasticci MB, Francisci D.	Viruses	10.3390/v15071577	2023
	Oral Microbiota Profile in Patients with Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis.	Esberg A, Johansson L, Berglin E, Mohammad AJ, Jonsson AP, Dahlqvist J, Stegmayr B, Johansson I, Rantapaa-Dahlqvist S.	Microorganisms	10.3390/microorganisms10081572	2022
	Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits.	Xu L, Peng B, He Y, Cui Y, Hu Q, Wu Y, Chen H, Zhou X, Chen L, Jiang M, Zuo L, Chen Q, Wu S, Liu Y, Qin Y, Shi X.	Front Microbiol	10.3389/fmicb.2021.799150	2021
Genetics	Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015-2019.	Bajanca-Lavado MP, Cavaco L, Fernandes M, Touret T, Candeias C, Simoes AS, Sa-Leao R.	Microorganisms	10.3390/microorganisms10101964	2022
Genetics	Pathogenic and genomic characterization of rabbit-sourced Pasteurella multocida serogroup F isolates recovered from dead rabbits with respiratory disease.	Wang J, Sun S, Chen D, Gao C, Sang L, Xie X.	Microbiol Spectr	10.1128/spectrum.03654-23	2024
	Clinical usefulness of a perioperative bacteriological culture to treat patients with postoperative pneumonia after esophagectomy.	Matsunaga T, Miyata H, Sugimura K, Asukai K, Yanagimoto Y, Takahashi Y, Tomokuni A, Yamamoto K, Akita H, Nishimura J, Wada H, Takahashi H, Yasui M, Omori T, Oue M, Yano M.	Ann Gastroenterol Surg	10.1002/ags3.12210	2019
	Maturation of the oral microbiota during primary teeth eruption: a longitudinal, preliminary study.	Xu H, Tian B, Shi W, Tian J, Wang W, Qin M.	J Oral Microbiol	10.1080/20002297.2022.2051352	2022
Genetics	The Cystic Fibrosis Upper and Lower Airway Metagenome.	Pienkowska K, Pust MM, Gessner M, Gaedcke S, Thavarasa A, Rosenboom I, Moran Losada P, Minso R, Arnold C, Hedtfeld S, Dorda M, Wiehlmann L, Mainz JG, Klockgether J, Tummler B.	Microbiol Spectr	10.1128/spectrum.03633-22	2023
Pathogenicity	Spectrum and antimicrobial resistance of common pathogenic bacteria isolated from patients with acute exacerbation of chronic obstructive pulmonary disease in mainland of China.	Ye F, He LX, Cai BQ, Wen FQ, Chen BY, Hadiarto M, Chen RC, Yuan JP, Sun HL.	Chin Med J (Engl)	10.3760/cma.j.issn.0366-6999.20122974	2013
	The Oral Microbiome in Periodontal Health.	Lenartova M, Tesinska B, Janatova T, Hrebicek O, Mysak J, Janata J, Najmanova L.	Front Cell Infect Microbiol	10.3389/fcimb.2021.629723	2021
	Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort.	Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J.	Infect Dis Ther	10.1007/s40121-023-00790-5	2023
	Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.	Pryor JC, Nieva C, Talley NJ, Eslick GD, Duncanson K, Burns GL, Hoedt EC, Keely S.	Gut Microbes	10.1080/19490976.2025.2500063	2025
	Gut Microbiota Composition and Its Metabolites in Different Stages of Chronic Kidney Disease.	Chen TH, Liu CW, Ho YH, Huang CK, Hung CS, Smith BH, Lin JC.	J Clin Med	10.3390/jcm10173881	2021
	Intratumoral microbiota: implications for cancer onset, progression, and therapy.	Wu J, Zhang P, Mei W, Zeng C.	Front Immunol	10.3389/fimmu.2023.1301506	2023
Pathogenicity	Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial.	Santamarina AB, Filho VN, de Freitas JA, Franco LAM, Martins RC, Fonseca JV, Orellana Turri JA, Hufnagel MT, Demarque DP, da Silva BFRB, Gusmao AF, Olivieri EHR, de Souza E, de Souza EA, Otoch JP, Pessoa AFM.	Mol Nutr Food Res	10.1002/mnfr.202400806	2025
	First Application of Fecal Microbiota Transplantation in Adult Asperger Syndrome With Digestive Symptoms-A Case Report.	Huang HL, Xu HM, Liu YD, Shou DW, Chen HT, Nie YQ, Li YQ, Zhou YJ.	Front Psychiatry	10.3389/fpsyt.2022.695481	2022
	Application of plasma metagenomic next-generation sequencing improves prognosis in hematology patients with neutropenia or hematopoietic stem cell transplantation for infection.	Chen Y, Wang J, Gan X, Li M, Liao Y, Zhou Y, Niu T.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1338307	2024
	Direct Real-Time PCR for the Detection and Serotyping of Haemophilus influenzae without DNA Extraction.	Marasini D, Whaley MJ, Jenkins LT, Hu F, Jiang W, Topaz N, Chen A, Schmink S, Dolan Thomas J, Harcourt BH, Marjuki H, Wang X.	J Clin Microbiol	10.1128/jcm.02111-21	2022
Enzymology	Rapid detection of Haemophilus influenzae and Haemophilus parainfluenzae in nasopharyngeal swabs by multiplex PCR.	Tian GZ, Zhang LJ, Wang XL, Zhang L, Li SF, Gu CM, Sun J, Cui BY.	Biomed Environ Sci	10.3967/0895-3988.2012.03.016	2012
	Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units.	Chien JY, Yu CJ, Hsueh PR.	Microbiol Spectr	10.1128/spectrum.00746-22	2022
Enzymology	[Pancreatic pseudocyst infection caused by Haemophilus parainfluenzae. Report of one case].	Martin-Berra M, Navarro-Lopez V, Sirvent E, Jimenez M.	Rev Med Chil	/s0034-98872011000200011	2011
	A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit.	Vongbhavit K, Salinero LK, Kalanetra KM, Masarweh C, Yu A, Taft DH, Mills DA, Underwood MA.	J Perinatol	10.1038/s41372-022-01452-z	2022
	coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies.	Calle ML, Pujolassos M, Susin A.	BMC Bioinformatics	10.1186/s12859-023-05205-3	2023
	A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.	Villani A, Fontana A, Panebianco C, Ferro C, Copetti M, Pavlovic R, Drago D, Fiorentini C, Terracciano F, Bazzocchi F, Canistro G, Pisati F, Maiello E, Latiano TP, Perri F, Pazienza V.	Gut Microbes	10.1080/19490976.2024.2375483	2024
	Development and clinical application of a endonuclease restriction real-time loop-mediated isothermal amplification (ERT-LAMP) assay for rapid detection of Haemophilus influenzae.	Cheng J, Zhou Y, Zhao X, Lu J, Wu J, Wang Y.	Front Microbiol	10.3389/fmicb.2022.1037343	2022
	Clinical helminth infections alter host gut and saliva microbiota.	Gobert GN, Atkinson LE, Lokko A, Yoonuan T, Phuphisut O, Poodeepiyasawat A, Homsuwan N, Mousley A, Adisakwattana P.	PLoS Negl Trop Dis	10.1371/journal.pntd.0010491	2022
	Case Report of Haemophilus parainfluenzae Sepsis in a Newborn Infant Following Water Birth and a Review of Literature.	Kaushik M, Bober B, Eisenfeld L, Hussain N.	AJP Rep	10.1055/s-0035-1556068	2015
	Trend of pathogens and respiratory co-infections in the province of Messina: from pediatric age to senescence.	Genovese C, Gorgone M, Genovese G, LA Spada G, Balsamo D, Calderone SM, Faranda I, Squeri R.	J Prev Med Hyg	10.15167/2421-4248/jpmh2024.65.3.3344	2024
	Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults.	Li X, Brejnrod A, Thorsen J, Zachariasen T, Trivedi U, Russel J, Vestergaard GA, Stokholm J, Rasmussen MA, Sorensen SJ.	Nat Commun	10.1038/s41467-023-44289-6	2023
	The Effect of Amino Sugars on the Composition and Metabolism of a Microcosm Biofilm and the Cariogenic Potential against Teeth and Dental Materials.	Zeng L, Walker AR, Calderon PDS, Xia X, Ren F, Esquivel-Upshaw JF.	J Funct Biomater	10.3390/jfb13040223	2022
	Prolonged mask wearing does not alter the oral microbiome, salivary flow rate or gingival health status - A pilot study.	Au S, Baraniya D, Dao J, Awan SB, Alvarez J, Sklar S, Chen T, Puri S, Al-Hebshi NN.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1039811	2022
Pathogenicity	Haemophilus parainfluenzae as a marker of the upper respiratory tract microbiota changes under the influence of preoperative prophylaxis with or without postoperative treatment in patients with lung cancer.	Kosikowska U, Biernasiuk A, Rybojad P, Los R, Malm A.	BMC Microbiol	10.1186/s12866-016-0679-6	2016
