Bacteroides stercoris (DSM 19555, ATCC 43183, CIP 104203)

Name: Bacteroides stercoris (DSM 19555, ATCC 43183, CIP 104203)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1618

Type strain

Strain Designation B5-21

Culture col. no. DSM 19555 ATCC 43183 CIP 104203 JCM 9496 CCUG 38733 3 more

NCBI tax ID(s) 449673 46506

Special Collections DSMZ CCUG JCM CIP

History <- JCM <- ATCC <- L. V. Moore; VPI B5-21 <- W. E. C. Moore ATCC 43183 <-- L. V. Moore VPI B5-21 <-- W. E. C. Moore. CIP <- 1994, ATCC <- L.V. Moore, VPI: strain B5-21 <- W.E.C. Moore

Links

Bacteroides stercoris B5-21 is an anaerobe, mesophilic prokaryote that was isolated from human faeces.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 46828

ATCC 43183,CIP 104203,JCM 9496,CCUG 38733,NCTC 13053,DSM 19555

@ref 20215

Last LPSN update 2025-12-16 09:47:09

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides stercoris

Full scientific name Bacteroides stercoris Johnson et al. 1986

BacDive ID	Other strains from **Bacteroides stercoris** (1)	Type strain
150546	B. stercoris CCUG 41561

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.4
125438	negative	92.865

Colony morphology

8172

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8172	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8172	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
34043	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
123313	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8172	positive	growth	37	mesophilic
34043	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8172	anaerobe
125438	anaerobe	91.958
125439	obligate anaerobe	98.5

Spore formation

@ref	Spore formation	Confidence
125439		99.9
125438		93.979

Observation

67770

Observationquinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	+	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	+	from API rID32A
68367	35581 ChEBI	indole	+	from API 20A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	+	3.2.1.23	from API zym
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	vitamin K metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	vitamin B12 metabolism	70.59	24 of 34
66794	propionate fermentation	70	7 of 10
66794	Entner Doudoroff pathway	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	purine metabolism	67.02	63 of 94
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	non-pathway related	55.26	21 of 38
66794	lipid metabolism	54.84	17 of 31
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	methionine metabolism	50	13 of 26
66794	ethanol fermentation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	tryptophan metabolism	50	19 of 38
66794	degradation of pentoses	46.43	13 of 28
66794	sulfate reduction	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	metabolism of disaccharids	45.45	5 of 11
66794	cysteine metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	oxidative phosphorylation	40.66	37 of 91
66794	coenzyme M biosynthesis	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	ascorbate metabolism	31.82	7 of 22
66794	urea cycle	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	heme metabolism	28.57	4 of 14
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9

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
54424	-	+	+	+	-	-	-	-	-	-	+	+	-	+	-	+	-	+	-	+

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
8172	+	-	+	-	+	+	+	-	+	-	-	-	-	-	+	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
54424	-	-	-	+	-	+	+	-	+	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
8172	-	-	-	+	-	+	+	-	-	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
8172	-	-	-	+	-	+	+	-	-	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
8172	human faeces	Texas	USA	USA	North America
54424	Human feces	Texas	USA	USA	North America
67770	Human feces
123313	Human, Feces	Texas	United States of America	USA	North America	1972

Taxonmaps

69479

Global distribution of 16S sequence X83953 (>99% sequence identity) for Bacteroides stercoris subclade from Microbeatlas

Aquatic Samples	3744
Soil Samples	1448
Animal Samples	95180
Plant Samples	326
Total Samples	100698

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
8172	yes, in single cases	1	Risk group (German classification) According to TRBA 466
123313		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
66792	ASM2514732v1 assembly for Bacteroides stercoris ATCC 43183	complete	GCA_025147325	449673.71	8079352516	449673	97.82
67770	ASM15452v1 assembly for Bacteroides stercoris ATCC 43183	scaffold	GCA_000154525	449673.7	641736196	449673	74.2
67770	IMG-taxon 2693429855 annotated assembly for Bacteroides stercoris DSM 19555	contig	GCA_900106605	46506.1562	2693429855	46506	64.62
66792	82B11 assembly for Bacteroides stercoris ATCC 43183	contig	GCA_900624775	449673.49	8119500756	449673	61.53
66792	82C1 assembly for Bacteroides stercoris ATCC 43183	contig	GCA_900624875	449673.50	2916293514	449673	59.9

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides stercoris gene for 16S ribosomal RNA, partial sequence, strain: JCM 9496	AB510708	1476	449673
20218	Bacteroides stercoris ATCC 43183 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	AY153429	673	449673
20218	Bacteroides stercoris ATCC 43183 16S ribosomal RNA gene, partial sequence	EU136684	1926	449673
20218	Bacteroides stercoris ATCC 43183 16S ribosomal RNA gene, partial sequence	U50417	59	449673
8172	Bacteroides stercoris 16S rRNA gene, type strain ATCC 43183T	X83953	1342	449673

GC content

@ref	GC-content (mol%)	Method
8172	46
67770	46	thermal denaturation, midpoint method (Tm)
67770	46.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacteroides stercoris ATCC 43183
PATRIC: 449673.71

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	no	69.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides stercoris ATCC 43183 ATCC 43183
NCBI: GCA_025147325.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.87	no
125438	anaerobic	anaerobicⓘ	yes	91.96	yes
125438	aerobic	aerobicⓘ	no	93.64	yes
125438	spore-forming	spore-formingⓘ	no	93.98	no
125438	thermophilic	thermophileⓘ	no	96.25	no
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	In Vitro Influence of Specific Bacteroidales Strains on Gut and Liver Health Related to Metabolic Dysfunction-Associated Fatty Liver Disease.	Garcia-Morena D, Fernandez-Cantos MV, Escalera SL, Lok J, Iannone V, Cancellieri P, Maathuis W, Panagiotou G, Aranzamendi C, Aidy SE, Kolehmainen M, El-Nezami H, Wellejus A, Kuipers OP.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10219-1	2025
	Increased Antibody Response to Fucosylated Oligosaccharides and Fucose-Carrying Bacteroides Species in Crohn's Disease.	Kappler K, Lasanajak Y, Smith DF, Opitz L, Hennet T.	Front Microbiol	10.3389/fmicb.2020.01553	2020
	Heterologous expression and antimicrobial potential of class II bacteriocins.	Elisa Heesemann Rosenkilde C, Olsen Lutzhoft D, Vazquez-Uribe R, Otto Alexander Sommer M.	Gut Microbes	10.1080/19490976.2024.2369338	2024
Metabolism	SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.	Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS.	Elife	10.7554/elife.82401	2023
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
Genetics	The prototypic crAssphage is a linear phage-plasmid.	Schmidtke DT, Hickey AS, Wirbel J, Lin JD, Liachko I, Sherlock G, Bhatt AS.	Cell Host Microbe	10.1016/j.chom.2025.07.004	2025
Phylogeny	16S rRNA gene sequencing reveals the correlation between the gut microbiota and the susceptibility to pathological scars.	Li M, Li M, Dai Y, Li D, Yu H, Liu J, Gao H, Zhong Y, Huang M, Lin J, Xie Y, Guo Z, Chen X.	Front Microbiol	10.3389/fmicb.2023.1215884	2023
	Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.	Mahajan T, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1013222	2025
Metabolism	Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.	Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2021.07.011	2021
Genetics	Microbial characterization based on multifractal analysis of metagenomes.	Xie XH, Huang YJ, Han GS, Yu ZG, Ma YL.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1117421	2023
Metabolism	Milk Formula Diet Alters Bacterial and Host Protein Profile in Comparison to Human Milk Diet in Neonatal Piglet Model.	Rosa F, Zybailov BL, Glazko GV, Rahmatallah Y, Byrum S, Mackintosh SG, Bowlin AK, Yeruva L.	Nutrients	10.3390/nu13113718	2021