	Haemophilus pittmaniae and Leptotrichia spp. Constitute a Multi-Marker Signature in a Cohort of Human Papillomavirus-Positive Head and Neck Cancer Patients.	Mougeot JC, Beckman MF, Langdon HC, Lalla RV, Brennan MT, Bahrani Mougeot FK.	Front Microbiol	10.3389/fmicb.2021.794546	2021
	Detection and characterization of bacterial nucleic acids in culture-negative synovial tissue and fluid samples from rheumatoid arthritis or osteoarthritis patients.	Zhao Y, Chen B, Li S, Yang L, Zhu D, Wang Y, Wang H, Wang T, Shi B, Gai Z, Yang J, Heng X, Yang J, Zhang L.	Sci Rep	10.1038/s41598-018-32675-w	2018
	The effect of dental material type and masticatory forces on periodontitis-derived subgingival microbiomes.	Montoya C, Baraniya D, Chen T, Al-Hebshi NN, Orrego S.	Biofilm	10.1016/j.bioflm.2024.100199	2024
	Efficacy of Omadacycline against Multidrug-Resistant Enterococcus faecium Strains in a Mouse Peritonitis Model.	Singh KV, Arias CA, Murray BE.	Antimicrob Agents Chemother	10.1128/aac.00709-21	2021
Genetics	miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.	Liu L, Cao S, Lin W, Gao Z, Yang L, Zhu L, Yang B, Zhang G, Zhu R, Wu D.	Gut Microbes	10.1080/19490976.2024.2434029	2024
	Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis.	Kosikowska U, Rybojad P, Stepien-Pysniak D, Zbikowska A, Malm A.	BMC Infect Dis	10.1186/s12879-016-1793-7	2016
Metabolism	Enrichment of polycyclic aromatic hydrocarbon metabolizing microorganisms on the oral mucosa of tobacco users.	Tao L, Chiarelli MP, Pavlova S, Kolokythas A, Schwartz J, DeFrancesco J, Salameh B, Green SJ, Adami G.	PeerJ	10.7717/peerj.16626	2024
	Chemical composition of essential oils of eight Tunisian Eucalyptus species and their antibacterial activity against strains responsible for otitis.	Ameur E, Sarra M, Yosra D, Mariem K, Nabil A, Lynen F, Larbi KM.	BMC Complement Med Ther	10.1186/s12906-021-03379-y	2021
	Oral pathobiont Klebsiella chaperon usher pili provide site-specific adaptation for the inflamed gut mucosa.	Guo Y, Kitamoto S, Caballero-Flores G, Kim Y, Watanabe D, Sugihara K, Nunez G, Alteri CJ, Inohara N, Kamada N.	Gut Microbes	10.1080/19490976.2024.2333463	2024
	Structural studies of the lipopolysaccharide from Haemophilus parainfluenzae strain 20.	Vitiazeva V, Twelkmeyer B, Young R, Hood DW, Schweda EK.	Carbohydr Res	10.1016/j.carres.2011.07.006	2011
	The functional landscape of the appendix microbiome under conditions of health and disease	Sagor M, Islam T, Tamanna N, Bappy M, Danishuddin, Haque M, Lackner M.	Gut Pathog		2025
Phylogeny	Variations in the oral microbiome and metabolome of methamphetamine users.	Wang D, Feng Y, Yang M, Sun H, Zhang Q, Wang R, Tong S, Su R, Jin Y, Wang Y, Lu Z, Han L, Sun Y.	mSystems	10.1128/msystems.00991-23	2024
Phylogeny	Dietary phytochemicals, gut microbiota composition, and health outcomes in human and animal models.	Mirmohammadali SN, Rosenkranz SK.	Biosci Microbiota Food Health	10.12938/bmfh.2022-078	2023
Transcriptome	Metatranscriptome Analysis of Nasopharyngeal Swabs across the Varying Severity of COVID-19 Disease Demonstrated Unprecedented Species Diversity.	Hyblova M, Hadzega D, Babisova K, Krumpolec P, Gnip A, Sabaka P, Lassan S, Minarik G.	Microorganisms	10.3390/microorganisms11071804	2023
	A potential oral microbiome signature associated with coronary artery disease in Tunisia.	Bouzid F, Gtif I, Alfadhli S, Charfeddine S, Ghorbel W, Abdelhedi R, Benmarzoug R, Abid L, Bouayed Abdelmoula N, Elloumi I, Masmoudi S, Rebai A, Kharrat N.	Biosci Rep	10.1042/bsr20220583	2022
	Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.	Jin D-M, Morton JT, Bonneau R.	mSystems	10.1128/msystems.00295-24	2024
	Molecular commensalism-how to investigate underappreciated health-associated polymicrobial communities.	Labossiere A, Ramsey M, Merritt J, Kreth J.	mBio	10.1128/mbio.01342-23	2023
	Prosthetic Joint Infection After Dental Work: Is the Correct Prophylaxis Being Prescribed? A Systematic Review.	Danilkowicz RM, Lachiewicz AM, Lorenzana DJ, Barton KD, Lachiewicz PF.	Arthroplast Today	10.1016/j.artd.2020.11.007	2021
	High-resolution computed tomography features associated with differentiation of tuberculosis among elderly patients with community-acquired pneumonia: a multi-institutional propensity-score matched study.	Komiya K, Yamasue M, Goto A, Nakamura Y, Hiramatsu K, Kadota JI, Kato S.	Sci Rep	10.1038/s41598-022-11625-7	2022
	Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study.	Bankvall M, Carda-Dieguez M, Mira A, Karlsson A, Hasseus B, Karlsson R, Robledo-Sierra J.	J Oral Microbiol	10.1080/20002297.2022.2161726	2023
	Susceptibility of microorganisms causing acute hand infections.	Fuchsjager N, Winterleitner H, Krause R, Feierl G, Koch H.	PLoS One	10.1371/journal.pone.0220555	2019
Pathogenicity	Detection of bile acids in bronchoalveolar lavage fluid defines the inflammatory and microbial landscape of the lower airways in infants with cystic fibrosis.	Caparros-Martin JA, Saladie M, Agudelo-Romero SP, Reen FJ, Ware RS, Sly PD, Stick SM, O'Gara F, COMBAT study group.	Microbiome	10.1186/s40168-023-01543-9	2023
	Etiology, Clinical Course, and Outcomes of Pneumonia in the Elderly: A Retrospective and Prospective Cohort Study in Thailand.	Osman M, Manosuthi W, Kaewkungwal J, Silachamroon U, Mansanguan C, Kamolratanakul S, Pitisuttithum P.	Am J Trop Med Hyg	10.4269/ajtmh.20-1393	2021
Pathogenicity	Diversion of the host humoral response: a novel virulence mechanism of Haemophilus influenzae mediated via outer membrane vesicles.	Deknuydt F, Nordstrom T, Riesbeck K.	J Leukoc Biol	10.1189/jlb.1013527	2014
Pathogenicity	In Vitro and Intracellular Activities of Omadacycline against Legionella pneumophila.	Dubois J, Dubois M, Martel JF.	Antimicrob Agents Chemother	10.1128/aac.01972-19	2020
Metabolism	Impacts of Cigarette Smoking Status on Metabolomic and Gut Microbiota Profile in Male Patients With Coronary Artery Disease: A Multi-Omics Study.	Hu X, Fan Y, Li H, Zhou R, Zhao X, Sun Y, Zhang S.	Front Cardiovasc Med	10.3389/fcvm.2021.766739	2021
	Changes in gut microbial community upon chronic kidney disease.	Liu W, Huang J, Liu T, Hu Y, Shi K, Zhou Y, Zhang N.	PLoS One	10.1371/journal.pone.0283389	2023
Transcriptome	The Colorectal Cancer Gut Environment Regulates Activity of the Microbiome and Promotes the Multidrug Resistant Phenotype of ESKAPE and Other Pathogens.	Lamaudiere MTF, Arasaradnam R, Weedall GD, Morozov IY.	mSphere	10.1128/msphere.00626-22	2023
	Nasal and Pharyngeal Colonization by Bacterial Pathogens: A Comparative Study between Preclinical and Clinical Sciences Medical Students.	Bhatta DR, Hamal D, Shrestha R, Parajuli R, Baral N, Subramanya SH, Nayak N, Gokhale S.	Can J Infect Dis Med Microbiol	10.1155/2018/7258672	2018
	Exploring the Potential of Oral Microbiome Biomarkers for Colorectal Cancer Diagnosis and Prognosis: A Systematic Review.	Negrut RL, Cote A, Maghiar AM.	Microorganisms	10.3390/microorganisms11061586	2023
	Management of Cepacia Syndrome With a Combination of Intravenous and Inhaled Antimicrobials in a Non-Cystic Fibrosis Pediatric Patient.	Branstetter JW, Yarbrough A, Poole C.	J Pediatr Pharmacol Ther	10.5863/1551-6776-25.8.730	2020
	Comparing Several Treatments with Antibiotics for Community-Acquired Pneumonia: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.	Bai F, Li X.	Iran J Public Health	10.18502/ijph.v50i6.6410	2021
	Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients.	Zhang F, Chen J, Huang H, Deng X, Zhang W, Zeng M, Liu R, Dai L, Wan Q.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-021-04254-x	2021
Phylogeny	Tongue Microbiota Composition and Dental Caries Experience in Primary School Children.	Zhang D, Takeshita T, Furuta M, Kageyama S, Asakawa M, Nambu K, Yamashita Y.	mSphere	10.1128/msphere.01252-20	2021
	Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study.	Bao R, Mei Q, Yang T, Zhang L, Zhu C, Fan X, Wang Y, Tong F, He Y, Fang X, Geng S, Yang Y, Sheng X, Pan A.	BMC Infect Dis	10.1186/s12879-023-08376-9	2023
	[An adult case of haemophilus parainfluenzae bacteremia and meningitis].	Kangas I.	Ugeskr Laeger		2010
	Evaluation of Staphylococcus aureus Colonization in Adult Patients Undergoing Tonsillectomy for Recurrent Tonsillitis.	Klagisa R, Racenis K, Broks R, Kise L, Kroica J.	Pathogens	10.3390/pathogens11040427	2022
	Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review.	Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.804644	2022
	Transesophageal Echocardiography vs. Transthoracic Echocardiography for Methicillin-Sensitive Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus Endocarditis.	Henriquez E, Fatima N, Sayabugari R, Nasim MH, Noorayingarath H, Bai K, Garcia A, Habib A, Patel TP, Shaikh F, Razzaq W, Abdin ZU, Gupta I.	Cureus	10.7759/cureus.39996	2023
Genetics	Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.	Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS, Kim SY.	BMC Microbiol	10.1186/s12866-023-03084-5	2023
	Respirable Metals, Bacteria, and Fungi during a Saharan-Sahelian Dust Event in Houston, Texas.	Das S, McEwen A, Prospero J, Spalink D, Chellam S.	Environ Sci Technol	10.1021/acs.est.3c04158	2023
	Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth.	Mendz GL, Petersen R, Quinlivan JA, Kaakoush NO.	BMJ Case Rep	10.1136/bcr-2014-205282	2014
Genetics	Dysbiosis by Eradication of Helicobacter pylori Infection Associated with Follicular Gastropathy and Pangastropathy	Gomez-Ramirez U, Nolasco-Romero C, Contreras-Rodriguez A, Zuniga G, Mendoza-Elizalde S, Prado-Galbarro F, Perez Aguilar F, Pedraza Tinoco J, Valencia-Mayoral P, Velazquez-Guadarrama N.	Microorganisms		2023
	The First Known Case of Liver Abscess Caused by Aggregatibacter aphrophilus in Japan.	Okumura T, Soya K, Hihara Y, Muraoka S, Nishimura Y, Inoue K, Maruyama A, Matsumoto G.	Intern Med	10.2169/internalmedicine.4220-19	2020
	The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients.	Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B, Sun Z.	Front Cell Infect Microbiol	10.3389/fcimb.2019.00090	2019
	Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections.	He P, Wang J, Ke R, Zhang W, Ning P, Zhang D, Yang X, Shi H, Fang P, Ming Z, Li W, Zhang J, Dong X, Liu Y, Zhou J, Xia H, Yang S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1042945	2022
	Haemophilus parainfluenzae infective endocarditis associated with pelvic abscess: an uncommon complication of endometriosis.	Miquel-Goulenok T, Le Tohic A, Laurichesse JJ, Iung B, Leport C, Longuet P.	Clin Exp Obstet Gynecol		2010
	Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.	Relvas M, Regueira-Iglesias A, Balsa-Castro C, Salazar F, Pacheco JJ, Cabral C, Henriques C, Tomas I.	Sci Rep	10.1038/s41598-020-79875-x	2021
	The Biofire® Filmarray® Pneumonia Plus panel for management of lower respiratory tract infection in mechanically-ventilated patients in the COVID-19 era: a diagnostic and cost-benefit evaluation.	Ferrer J, Clari MA, Gimenez E, Carbonell N, Torres I, Blasco ML, Albert E, Navarro D.	Diagn Microbiol Infect Dis	10.1016/j.diagmicrobio.2022.115847	2023
Phylogeny	Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study.	Frid P, Baraniya D, Halbig J, Rypdal V, Songstad NT, Rosen A, Berstad JR, Flato B, Alakwaa F, Gil EG, Cetrelli L, Chen T, Al-Hebshi NN, Nordal E, Al-Haroni M.	Front Cell Infect Microbiol	10.3389/fcimb.2020.602239	2020
Genetics	Identification of hidden N4-like viruses and their interactions with hosts.	Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang Y-Z, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M.	mSystems	10.1128/msystems.00197-23	2023
Pathogenicity	Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis.	Choo JM, Abell GCJ, Thomson R, Morgan L, Waterer G, Gordon DL, Taylor SL, Leong LEX, Wesselingh SL, Burr LD, Rogers GB.	mSphere	10.1128/msphere.00103-18	2018
	Multicenter Clinical Performance Evaluation of Omadacycline Susceptibility Testing of Enterobacterales on VITEK 2 Systems.	Csiki-Fejer E, Traczewski M, Procop GW, Davis TE, Hackel M, Dwivedi HP, Pincus DH.	J Clin Microbiol	10.1128/jcm.00174-23	2023
	Infections and immune dysregulation in ataxia-telangiectasia children with hyper-IgM and non-hyper-IgM phenotypes: A single-center experience.	Szczawinska-Poplonyk A, Tapolska-Jozwiak K, Schwartzmann E, Pietrucha B.	Front Pediatr	10.3389/fped.2022.972952	2022
	Replication-associated inversions are the dominant form of bacterial chromosome structural variation.	D'Iorio M, Dewar K.	Life Sci Alliance	10.26508/lsa.202201434	2023
Pathogenicity	Ocular surface infections in northeastern state of malaysia: a 10-year review of bacterial isolates and antimicrobial susceptibility.	Rahman ZA, Harun A, Hasan H, Mohamed Z, Noor SS, Deris ZZ, Ismail N, Hassan AS, Ahmad F, Yaakub A.	Eye Contact Lens	10.1097/icl.0b013e3182a3026b	2013
	Bank1 deficiency reshapes the gut microbiota of lupus mice towards an anti-inflammatory composition.	Galicia G, Botia-Sanchez M, Toro-Dominguez D, Garcia AL, Valera JR, Gomez Hernandez G, Fernandez RM, Carmona N, Luque G, Morell M, Varela N, Perez-Cozar F, Margolles A, Aguilera M, Alarcon-Riquelme ME.	Front Immunol	10.3389/fimmu.2025.1586025	2025
	Interactions and effects of a stannous-containing sodium fluoride dentifrice on oral pathogens and the oral microbiome.	Chen D, Chew D, Xiang Q, Lam T, Dai Y, Liu J, Wang L, He T, Strand R, Zhang X, Lim L, Xu J, Shi Y, Dong W.	Front Microbiol	10.3389/fmicb.2024.1327913	2024
Genetics	Guild-level signature of gut microbiome for diabetic kidney disease.	Tang S, Wu G, Liu Y, Xue B, Zhang S, Zhang W, Jia Y, Xie Q, Liang C, Wang L, Heng H, Wei W, Shi X, Hu Y, Yang J, Zhao L, Wang X, Zhao L, Yuan H.	mBio	10.1128/mbio.00735-24	2024
	Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia.	Tesfaw G, Siraj DS, Abdissa A, Jakobsen RR, Johansen OH, Zangenberg M, Hanevik K, Mekonnen Z, Langeland N, Bjorang O, Safdar N, Mapes AC, Kates A, Krych L, Castro-Mejia JL, Nielsen DS.	Nat Commun	10.1038/s41467-024-51464-w	2024
	Staphylococcus aureus and other skin and soft tissue infections among basic military trainees, Lackland Air Force Base, Texas, 2008-2012.	Webber BJ, Federinko SP, Tchandja JN, Cropper TL, Keller PL.	MSMR		2013
	Efficacy of Delafloxacin versus Moxifloxacin against Bacterial Respiratory Pathogens in Adults with Community-Acquired Bacterial Pneumonia (CABP): Microbiology Results from the Delafloxacin Phase 3 CABP Trial.	McCurdy S, Keedy K, Lawrence L, Nenninger A, Sheets A, Quintas M, Cammarata S.	Antimicrob Agents Chemother	10.1128/aac.01949-19	2020
	Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases.	Chung M, Zhao N, Meier R, Koestler DC, Wu G, de Castillo E, Paster BJ, Charpentier K, Izard J, Kelsey KT, Michaud DS.	J Oral Microbiol	10.1080/20002297.2021.1887680	2021
Transcriptome	Establishing diagnosis of Haemophilus parainfluenzae as etiology of culture-negative endocarditis using DNA sequence analysis on tissue specimen.	Kelesidis T, Kelesidis I, Lewinski MA, Humphries R.	Am J Med	10.1016/j.amjmed.2011.02.026	2011
	AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain.	Kim GE, Park HH.	Nucleic Acids Res	10.1093/nar/gkae357	2024
	The Role of Indoor Microbiome and Metabolites in Shaping Children's Nasal and Oral Microbiota: A Pilot Multi-Omic Analysis.	Zhang M, Tang H, Yuan Y, Ou Z, Chen Z, Xu Y, Fu X, Zhao Z, Sun Y.	Metabolites	10.3390/metabo13101040	2023
Phylogeny	Identifying the oral microbiome of adolescents with and without dental fluorosis based on full-length 16S rRNA gene sequencing.	Luo S, Shao R, Hong Y, Zhang T, Zhou Q, Zhou Q, Rao F, Zhao X, Dong Y, Zhu R, Ling P, Cui G, Guan Z, Luo P, He Y, Qi X, Liao J, Hong W.	Front Microbiol	10.3389/fmicb.2024.1296753	2024
Metabolism	2'-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations.	Versluis DM, Schoemaker R, Looijesteijn E, Geurts JMW, Merks RMH.	iScience	10.1016/j.isci.2024.109085	2024
	The effect of physical and psychological stress on the oral microbiome.	Stoy S, McMillan A, Ericsson AC, Brooks AE.	Front Psychol	10.3389/fpsyg.2023.1166168	2023
Genetics	Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients.	Kouraki A, Zheng AS, Miller S, Kelly A, Ashraf W, Bazzani D, Bonadiman A, Tonidandel G, Bolzan M, Vijay A, Nightingale J, Menni C, Ollivere BJ, Valdes AM.	iScience	10.1016/j.isci.2024.110783	2024
	Induced sputum compared to bronchoalveolar lavage in young, non-expectorating cystic fibrosis children.	Blau H, Linnane B, Carzino R, Tannenbaum EL, Skoric B, Robinson PJ, Robertson C, Ranganathan SC.	J Cyst Fibros	10.1016/j.jcf.2013.05.013	2014
Metabolism	Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3.	Tang Z, Xu W, Zhou Z, Qiao Y, Zheng S, Rong W.	PeerJ	10.7717/peerj.13529	2022
	Benefits of Gut Microbiota Reconstitution by Beta 1,3-1,6 Glucans in Subjects with Autism Spectrum Disorder and Other Neurodegenerative Diseases.	Raghavan K, Dedeepiya VD, Yamamoto N, Ikewaki N, Sonoda T, Iwasaki M, Kandaswamy RS, Senthilkumar R, Preethy S, Abraham SJK.	J Alzheimers Dis	10.3233/jad-220388	2023
	Sensitivity of ivacaftor to drug-drug interactions with rifampin, a cytochrome P450 3A4 inducer.	Guimbellot JS, Acosta EP, Rowe SM.	Pediatr Pulmonol	10.1002/ppul.23971	2018
Enzymology	Ocular penetration of topical antibiotics: study on the penetration of chloramphenicol, tobramycin and netilmicin into the anterior chamber after topical administration.	Cagini C, Piccinelli F, Lupidi M, Messina M, Cerquaglia A, Manes S, Fiore T, Pellegrino RM.	Clin Exp Ophthalmol	10.1111/ceo.12087	2013
	Factors associated with gravity-dependent distribution on chest CT in elderly patients with community-acquired pneumonia: a retrospective observational study.	Komiya K, Yamamoto T, Yoshikawa H, Goto A, Umeki K, Johkoh T, Hiramatsu K, Kadota JI.	Sci Rep	10.1038/s41598-022-12092-w	2022
Enzymology	Tricuspid valve endocarditis caused by Haemophilus parainfluenzae: a case report and review of the literature.	Nwaohiri N, Urban C, Gluck J, Ahluwalia M, Wehbeh W.	Diagn Microbiol Infect Dis	10.1016/j.diagmicrobio.2009.02.015	2009
	SAELGMDA: Identifying human microbe-disease associations based on sparse autoencoder and LightGBM.	Wang F, Yang H, Wu Y, Peng L, Li X.	Front Microbiol	10.3389/fmicb.2023.1207209	2023
	Autologous transplantation of P63⁺ lung progenitor cells in patients with bronchiectasis: A randomized, single-blind, controlled trial.	Yan J, Zhang W, Feng Y, Liu X, Niu L, Guo Y, Zhou L, Shi M, Di C, Zhang Q, Wang X, Zhou J, Dai R, Ni L, Bao Z, Yan T, Hu Y, Wang P, Zhang T, Zhou M, Zuo W, Qu J.	Cell Rep Med	10.1016/j.xcrm.2024.101819	2024
	The Influence and Role of Microbial Factors in Autoimmune Kidney Diseases: A Systematic Review.	Kronbichler A, Kerschbaum J, Mayer G.	J Immunol Res	10.1155/2015/858027	2015
	Metagenomics analysis of the neonatal intestinal resistome.	Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P.	Front Pediatr	10.3389/fped.2023.1169651	2023
	Septic arthritis of the acromioclavicular joint: a case series and review of the literature.	Steinmetz RG, Maupin JJ, Smith JN, White CB.	Shoulder Elbow	10.1177/1758573218815289	2020
	Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis.	Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJ, Yen JH.	Int J Mol Sci	10.3390/ijms23179883	2022
Phylogeny	EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale.	Nagpal S, Mande SS, Hooda H, Dutta U, Taneja B.	Microbiol Spectr	10.1128/spectrum.04150-23	2024
	Variations in oral microbiome profiles in rheumatoid arthritis and osteoarthritis with potential biomarkers for arthritis screening.	Chen B, Zhao Y, Li S, Yang L, Wang H, Wang T, Bin Shi, Gai Z, Heng X, Zhang C, Yang J, Zhang L.	Sci Rep	10.1038/s41598-018-35473-6	2018
	A Five-Year Retrospective Study of 746 Cases with Maxillofacial Space Infection in Western China.	Wang P, Huang Y, Long J.	Infect Drug Resist	10.2147/idr.s377657	2022
	Characterization and Fitness Cost of Tn7100, a Novel Integrative and Conjugative Element Conferring Multidrug Resistance in Haemophilus influenzae.	Johannessen H, Anthonisen IL, Zecic N, Hegstad K, Ranheim TE, Skaare D.	Front Microbiol	10.3389/fmicb.2022.945411	2022
	Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF^beta-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1.	Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fabian Z, Gambus A, Mailand N, Duxin JP, Nielsen ML.	Nat Commun	10.1038/s41467-023-43873-0	2023
	Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.	Wang Y, Chen J, Ni Y, Liu Y, Gao X, Tse MA, Panagiotou G, Xu A.	Gut Microbes	10.1080/19490976.2024.2416928	2024
	The intestinal microbiome of inflammatory bowel disease across the pediatric age range.	Conrad MA, Bittinger K, Ren Y, Kachelries K, Vales J, Li H, Wu GD, Bushman FD, Devoto M, Baldassano RN, Kelsen JR.	Gut Microbes	10.1080/19490976.2024.2317932	2024
	Checkpoint inhibitor responses can be regulated by the gut microbiota - A systematic review.	Zeriouh M, Raskov H, Kvich L, Gogenur I, Bennedsen ALB.	Neoplasia	10.1016/j.neo.2023.100923	2023
Phylogeny	Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community.	Leitao Filho FS, Monica Peters C, Sheel AW, Yang J, Nislow C, Lam S, Leung JM, Sin DD.	Biomedicines	10.3390/biomedicines11030841	2023
	Vertebral Osteomyelitis, Discitis, and Epidural Abscess: A Rare Complication of Cardiobacterium Endocarditis.	Yadava SK, Eranki A.	J Investig Med High Impact Case Rep	10.1177/2324709618807504	2018
Phylogeny	Gut microbiome characteristics of comorbid generalized anxiety disorder and functional gastrointestinal disease: Correlation with alexithymia and personality traits.	Guo X, Lin F, Yang F, Chen J, Cai W, Zou T.	Front Psychiatry	10.3389/fpsyt.2022.946808	2022
	Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students.	Ahrens AP, Sanchez-Padilla DE, Drew JC, Oli MW, Roesch LFW, Triplett EW.	Sci Rep	10.1038/s41598-022-18020-2	2022
	The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey.	Yang X, He L, Yan S, Chen X, Que G.	BMC Oral Health	10.1186/s12903-021-01683-0	2021