	Mapping the T cell repertoire to a complex gut bacterial community.	Nagashima K, Zhao A, Atabakhsh K, Bae M, Blum JE, Weakley A, Jain S, Meng X, Cheng AG, Wang M, Higginbottom S, Dimas A, Murugkar P, Sattely ES, Moon JJ, Balskus EP, Fischbach MA.	Nature	10.1038/s41586-023-06431-8	2023
Genetics	MINTIA: a metagenomic INserT integrated assembly and annotation tool.	Bardou P, Laguerre S, Maman Haddad S, Legoueix Rodriguez S, Laville E, Dumon C, Potocki-Veronese G, Klopp C.	PeerJ	10.7717/peerj.11885	2021
	Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.	Ishaq HM, Mohammad IS, Hussain R, Parveen R, Shirazi JH, Fan Y, Shahzad M, Hayat K, Li H, Ihsan A, Muhammad KS, Usman M, Zhang S, Yuan L, Ullah S, Paiva-Santos AC, Xu J.	J Cancer	10.7150/jca.66816	2022
	The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.	Wang J, Qie J, Zhu D, Zhang X, Zhang Q, Xu Y, Wang Y, Mi K, Pei Y, Liu Y, Ji G, Liu X.	Gut Microbes	10.1080/19490976.2022.2107288	2022
	Deep learning for HGT insertion sites recognition.	Li C, Chen J, Li SC.	BMC Genomics	10.1186/s12864-020-07296-1	2020
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
	Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.	Arias MC, Danchin EG, Coutinho P, Henrissat B, Ball S.	Mob Genet Elements	10.4161/mge.20375	2012
Metabolism	The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides.	Benitez-Paez A, Gomez Del Pulgar EM, Sanz Y.	Front Cell Infect Microbiol	10.3389/fcimb.2017.00383	2017
Metabolism	Depletion of microbiome-derived molecules in the host using Clostridium genetics.	Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA.	Science	10.1126/science.aav1282	2019
Metabolism	Mobilization of vitamin B₁₂ transporters alters competitive dynamics in a human gut microbe.	Frye KA, Piamthai V, Hsiao A, Degnan PH.	Cell Rep	10.1016/j.celrep.2021.110164	2021
	The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.	Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D.	Stand Genomic Sci	10.4056/sigs.2675953	2012
Metabolism	Role of glycoside phosphorylases in mannose foraging by human gut bacteria.	Ladeveze S, Tarquis L, Cecchini DA, Bercovici J, Andre I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, Potocki-Veronese G.	J Biol Chem	10.1074/jbc.m113.483628	2013
Metabolism	Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.	Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Dore J, Monsan P, Remaud-Simeon M, Potocki-Veronese G.	Genome Res	10.1101/gr.108332.110	2010
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
	The prevalence of species and strains in the human microbiome: a resource for experimental efforts.	Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M.	PLoS One	10.1371/journal.pone.0097279	2014
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
Metabolism	An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.	Antharam VC, McEwen DC, Garrett TJ, Dossey AT, Li EC, Kozlov AN, Mesbah Z, Wang GP.	PLoS One	10.1371/journal.pone.0148824	2016
Genetics	Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.	Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG.	BMC Bioinformatics	10.1186/s12859-015-0875-7	2016
Metabolism	Cofactor requirement of HpyAV restriction endonuclease.	Chan SH, Opitz L, Higgins L, O'loane D, Xu SY.	PLoS One	10.1371/journal.pone.0009071	2010