Phylogeny	Development of a Novel Metagenomic Biomarker for Prediction of Upper Gastrointestinal Tract Involvement in Patients With Crohn's Disease.	Kwak MS, Cha JM, Shin HP, Jeon JW, Yoon JY.	Front Microbiol	10.3389/fmicb.2020.01162	2020
	Omics community detection using multi-resolution clustering.	Rahnavard A, Chatterjee S, Sayoldin B, Crandall KA, Tekola-Ayele F, Mallick H.	Bioinformatics	10.1093/bioinformatics/btab317	2021
	A systematic review and meta-analysis of the benefits of a gluten-free diet and/or casein-free diet for children with autism spectrum disorder.	Quan L, Xu X, Cui Y, Han H, Hendren RL, Zhao L, You X.	Nutr Rev	10.1093/nutrit/nuab073	2022
Pathogenicity	Oral polymicrobial communities: Assembly, function, and impact on diseases.	Hajishengallis G, Lamont RJ, Koo H.	Cell Host Microbe	10.1016/j.chom.2023.02.009	2023
Genetics	The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.	Kazarina A, Petersone-Gordina E, Kimsis J, Kuzmicka J, Zayakin P, Griskjans Z, Gerhards G, Ranka R.	Genes (Basel)	10.3390/genes12020309	2021
	Acromioclavicular septic arthritis: a case report of a novel pathogen.	Carey TW, Jackson K, Roure R, Abell BE.	Am J Orthop (Belle Mead NJ)		2010
	Infective Endocarditis among Pediatric Patients with Prosthetic Valves and Cardiac Devices: A Review and Update of Recent Emerging Diagnostic and Management Strategies.	Dardari M, Cinteza E, Vasile CM, Padovani P, Vatasescu R.	J Clin Med	10.3390/jcm12154941	2023
	Abiotrophia defectiva liver abscess in a teenage boy after a supposedly mild blunt abdominal trauma: a case report.	Rasic P, Bosnic S, Vasiljevic ZV, Djuricic SM, Topic V, Milickovic M, Savic D.	BMC Gastroenterol	10.1186/s12876-020-01409-6	2020
	The Association of Chronic Hepatitis C with Respiratory Microbiota Disturbance on the Basis of Decreased Haemophilus Spp. Colonization.	Kosikowska U, Biernasiuk A, Korona-Glowniak I, Kiciak S, Tomasiewicz K, Malm A.	Med Sci Monit	10.12659/msm.895544	2016
Enzymology	Integrative population pharmacokinetic/pharmacodynamic analysis of nemonoxacin capsule in Chinese patients with community-acquired pneumonia.	Chen Y, Wu X, Tsai C, Chang L, Yu J, Cao G, Guo B, Shi Y, Zhu D, Hu F, Yuan J, Liu Y, Zhao X, Zhang Y, Wu J, Zhang J.	Front Pharmacol	10.3389/fphar.2023.912962	2023
Enzymology	Purulent pericarditis caused by Haemophilus parainfluenzae.	Latyshev Y, Mathew A, Jacobson JM, Sturm E.	Tex Heart Inst J		2013
	Colonoscopy aspiration lavages for mucosal metataxonomic profiling of spondylarthritis-associated gastrointestinal tract alterations.	Marquez-Ortiz RA, Leon M, Abril D, Escobar-Perez J, Florez-Sarmiento C, Parra-Izquierdo V, Chalem P, Romero-Sanchez C.	Sci Rep	10.1038/s41598-023-33597-y	2023
	Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.	Chen ZL, Wang C, Wang F.	World J Gastroenterol	10.3748/wjg.v31.i24.108021	2025
	Multiomics Analysis Reveals Gut Virome-Bacteria-Metabolite Interactions and Their Associations with Symptoms in Patients with IBS-D.	Xie P, Luo M, Fan J, Xiong L.	Viruses	10.3390/v16071054	2024
Phylogeny	Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma.	Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ.	Microbiol Spectr	10.1128/spectrum.03088-22	2022
	Lack of Additional Diagnostic Yield of 16s rRNA Gene PCR for Prosthetic Joint Infections.	Lane MA, Ganeshraj N, Gu A, Warren DK, Burnham CD.	J Appl Lab Med	10.1373/jalm.2018.027003	2019
	Haemophilus parainfluenzae meningitis in an adult associated with acute otitis media.	Cardines R, Giufre M, Ciofi degli Atti ML, Accogli M, Mastrantonio P, Cerquetti M.	New Microbiol		2009
	Surgical site infections after gracilis free flap reconstruction for facial paralysis.	Lee LN, Susarla SM, Henstrom DK, Hohman MH, Durand ML, Cheney ML, Hadlock TA.	Otolaryngol Head Neck Surg	10.1177/0194599812444262	2012
	A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients.	Obuya S, Elkholy A, Avuthu N, Behring M, Bajpai P, Agarwal S, Kim HG, El-Nikhely N, Akinyi P, Orwa J, Afaq F, Abdalla M, Michael A, Farouk M, Bateman LB, Fouad M, Saleh M, Guda C, Manne U, Arafat W.	J Gastrointest Oncol	10.21037/jgo-22-116	2022
	Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.	Kang Y, Sun B, Chen Y, Lou Y, Zheng M, Li Z.	mSphere	10.1128/msphere.00162-21	2021
	Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation.	Tian H, Ye C, Yang B, Cui J, Zheng Z, Wu C, Zhou S, Lv X, Qin N, Qin H, Li N, Chen Q.	Front Med (Lausanne)	10.3389/fmed.2021.777961	2021
	Microbial Associations With Microscopic Colitis.	Sun S, Blakley IC, Fodor AA, Keku TO, Woosley JT, Peery AF, Sandler RS.	Clin Transl Gastroenterol	10.14309/ctg.0000000000000528	2022
	The impact of fixed orthodontic appliances on oral microbiome dynamics in Japanese patients.	Kado I, Hisatsune J, Tsuruda K, Tanimoto K, Sugai M.	Sci Rep	10.1038/s41598-020-78971-2	2020
	Infective endocarditis caused by Cardiobacterium valvarum.	Washio Y, Sakamoto SI, Saito R, Nei T, Morishima M, Shinoyama A, Tashiro A, Sugimoto R.	Access Microbiol	10.1099/acmi.0.000040	2019
	Dysregulation of the Intestinal Microbiome in Patients With Haploinsufficiency of A20.	Toyofuku E, Takeshita K, Ohnishi H, Kiridoshi Y, Masuoka H, Kadowaki T, Nishikomori R, Nishimura K, Kobayashi C, Ebato T, Shigemura T, Inoue Y, Suda W, Hattori M, Morio T, Honda K, Kanegane H.	Front Cell Infect Microbiol	10.3389/fcimb.2021.787667	2021
Pathogenicity	Bacteria and Candida yeasts in inflammations of the oral mucosa in children with secondary immunodeficiency.	Olczak-Kowalczyk D, Daszkiewicz M, Krasuska-Slawinska, Dembowska-Baginska B, Gozdowski D, Daszkiewicz P, Fronc B, Semczuk K.	J Oral Pathol Med	10.1111/j.1600-0714.2012.01146.x	2012
	Polymicrobial endocarditis in intravenous heroin and fentanyl abuse.	Mehrzad R, Sublette M, Barza M.	J Clin Diagn Res	10.7860/jcdr/2013/7303.3817	2013
	Deciphering salivary microbiome signature in Crohn's disease patients with different factors contributing to dysbiosis.	Elzayat H, Malik T, Al-Awadhi H, Taha M, Elghazali G, Al-Marzooq F.	Sci Rep	10.1038/s41598-023-46714-8	2023
	Fecal Immunoglobulin Levels as a Modifier of the Gut Microbiome in Patients with Common Variable Immunodeficiency.	Noltner C, Bulashevska A, Hubscher K, Haberstroh H, Grimbacher B, Proietti M.	J Clin Immunol	10.1007/s10875-023-01469-9	2023
	A case of bronchiolitis obliterans organising pneumonia associated with SAPHO (synovitis-acne-pustulosis-hyperostosis-osteitis) syndrome.	Hameed F, Steer H.	BMJ Case Rep	10.1136/bcr-2017-219822	2017
	The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease.	Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, Voskuil MD, Fu J, Wijmenga C, Zhernakova A, Weersma RK, Vich Vila A.	J Crohns Colitis	10.1093/ecco-jcc/jjab020	2021
	Poliprotect vs Omeprazole in the Relief of Heartburn, Epigastric Pain, and Burning in Patients Without Erosive Esophagitis and Gastroduodenal Lesions: A Randomized, Controlled Trial.	Corazziari ES, Gasbarrini A, D'Alba L, D'Ovidio V, Riggio O, Passaretti S, Annibale B, Cicala M, Repici A, Bassotti G, Ciacci C, Di Sabatino A, Neri M, Bragazzi MC, Ribichini E, Radocchia G, Iovino P, Marazzato M, Schippa S, Badiali D.	Am J Gastroenterol	10.14309/ajg.0000000000002360	2023
	Intestinal and esophageal microbiota in esophageal cancer development and treatment.	Baba Y, Tajima K, Yoshimura K.	Gut Microbes	10.1080/19490976.2025.2505118	2025
Enzymology	Haemophilus parainfluenzae prosthetic valve endocarditis complicated by septic emboli to brain.	Liang JJ, Swiecicki PL, Killu AM, Sohail MR.	BMJ Case Rep	10.1136/bcr-2013-009744	2013
	Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease.	Qiu C, Zhou W, Shen H, Wang J, Tang R, Wang T, Xie X, Hong B, Ren R, Wang G, Song Z.	Alzheimers Res Ther	10.1186/s13195-024-01402-1	2024
	Structural characterization of Haemophilus parainfluenzae lipooligosaccharide and elucidation of its role in adherence using an outer core mutant.	Pollard A, St Michael F, Connor L, Nichols W, Cox A.	Can J Microbiol	10.1139/w08-082	2008
Phylogeny	Oral Dysbiosis in Severe Forms of Periodontitis Is Associated With Gut Dysbiosis and Correlated With Salivary Inflammatory Mediators: A Preliminary Study.	Kawamoto D, Borges R, Ribeiro RA, de Souza RF, Amado PPP, Saraiva L, Horliana ACRT, Faveri M, Mayer MPA.	Front Oral Health	10.3389/froh.2021.722495	2021
	PM_2.5-associated bacteria in ambient air: Is PM_2.5 exposure associated with the acquisition of community-acquired staphylococcal infections?	Karimi H, Nikaeen M, Gholipour S, Hatamzadeh M, Hassanzadeh A, Hajizadeh Y.	J Environ Health Sci Eng	10.1007/s40201-020-00522-8	2020
	The exudative-constrictive tuberculosis pericarditis diagnosed by toracoscopic biopsy.	Blagova OV, Alijeva IN, Nedostup AV, Senchihin PV, Parshin VD, Kogan EA.	J Clin Tuberc Other Mycobact Dis	10.1016/j.jctube.2020.100165	2020
Pathogenicity	Extracellular Vesicles, a Key Mediator to Link Environmental Microbiota to Airway Immunity.	Choi Y, Park H, Park HS, Kim YK.	Allergy Asthma Immunol Res	10.4168/aair.2017.9.2.101	2017
	Identification of the nasopharyngeal carriage of Neisseria meningitidis by 16S rRNA Gene sequencing in asymptomatic adolescents and young adults in Cartagena, Colombia (2019-2020).	Macias-Mendoza M, Montes-Robledo A, Arteta-Acosta C, Baldiris-Avila R, Coronell-Rodriguez W.	Braz J Infect Dis	10.1016/j.bjid.2022.102330	2022
	Oral microbiome, periodontal disease and systemic bone-related diseases in the era of homeostatic medicine.	Hu W, Chen S, Zou X, Chen Y, Luo J, Zhong P, Ma D.	J Adv Res	10.1016/j.jare.2024.08.019	2025
Pathogenicity	Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.	Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.	Sci Rep	10.1038/s41598-024-53784-9	2024
	Prospective Surveillance of Respiratory Infections in British Antarctic Survey Bases During the COVID-19 Pandemic.	Ganly KH, Bowyer JC, Bird PW, Willford NJ, Shaw J, Odedra M, Osborn G, Everett T, Warner M, Horne S, Dinn M, McMurray CL, Holmes CW, Koo SSF, Tang JW.	J Infect Dis	10.1093/infdis/jiac412	2022
	Investigating the Properties and Characterization of a Hybrid 3D Printed Antimicrobial Composite Material Using FFF Process: Innovative and Swift.	Ahmed W, Al-Marzouqi AH, Nazir MH, Rizvi TA, Zaneldin E, Khan M, Aziz M.	Int J Mol Sci	10.3390/ijms24108895	2023
	Clinical Microbial Identification of Severe Oral Infections by MALDI-TOF Mass Spectrometry in Stockholm County: an 11-Year (2010 to 2020) Epidemiological Investigation.	Al-Manei K, Ghorbani M, Naud S, Al-Manei KK, Sobkowiak MJ, Lund B, Hazirolan G, Sallberg Chen M, Ozenci V.	Microbiol Spectr	10.1128/spectrum.02487-22	2022
	Human Lung Microbiome on the Way to Cancer.	Kovaleva OV, Romashin D, Zborovskaya IB, Davydov MM, Shogenov MS, Gratchev A.	J Immunol Res	10.1155/2019/1394191	2019
	Prosthetic Valve Endocarditis caused by HACEK Organisms: a Case Reports and Systematic Review of the Literature.	Choi HN, Park KH, Park S, Kim JM, Kang HJ, Park JH, Lee MS.	Infect Chemother	10.3947/ic.2017.49.4.282	2017
	Characteristics of the Salivary Microbiota in Periodontal Diseases and Potential Roles of Individual Bacterial Species To Predict the Severity of Periodontal Disease.	Ji S, Kook JK, Park SN, Lim YK, Choi GH, Jung JS.	Microbiol Spectr	10.1128/spectrum.04327-22	2023
Transcriptome	Respiratory immune status and microbiome in recovered COVID-19 patients revealed by metatranscriptomic analyses.	Meng H, Wang S, Tang X, Guo J, Xu X, Wang D, Jin F, Zheng M, Yin S, He C, Han Y, Chen J, Han J, Ren C, Gao Y, Liu H, Wang Y, Jin R.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1011672	2022
Genetics	BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species.	Topaz N, Boxrud D, Retchless AC, Nichols M, Chang HY, Hu F, Wang X.	BMC Infect Dis	10.1186/s12879-018-3324-1	2018
Enzymology	Combining culture and culture-independent methods reveals new microbial composition of halitosis patients' tongue biofilm.	Bernardi S, Karygianni L, Filippi A, Anderson AC, Zurcher A, Hellwig E, Vach K, Macchiarelli G, Al-Ahmad A.	Microbiologyopen	10.1002/mbo3.958	2020
	Kidney Injury due to Ureteral Obstruction Caused by Compression from Infected Simple Hepatic Cyst.	Sawada N, Endo T, Mikami K, Igarashi G, Sakamoto J, Tono H, Fukuda S.	Case Rep Gastroenterol	10.1159/000475919	2017
	Association between antibiotics and asthma risk among adults aged over 40 years: a nationally representative retrospective cohort study.	Choi J, Park SJ, Park YJ, Hong J, Jeong S, Chang J, Kim SM, Song J, Cho Y, Park SM.	BMJ Open Respir Res	10.1136/bmjresp-2023-001643	2023
Genetics	Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance.	Martin Rihova J, Gupta S, Darby AC, Novakova E, Hypsa V.	mSystems	10.1128/msystems.00706-23	2023
Phylogeny	Subgingival microbiome of experimental gingivitis: shifts associated with the use of chlorhexidine and N-acetyl cysteine mouthwashes.	Al-Kamel A, Baraniya D, Al-Hajj WA, Halboub E, Abdulrab S, Chen T, Al-Hebshi NN.	J Oral Microbiol	10.1080/20002297.2019.1608141	2019
	Infective endocarditis in children without underlying heart disease.	Lin YT, Hsieh KS, Chen YS, Huang IF, Cheng MF.	J Microbiol Immunol Infect	10.1016/j.jmii.2012.05.001	2013
Genetics	Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis.	Wang J, Han Y, Feng J.	BMC Pulm Med	10.1186/s12890-019-1022-4	2019
Pathogenicity	Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis.	Rausch P, Hartmann M, Baines JF, von Bismarck P.	Arthritis Res Ther	10.1186/s13075-021-02711-8	2022
	Anti-CRISPR AcrIIC5 is a dsDNA mimic that inhibits type II-C Cas9 effectors by blocking PAM recognition.	Sun W, Zhao X, Wang J, Yang X, Cheng Z, Liu S, Wang J, Sheng G, Wang Y.	Nucleic Acids Res	10.1093/nar/gkad052	2023
	Etiology and characteristics of patients with bronchiectasis in Taiwan: a cohort study from 2002 to 2016.	Huang HY, Chung FT, Lo CY, Lin HC, Huang YT, Yeh CH, Lin CW, Huang YC, Wang CH.	BMC Pulm Med	10.1186/s12890-020-1080-7	2020
	Exploring the etiology of colitis: insights from gut microbiota research	Qian G, Chen X, Liu G, Yu J, Zhong S, Yang J, Sun Y, Zhou J.	Gut microbes		2025
Enzymology	Nasopharyngeal and Adenoid Colonization by Haemophilus influenzae and Haemophilus parainfluenzae in Children Undergoing Adenoidectomy and the Ability of Bacterial Isolates to Biofilm Production.	Kosikowska U, Korona-Glowniak I, Niedzielski A, Malm A.	Medicine (Baltimore)	10.1097/md.0000000000000799	2015
Genetics	Global compositional and functional states of the human gut microbiome in health and disease.	Lee S, Portlock T, Le Chatelier E, Garcia-Guevara F, Clasen F, Onate FP, Pons N, Begum N, Harzandi A, Proffitt C, Rosario D, Vaga S, Park J, von Feilitzen K, Johansson F, Zhang C, Edwards LA, Lombard V, Gauthier F, Steves CJ, Gomez-Cabrero D, Henrissat B, Lee D, Engstrand L, Shawcross DL, Proctor G, Almeida M, Nielsen J, Mardinoglu A, Moyes DL, Ehrlich SD, Uhlen M, Shoaie S.	Genome Res	10.1101/gr.278637.123	2024
	Prevalence of Fungal and Bacterial Co-Infection in Pulmonary Fungal Infections: A Metagenomic Next Generation Sequencing-Based Study.	Zhao Z, Song J, Yang C, Yang L, Chen J, Li X, Wang Y, Feng J.	Front Cell Infect Microbiol	10.3389/fcimb.2021.749905	2021
Pathogenicity	Disseminated Herpes Simplex Infection Presenting as Acute Supraglottitis in an Adult.	Bowers EMR, Esianor BI, Kimura K, Lewis JS, Topf MC.	Head Neck Pathol	10.1007/s12105-020-01255-8	2021
Genetics	Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease.	Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, Vlamakis H, Sokol H, Xavier RJ.	Gastroenterology	10.1053/j.gastro.2020.08.045	2020
Pathogenicity	[Distribution and drug resistance of the isolated bacteria from children with acute respiratory infection].	Guo J, Cui ZZ, Huang Y, Yu AM.	Zhongguo Dang Dai Er Ke Za Zhi		2008
Metabolism	Defining Metaniches in the Oral Cavity According to Their Microbial Composition and Cytokine Profile.	Seidel CL, Gerlach RG, Wiedemann P, Weider M, Rodrian G, Hader M, Frey B, Gaipl US, Bozec A, Cieplik F, Kirschneck C, Bogdan C, Golz L.	Int J Mol Sci	10.3390/ijms21218218	2020
Pathogenicity	Emergence of extensively drug-resistant Haemophilus parainfluenzae in Switzerland.	Tinguely R, Seiffert SN, Furrer H, Perreten V, Droz S, Endimiani A.	Antimicrob Agents Chemother	10.1128/aac.00221-13	2013
	[Haemophilus parainfluenzae--a rare cause of endocarditis].	Ledina D, Karanovic J, Ivic I, Karanovic N, Ledina D.	Acta Med Croatica		2007
Pathogenicity	Influence of Oral Microbiota on the Presence of IgA Anti-Citrullinated Protein Antibodies in Gingival Crevicular Fluid.	de Smit MJ, Rahajoe PS, Raveling-Eelsing E, Lisotto P, Harmsen HJM, Kertia N, Vissink A, Westra J.	Front Oral Health	10.3389/froh.2022.904711	2022
Pathogenicity	Clinically Healthy Human Gingival Tissues Show Significant Inter-individual Variability in GCF Chemokine Expression and Subgingival Plaque Microbial Composition.	Bamashmous S, Kotsakis GA, Jain S, Chang AM, McLean JS, Darveau RP.	Front Oral Health	10.3389/froh.2021.689475	2021
	Phylogeny-guided microbiome OTU-specific association test (POST).	Huang C, Callahan BJ, Wu MC, Holloway ST, Brochu H, Lu W, Peng X, Tzeng JY.	Microbiome	10.1186/s40168-022-01266-3	2022
	A Novel Mutation in the NCF2 Gene in a CGD Patient With Chronic Recurrent Pneumopathy.	de Albuquerque JAT, Lima AM, de Oliveira Junior EB, Ishizuka EK, Aragao-Filho WC, Bengala Zurro N, Mayumi Chiba S, Fernandes FR, Condino-Neto A.	Front Pediatr	10.3389/fped.2019.00391	2019
	Microbiota of preterm infant develops over time along with the first teeth eruption.	Zhang Y, Wu YP, Feng V, Cao GZ, Feng XP, Chen X.	Front Microbiol	10.3389/fmicb.2022.1049021	2022
Phylogeny	Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis.	Kim MS, Chang J, Kim MN, Choi SH, Jung SH, Lee JW, Sung H.	Ann Lab Med	10.3343/alm.2017.37.6.505	2017
Enzymology	Characterization of extended-spectrum beta-lactamase-producing isolates of Haemophilus parainfluenzae.	Tristram SG, Pitout MJ, Forward K, Campbell S, Nichols S, Davidson RJ.	J Antimicrob Chemother	10.1093/jac/dkm523	2008
	Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air-liquid interface respiratory epithelial cultures.	Horvath M, Yang R, Castaneda DC, Callender M, Aiken ES, Voigt AY, Caldwell R, Fachi J, Di Luccia B, Scholar Z, Yu P, Salner A, Colonna M, Palucka K, Oh J.	BMC Biol	10.1186/s12915-025-02129-7	2025
	Mounier-Kuhn syndrome: a case of tracheal smooth muscle remodeling.	Cook DP, Adam RJ, Abou Alaiwa MH, Eberlein M, Klesney-Tait JA, Parekh KR, Meyerholz DK, Stoltz DA.	Clin Case Rep	10.1002/ccr3.794	2017
	Extensive eye-oral-bronchial mucosal nodules with eosinopgillia: a rare case report and literature review.	Wu L, Leng Q, Wang Y, Wang D, Yang D.	BMC Pulm Med	10.1186/s12890-020-01340-2	2020
Enzymology	Identification of bacterial DNA in noninfectious pleural fluid with a highly sensitive PCR method.	Cremades R, Galiana A, Rodriguez JC, Santos A, Lopez P, Ruiz M, Garcia-Pachon E, Royo G.	Respiration	10.1159/000322003	2011
	43-Year Temporal Trends in Immune Response to Oral Bacteria in a Swedish Population.	Esberg A, Johansson A, Claesson R, Johansson I.	Pathogens	10.3390/pathogens9070544	2020
Enzymology	[Etiology of acute respiratory tract infection in hospitalized children in Suzhou from 2005 to 2011].	Ji W, Chen ZR, Zhou WF, Sun HM, Li BQ, Cai LH, Yan YD.	Zhonghua Yu Fang Yi Xue Za Zhi		2013
	Urinary tract infection caused by Haemophilus influenzae and Haemophilus parainfluenzae in children.	Hansson S, Svedhem A, Wennerstrom M, Jodal U.	Pediatr Nephrol	10.1007/s00467-007-0531-1	2007
Genetics	Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease.	Hu S, Png E, Gowans M, Ong DEH, de Sessions PF, Song J, Nagarajan N.	Gut Pathog	10.1186/s13099-021-00409-5	2021
	Concurrent Acute Glomerulonephritis and Retropharyngeal Abscess in 10 Year Boy: A Case Report.	Yadav S, Garg D, Vaswani ND, Kaushik JS, Rohilla S.	J Clin Diagn Res	10.7860/jcdr/2017/26421.10299	2017
Metabolism	Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease.	Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, Gonzalez A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmuller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I.	Sci Rep	10.1038/s41598-024-55960-3	2024
Phylogeny	Detection of Microbial 16S rRNA Gene in the Serum of Patients With Gastric Cancer.	Dong Z, Chen B, Pan H, Wang D, Liu M, Yang Y, Zou M, Yang J, Xiao K, Zhao R, Zheng X, Zhang L, Zhang Y.	Front Oncol	10.3389/fonc.2019.00608	2019
Metabolism	Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi.	Toro I, Petrutz C, Pacello F, D'Orazio M, Battistoni A, Djinovic-Carugo K.	J Mol Biol	10.1016/j.jmb.2008.12.004	2009
	A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples.	Bogus MI, Wronska AK, Kaczmarek A, Drozdowski M, Laskowski Z, Myczka A, Cybulska A, Golebiowski M, Chwir-Golebiowska A, Siecinska L, Mokijewska E.	PLoS One	10.1371/journal.pone.0280810	2023
Phylogeny	Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging.	Yang CY, Yeh YM, Yu HY, Chin CY, Hsu CW, Liu H, Huang PJ, Hu SN, Liao CT, Chang KP, Chang YL.	Front Microbiol	10.3389/fmicb.2018.00862	2018
	An Overview of the Evidence and Mechanism of Drug-Herb Interactions Between Propolis and Pharmaceutical Drugs.	Hossain S, Yousaf M, Liu Y, Chang D, Zhou X.	Front Pharmacol	10.3389/fphar.2022.876183	2022
	Screening of Health-Associated Oral Bacteria for Anticancer Properties in vitro.	Baraniya D, Jain V, Lucarelli R, Tam V, Vanderveer L, Puri S, Yang M, Al-Hebshi NN.	Front Cell Infect Microbiol	10.3389/fcimb.2020.575656	2020
	The etiology of community-acquired pneumonia among children under 5 years of age in mainland China, 2001-2015: A systematic review.	Ning G, Wang X, Wu D, Yin Z, Li Y, Wang H, Yang W.	Hum Vaccin Immunother	10.1080/21645515.2017.1371381	2017
	Tolerance to intraoral biofilms and their effectiveness in improving mouth dryness and modifying oral microbiota in patients with primary Sjögren's syndrome: "Predelfi study".	Orliaguet M, Fong SB, Le Pottier L, Meuric V, Boisrame S, Bonnaure-Mallet M, Pers JO.	Front Microbiol	10.3389/fmicb.2023.1071683	2023
	Selective expansion of T cell receptor (TCR) V beta 6 in tonsillar and peripheral blood T cells and its induction by in vitro stimulation with Haemophilus parainfluenzae in patients with IgA nephropathy.	Nozawa H, Takahara M, Yoshizaki T, Goto T, Bandoh N, Harabuchi Y.	Clin Exp Immunol	10.1111/j.1365-2249.2007.03523.x	2008