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Enzymology	Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against beta-lactam antibiotics.	Stentz R, Horn N, Cross K, Salt L, Brearley C, Livermore DM, Carding SR.	J Antimicrob Chemother	10.1093/jac/dku466	2015
Phylogeny	PCR assay for species-specific identification of Bacteroides thetaiotaomicron.	Teng LJ, Hsueh PR, Tsai JC, Chiang FL, Chen CY, Ho SW, Luh KT.	J Clin Microbiol	10.1128/jcm.38.4.1672-1675.2000	2000
Pathogenicity	Fish oil enhances recovery of intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplant.	Li Q, Zhang Q, Wang C, Tang C, Zhang Y, Li N, Li J.	PLoS One	10.1371/journal.pone.0020460	2011
	Characterizing the interactions between a naturally primed immunoglobulin A and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice.	Peterson DA, Planer JD, Guruge JL, Xue L, Downey-Virgin W, Goodman AL, Seedorf H, Gordon JI.	J Biol Chem	10.1074/jbc.m114.633800	2015
Phylogeny	Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.	Martinez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J.	Appl Environ Microbiol	10.1128/aem.00380-09	2009
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
Phylogeny	Rapid and correct identification of intestinal Bacteroides spp. with chromosomal DNA probes by whole-cell dot blot hybridization.	Morotomi M, Ohno T, Mutai M.	Appl Environ Microbiol	10.1128/aem.54.5.1158-1162.1988	1988
Genetics	Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics.	Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP.	BMC Genomics	10.1186/1471-2164-11-99	2010
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
	Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes.	Matsumoto W, Takemura M, Nanaura H, Ami Y, Maoka T, Shindo K, Kurihara S, Misawa N.	Eng Microbiol	10.1016/j.engmic.2024.100147	2024
Metabolism	Probiotics in human gut microbiota can degrade host glycosaminoglycans.	Kawai K, Kamochi R, Oiki S, Murata K, Hashimoto W.	Sci Rep	10.1038/s41598-018-28886-w	2018
	Causal relationship between gut microbiota and hepatocellular carcinoma: a two-sample Mendelian randomization and case-control study.	Yang L, Wei W, Wang Y, Kuai W, Xu L.	Discov Oncol	10.1007/s12672-025-02806-7	2025
	Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.	Wang K, Wang H, Zhao Z, Shen X, Zhao J, Zhang H.	mSystems	10.1128/msystems.00862-25	2025
Metabolism	Altered tryptophan metabolism and gut immune crosstalk in hypertensive middle-aged women.	Shah S, Mu C, Shen-Tu G, Schlicht K, Forkert ND, Laudes M, Kofeler HC, Shearer J.	Am J Physiol Heart Circ Physiol	10.1152/ajpheart.00395.2025	2025
Pathogenicity	The Role of 473 Intestinal Microbiota and 91 Inflammatory Factors in Breast Cancer Risk: Insights From Mendel Randomization and its Implications for Diagnosis and Treatment.	Zhu R, Qiu J, Xian D, Yang K.	Clin Breast Cancer	10.1016/j.clbc.2025.06.001	2025
	The ecology of the microbiota in children with obesity is associated with the intake of carbohydrates and insulin resistance.	Prodam F, Ricotti R, Caramaschi A, Mancioppi V, Antoniotti V, Caputo M, Archero F, Filigheddu N, Tini S, Celano S, Manfredi M, Massa N, Bellone S, Bona E.	Clin Nutr	10.1016/j.clnu.2025.08.018	2025
Enzymology	Altered intestinal Streptococcus anginosus and 5alpha-reductase gene levels in patients with hepatocellular carcinoma and elevated Bacteroides stercoris in atezolizumab/bevacizumab non-responders.	Fujii T, Kuzuya T, Kondo N, Funasaka K, Ohno E, Hirooka Y, Tochio T.	J Med Microbiol	10.1099/jmm.0.001878	2024