Genetics	Evaluation of Extraction Methods for Clinical Metagenomic Assay.	Farraj SA, El-Kafrawy SA, Kumosani TA, Yousef JM, Azhar EI.	Microorganisms	10.3390/microorganisms8081128	2020
Enzymology	Impact of a vegan diet on the human salivary microbiota.	Hansen TH, Kern T, Bak EG, Kashani A, Allin KH, Nielsen T, Hansen T, Pedersen O.	Sci Rep	10.1038/s41598-018-24207-3	2018
	Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis.	Sousa V, Spratt D, Davrandi M, Mardas N, Beltran V, Donos N.	Int J Environ Res Public Health	10.3390/ijerph192114088	2022
	Microbial Dynamics in Newly Diagnosed and Treatment Naïve IBD Patients in the Mediterranean.	Rausch P, Ellul S, Pisani A, Bang C, Tabone T, Marantidis Cordina C, Zahra G, Franke A, Ellul P.	Inflamm Bowel Dis	10.1093/ibd/izad004	2023
	Oral microbiome contributes to the failure of orthodontic temporary anchorage devices (TADs).	Zhao N, Zhang Q, Guo Y, Cui S, Tian Y, Zhang Y, Zhou Y, Wang X.	BMC Oral Health	10.1186/s12903-023-02715-7	2023
	Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands.	Musial N, Bogucka A, Tretiakow D, Skorek A, Ryl J, Czaplewska P.	Clin Proteomics	10.1186/s12014-023-09402-3	2023
	Essential role of IL-17 in acute exacerbation of pulmonary fibrosis induced by non-typeable Haemophilus influenzae.	Chen S, Zhang X, Yang C, Wang S, Shen H.	Theranostics	10.7150/thno.74809	2022
	Assessment of Long-Term Macrolide Exposure on the Oropharyngeal Microbiome and Macrolide Resistance in Healthy Adults and Consequences for Onward Transmission of Resistance.	Burr LD, Taylor SL, Richard A, Schreiber V, Lingman S, Martin M, Papanicolas LE, Choo JM, Rogers GB.	Antimicrob Agents Chemother	10.1128/aac.02246-21	2022
	Nutritional composition, heavy metal content and in vitro effect on the human gut microbiota of Talitrus saltator, an underutilized crustacean from the Atlantic coast.	Lopez-Santamarina A, Cardelle-Cobas A, Lamas A, Mondragon-Portocarrero A, Cepeda A, Miranda JM.	Front Nutr	10.3389/fnut.2022.943133	2022
	Detection of viral and bacterial pathogens in hospitalized children with acute respiratory illnesses, Chongqing, 2009-2013.	Wei L, Liu W, Zhang XA, Liu EM, Wo Y, Cowling BJ, Cao WC.	Medicine (Baltimore)	10.1097/md.0000000000000742	2015
	Systematic review of ceftaroline fosamil in the management of patients with methicillin-resistant Staphylococcus aureus pneumonia.	Torres A, Kuraieva A, Stone GG, Cilloniz C.	Eur Respir Rev	10.1183/16000617.0117-2023	2023
	Re-establishing the utility of tetracycline-class antibiotics for current challenges with antibiotic resistance.	LaPlante KL, Dhand A, Wright K, Lauterio M.	Ann Med	10.1080/07853890.2022.2085881	2022
	Extended Interval Tobramycin Pharmacokinetics in a Pediatric Patient With Primary Ciliary Dyskinesia Presenting With an Acute Respiratory Exacerbation.	Higgins KL, Noda C, Stultz JS.	J Pediatr Pharmacol Ther	10.5863/1551-6776-23.2.159	2018
Genetics	A metagenomics workflow for SARS-CoV-2 identification, co-pathogen detection, and overall diversity.	Castaneda-Mogollon D, Kamaliddin C, Oberding L, Liu Y, Mohon AN, Faridi RM, Khan F, Pillai DR.	J Clin Virol	10.1016/j.jcv.2021.105025	2021
	Application of Metagenomic Next-Generation Sequencing in the Etiological Diagnosis of Infective Endocarditis During the Perioperative Period of Cardiac Surgery: A Prospective Cohort Study.	Zeng X, Wu J, Li X, Xiong W, Tang L, Li X, Zhuang J, Yu R, Chen J, Jian X, Lei L.	Front Cardiovasc Med	10.3389/fcvm.2022.811492	2022
	Changes in microbiota during experimental human Rhinovirus infection.	Hofstra JJ, Matamoros S, van de Pol MA, de Wever B, Tanck MW, Wendt-Knol H, Deijs M, van der Hoek L, Wolthers KC, Molenkamp R, Visser CE, Sterk PJ, Lutter R, de Jong MD.	BMC Infect Dis	10.1186/s12879-015-1081-y	2015
Transcriptome	Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells.	Bastakoti S, Pesonen M, Ajayi C, Julin K, Corander J, Johannessen M, Hanssen AM.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1326730	2024
	Microbiota - The Unseen Players in Adult Asthmatic Airways.	Ozturk AB, Ranjan R, Rani A, Yazici D, Bavbek S.	Turk Thorac J	10.5152/turkthoracj.2020.19085	2021
	Gut Microbiota-Targeted Interventions in the Management of Chronic Kidney Disease.	Sumida K, Pierre JF, Yuzefpolskaya M, Colombo PC, Demmer RT, Kovesdy CP.	Semin Nephrol	10.1016/j.semnephrol.2023.151408	2023
	Dysbiosis: An Indicator of COVID-19 Severity in Critically Ill Patients.	Cuenca S, Soler Z, Serrano-Gomez G, Xie Z, Barquinero J, Roca J, Sirvent JM, Manichanh C.	Int J Mol Sci	10.3390/ijms232415808	2022
Phenotype	Patterns of Human Milk Oligosaccharides in Mature Milk Are Associated with Certain Gut Microbiota in Infants.	Mao S, Zhao A, Jiang H, Yan J, Zhong W, Xun Y, Zhang Y.	Nutrients	10.3390/nu16091287	2024
Pathogenicity	Antibiotic-Associated Apoptotic Enterocolitis in the Absence of a Defined Pathogen: The Role of Intestinal Microbiota Depletion.	Wurm P, Spindelboeck W, Krause R, Plank J, Fuchs G, Bashir M, Petritsch W, Halwachs B, Langner C, Hogenauer C, Gorkiewicz G.	Crit Care Med	10.1097/ccm.0000000000002310	2017
	A Case of Unresolved and Worsening Retroperitoneal Abscess.	Bansal R, Barakat M, Chun S, Rosberger S, Baum J, Tiba M.	Case Rep Gastrointest Med	10.1155/2018/6740734	2018
Phylogeny	Bacterial symbionts of the brown planthopper, Nilaparvata lugens (Homoptera: Delphacidae).	Tang M, Lv L, Jing S, Zhu L, He G.	Appl Environ Microbiol	10.1128/aem.02240-09	2010
Enzymology	Simultaneous detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae by use of molecular beacons in a duplex real-time PCR.	Gullsby K, Storm M, Bondeson K.	J Clin Microbiol	10.1128/jcm.01540-07	2008
Genetics	Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease.	Ricanek P, Lothe SM, Frye SA, Rydning A, Vatn MH, Tonjum T.	Clin Exp Gastroenterol	10.2147/ceg.s33858	2012
Enzymology	A loop-mediated isothermal amplification procedure targeting the sodA gene for rapid and specific identification of Gallibacterium anatis.	Stepien-Pysniak D, Kosikowska U, Hauschild T, Burzynski A, Wilczynski J, Kolinska A, Nowaczek A, Marek A	Poult Sci	10.3382/ps/pex420	2018
	Haemophilus parainfluenzae Strain ATCC 33392 Forms Biofilms In Vitro and during Experimental Otitis Media Infections.	Pang B, Swords WE	Infect Immun	10.1128/IAI.01070-16	2017
Phylogeny	Dentiradicibacter hellwigii gen. nov., sp. nov., isolated from a secondary infected root canal in the human oral cavity.	Bartsch S, Wittmer A, Weber AK, Neumann-Schaal M, Wolf J, Gronow S, Turnbull JD, Tennert C, Hacker G, Cieplik F, Al-Ahmad A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006690	2025

References

#3450	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8978
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#33555	; Curators of the CIP;
#45838	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12836
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68377	Automatically annotated from API NH .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#121563	Collection of Institut Pasteur ; Curators of the CIP; CIP 102513
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Haemophilus parainfluenzae (DSM 8978, ATCC 33392, NCTC 7857)

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