	Antimicrobial resistance pattern of the Bacteroides fragilis group strains isolated at a teaching hospital in China.	Wu ZC, Feng HX, Wu L, Zhang M, Gu Z.	Acta Microbiol Immunol Hung	10.1556/030.2025.02400	2025
	The development and excretion of Toxoplasma gondii oocyst manipulate the gut microbiota in its definitive host.	Zhao GH, Zhou BB, Cao ZH, Xiao T, Li YN, Zhu WJ, Sun H, Xie HH, Xie XM, Zhang JM, Wang Q, Zhang X, Xie JJ, Dong HJ, Xu C, Yin K.	Parasit Vectors	10.1186/s13071-025-06925-6	2025
Genetics	Dysbiosis of Gut Microbiota in Microscopic Colitis: Diagnostic and Therapeutic Implications.	Dragasevic S, Nikolic A, Zgradic S, Stojkovic Lalosevic M, Stojkovic S, Matovic Zaric V, Lukic S, Glisic T, Kmezic S, Saponjski D, Popovic D.	Diagnostics (Basel)	10.3390/diagnostics15141733	2025
Genetics	Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes?	Sanville J, O'Toole GA, Madan J, Coker M.	J Pediatr Gastroenterol Nutr	10.1002/jpn3.12350	2024
	Anti-obesity activity of human gut microbiota Bacteroides stercoris KGMB02265.	Ryu SW, Moon JC, Oh BS, Yu SY, Bak JE, Heo ES, Jeong JH, Lee JH.	Arch Microbiol	10.1007/s00203-023-03750-2	2023
	Analysis of Gut Microbiota and Their Metabolites in CADASIL Patients.	Watanabe-Hosomi A, Inoue R, Mizuta I, Matsuura J, Matsuura H, Fukunaga D, Ohara T, Naito Y, Mizuno T.	J Clin Neurol	10.3988/jcn.2025.0231	2025
	Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma.	Esparteiro D, Fouquet G, Courtois A, Naassila M, Nguyen-Khac E, Marcq I.	Gastro Hep Adv	10.1016/j.gastha.2024.07.020	2025
Genetics	Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.	Luo L, Chen B, Zeng S, Li Y, Chen X, Zhang J, Guo X, Li S, Ruan L, Zhu S, Gao C, Zhang C, Li T.	Front Microbiol	10.3389/fmicb.2025.1586195	2025
	Intestinal Microbiome Associated with Efficacy of Atezolizumab and Bevacizumab Therapy for Hepatocellular Carcinoma.	Inukai Y, Yamamoto K, Honda T, Yokoyama S, Ito T, Imai N, Ishizu Y, Nakamura M, Ishigami M, Kawashima H.	Cancers (Basel)	10.3390/cancers16091675	2024
	Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.	Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G.	mSystems	10.1128/msystems.01303-23	2024
Phylogeny	Longitudinal Pilot Evaluation of the Gut Microbiota Comparing Patients With and Without Chronic Kidney Disease.	Pourafshar S, Sharma B, Allen J, Hoang M, Lee H, Dressman H, Tyson CC, Mallawaarachchi I, Kumar P, Ma JZ, Lin PH, Scialla JJ.	J Ren Nutr	10.1053/j.jrn.2024.01.003	2024
	Gut microbiota-metabolome remodeling associated with low bone mass: an integrated multi-omics study in fracture patients.	Zhao X, Wu B, Han P, Wang Z, Cao R, Chen S, Cheng C, Lian H, Zha Y, Li M.	Front Mol Biosci	10.3389/fmolb.2025.1646361	2025
	Gut microbiota, physical activity and/or metabolic markers in healthy individuals - towards new biomarkers of health.	Myhrstad MCW, Ruud E, Gaundal L, Gjovaag T, Rud I, Retterstol K, Ulven SM, Holven KB, Koehler K, Telle-Hansen VH.	Front Nutr	10.3389/fnut.2024.1438876	2024
	Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations.	Ni Y, Qian L, Siliceo SL, Long X, Nychas E, Liu Y, Ismaiah MJ, Leung H, Zhang L, Gao Q, Wu Q, Zhang Y, Jia X, Liu S, Yuan R, Zhou L, Wang X, Li Q, Zhao Y, El-Nezami H, Xu A, Xu G, Li H, Panagiotou G, Jia W.	Cell Metab	10.1016/j.cmet.2023.08.002	2023
	Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.	Ai X, Huang C, Liu Q, Duan R, Ma X, Li L, Shu Z, Miao Y, Shen H, Lv Y, Jiang Z, Luo H, Long Z.	Front Microbiol	10.3389/fmicb.2025.1629811	2025
	Parity influences postpartum adaptations in the maternal gut microbiota.	Jarmukhanov Z, Vinogradova E, Mukhanbetzhanov N, Kozhakhmetov S, Khassenbekova D, Kushugulova A.	Sci Rep	10.1038/s41598-025-02013-y	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
	Intestinal bacteria associated with irritable bowel syndrome and chronic fatigue.	El-Salhy M.	Neurogastroenterol Motil	10.1111/nmo.14621	2023
Enzymology	Gut microbiota and metabolite profiles in HBV cirrhosis with persistent liver enzyme abnormalities.	He H, Zou R, Liao X, Lan Y.	Front Microbiol	10.3389/fmicb.2025.1645023	2025
	Dynamic development of gut microbiota and metabolism during and after weaning of kittens.	Zhang H, Ren Y, Wei S, Jin H, Wang Y, Jin M.	Anim Microbiome	10.1186/s42523-024-00373-w	2025
	Gut microbiota dysbiosis in people living with HIV who have cancer: novel insights and diagnostic potential.	Xie Z, Huang Q, Wen L, Luo T, Ai S, Ruan G, Liu N, Wei Y, Lan Y, Cui P, Cao Q, Liang H, Ye L, Zhou J, Huang J.	Front Immunol	10.3389/fimmu.2025.1598650	2025
Metabolism	Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.	Kuo TH, Wu PH, Liu PY, Chuang YS, Tai CJ, Kuo MC, Chiu YW, Lin YT.	Int J Mol Sci	10.3390/ijms262110463	2025
	Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.	Ito E, Ohki T, Toya N, Emoto T, Yamashita T, Sugiyama T, Yamada T, Mori H, Toyoda A, Hirata KI.	Ann Vasc Dis	10.3400/avd.oa.24-00105	2025
	Postoperative Gut Microbiota Changes after Colorectal Cancer Surgery: A Comparative Study Based on Resection Sites.	Hattori Y, Fujii T, Tochio T, Kumamoto T, Hiro J, Matsuoka H, Masumori K, Funasaka K, Ohno E, Hirooka Y, Suda K, Otsuka K.	J Anus Rectum Colon	10.23922/jarc.2025-048	2025
	The differences in intestinal flora and metabolites between H-type hypertension and non-H-type hypertension.	Wu J, Zhao J, Cheng Y, Zhou H, Shen G, Ding H, Lv J, Dong S, Tang O.	J Transl Med	10.1186/s12967-025-06295-8	2025
	Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication.	Stiernborg M, Debelius JW, Yang LL, Skott E, Millischer V, Giacobini M, Melas PA, Boulund F, Lavebratt C.	Brain Behav Immun	10.1016/j.bbi.2023.03.012	2023
	Association between gut microbiota composition and physical functioning in patients with knee osteoarthritis: a machine learning study.	de Sire A, Mancuso E, Marotta N, Massimino M, Zito R, Averta C, Bartalotta I, Palummo A, Cerantonio A, Citrigno L, Soverini M, Castagnetti A, Mannino GC, Ammendolia A, Andreozzi F.	Sci Rep	10.1038/s41598-025-24500-y	2025
Genetics	Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.	Xiang J, Chai N, Li L, Hao X, Linghu E.	Turk J Gastroenterol	10.5152/tjg.2024.24294	2024
Phylogeny	A Comparative Assessment of Flaxseed (Linum usitatissimum L.) and Chia Seed (Salvia hispanica L.) in Modulating Fecal Microbiota Composition and Function In Vitro.	Arioglu-Tuncil S.	Food Sci Nutr	10.1002/fsn3.70243	2025
	Gut microbiota profile in adults with abdominal obesity and non-abdominal obesity: links to body composition and macronutrient intake in Semarang, Indonesia-a brief research report.	Fadhillah FS, Arafat FB, Maharani N, Fadhilah J, Zariyah H, Sobirin MA, Tsutsui H, Wibowo A, Juniarto AZ, Pramono A.	Front Nutr	10.3389/fnut.2025.1648575	2025
	Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.	Raziq MF, Khan N, Manzoor H, Tariq HMA, Rafiq M, Rasool S, Kayani MUR, Huang L.	J Transl Med	10.1186/s12967-025-06370-0	2025
	Gut microbiota influences lung cancer risk through circulating cytokines-Insights from a Mendelian randomization study.	Shen W, Hou R, Zhang J, Liu C, Zhang C, Liu X.	Medicine (Baltimore)	10.1097/md.0000000000044897	2025
Pathogenicity	The antibacterial activity of a prophage-encoded fitness factor is neutralized by two cognate immunity proteins.	Alexei AG, Bullen NP, Garrett SR, Sychantha D, Whitney JC.	J Biol Chem	10.1016/j.jbc.2024.108007	2024
	Community characteristics and relationship between gut microbiota and intratumoral microbiota in hepatocellular carcinoma.	Lin H, Ma Z, Li J, Zhu H, Huang X, Chen H, Tu L, Lian Y, Su Y.	Front Immunol	10.3389/fimmu.2024.1500863	2024
	Intestinal deguelin drives resistance to acetaminophen-induced hepatotoxicity in female mice.	Gong S, Zeng Y, Wang Z, Li Y, Wu R, Li L, Hu H, Qin P, Yu Z, Huang X, Guo P, Yang H, He Y, Zhao Z, Xiao W, Zhao X, Gao L, Cai S, Zeng Z.	Gut Microbes	10.1080/19490976.2024.2404138	2024
	Microbe-immune interactions: new perspectives on coagulation deficiencies, purpura, and other hemorrhagic conditions under the regulation of the gut microbiota.	Ren R, Huang X, Wei D, Guo Q, Wang C, Li M, Yang L, Lang H, Chen S.	Front Immunol	10.3389/fimmu.2024.1461221	2024
Phylogeny	Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.	Cho HY, Park HJ, Choi JS, Kim SH, Ryu MO, Seo KW.	Front Vet Sci	10.3389/fvets.2025.1571107	2025
Genetics	Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.	Ghozlane A, Thirion F, Plaza Onate F, Gauthier F, Le Chatelier E, Annamale A, Almeida M, Ehrlich SD, Pons N.	Microbiome	10.1186/s40168-025-02249-w	2025
	mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.	Qi C, Cai Y, He G, Qian K, Guo M, Cheng L.	Gut Microbes	10.1080/19490976.2025.2552347	2025
	The role of the gut microbiota in chemotherapy response, efficacy and toxicity: a systematic review.	Bohm D, Russ E, Guchelaar HJ, Ziemons J, Penders J, Smidt ML, van Best N, Deenen MJ.	NPJ Precis Oncol	10.1038/s41698-025-01034-0	2025
Metabolism	Characteristics of the gut microbiota and serum metabolites in postmenopausal women with reduced bone mineral density.	Yan L, Wang X, Yu T, Qi Z, Li H, Nan H, Wang K, Luo D, Hua F, Wang W.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1367325	2024
	Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.	Vargas BO, Carazzolle MF, Galhardo JP, Jose J, de Souza BC, Correia JBL, Santos JRD, Pereira GAG, de de Mello FDSB.	Biotechnol J	10.1002/biot.70050	2025
	Are Bifidobacterium Species Key Players in the Progression of Type 1 Diabetes? A Systematic Review.	Vergoz V, Jeong D, Hamilton-Williams EE.	Endocrinol Diabetes Metab	10.1002/edm2.70120	2025
Genetics	Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.	Albaijan D, Albaijan D, Akbar A.	Curr Issues Mol Biol	10.3390/cimb47110890	2025
	Decreased Lactococcus lactis and Propionic Acid in Feces of Patients with Moyamoya Disease: Possible Implications of Immune Dysregulation.	Otomo M, Tashiro R, Tokuno H, Kanoke A, Tominaga K, Nagai A, Aikawa T, Ando D, Sakata H, Sato T, Abe T, Endo H, Niizuma K, Tominaga T.	Cerebrovasc Dis	10.1159/000545478	2025
	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
	The effect of culturing temperature on the growth of the most dominant bacterial species of human gut microbiota and harmful bacterial species.	Shimokawa H, Sakakibara H, Ami Y, Hirano R, Kurihara S.	Biosci Microbiota Food Health	10.12938/bmfh.2024-087	2025
	Changes in Human Colonic Microbiota Promoted by Synbiotic Açai Juice Composed of Gluco-Oligosaccharides, Dextran, and Bifidobacterium breve NRRL B-41408.	Reges BM, da Silva Oliveira FA, Fonteles TV, Rodrigues S.	Foods	10.3390/foods13244121	2024
	Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.	Ma C, Zhang Y, Jiang S, Teng F, Huang S, Zhang J.	mSystems	10.1128/msystems.00828-23	2023
Metabolism	Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.	Yang MT, Xie LH, Wang L, Gao YQ, Liu R, Ma H, Lei CC, Jiang J, Su JW, Zhang XX, Ni HB, Nan FL.	Poult Sci	10.1016/j.psj.2025.105956	2025
Enzymology	Reduced Enterohepatic Recirculation of Mycophenolate and Lower Blood Concentrations Are Associated with the Stool Bacterial Microbiome after Hematopoietic Cell Transplantation.	Saqr A, Carlson B, Staley C, Rashidi A, Al-Kofahi M, Kaiser T, Holtan S, MacMillan M, Young JA, Jurdi NE, Weisdorf D, Khoruts A, Jacobson PA.	Transplant Cell Ther	10.1016/j.jtct.2022.04.018	2022
	The gut microbiota and diabetic nephropathy: an observational study review and bidirectional Mendelian randomization study.	Han YZ, Wang YZY, Zhu XY, Du BX, Wang YX, Zhang XQ, Jia JM, Liu WJ, Zheng HJ.	Trials	10.1186/s13063-025-08755-4	2025
Enzymology	Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.	Wang Y, Bai Z, Liu Y, Wang Y, Xu J, Lai Z.	Front Microbiol	10.3389/fmicb.2025.1616985	2025
	Gut dysbiosis, inflammation and type 2 diabetes in mice using synthetic gut microbiota from diabetic humans.	Liaqat I, Ali NM, Arshad N, Sajjad S, Rashid F, Hanif U, Ara C, Ulfat M, Andleeb S, Awan UF, Bibi A, Mubin M, Ali S, Tahir HM, Ul-Haq I.	Braz J Biol	10.1590/1519-6984.242818	2021
Phylogeny	TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.	Shen Q, Fan X, Sun Y, Gao H, Su X.	BMC Bioinformatics	10.1186/s12859-025-06156-7	2025
Pathogenicity	Gut microbiota is associated with dietary intake and metabolic markers in healthy individuals.	Gaundal L, Myhrstad MCW, Rud I, Gjovaag T, Byfuglien MG, Retterstol K, Holven KB, Ulven SM, Telle-Hansen VH.	Food Nutr Res	10.29219/fnr.v66.8580	2022
Pathogenicity	Evaluation of the therapeutic effect of Berberine microcapsules on Salmonella enteritidis-infected mice.	Yang L, Qiao Y, Chen R, Wang M, Zhou B, Zhang X, Zhao Y, Shi H, Xia L, Fu Q.	BMC Vet Res	10.1186/s12917-025-04986-4	2025
	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
	Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis.	Yan J, Chen H, Zhang Y, Peng L, Wang Z, Lan X, Yu S, Yang Y.	Gut Microbes	10.1080/19490976.2024.2353396	2024
Phylogeny	Distinct gut microbial species, but not phylum-to-genus composition, associate with insulin resistance: a unique perspective from the Kazakh population.	Abildinova GZ, Benberin VV, Vochshenkova TA, Mussin NM, Afshar A, Tamadon A.	Front Microbiol	10.3389/fmicb.2025.1683885	2025
Pathogenicity	Gut Microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.	Scalzo PL, Marshall AG, Soriano S, Curry K, Dulay M, Hodics T, Quigley EMM, Treangen TJ, Piskorz MM, Villapol S.	J Transl Med	10.1186/s12967-025-06348-y	2025
	Correlation study on gut microbiota and myosteatosis in patients with liver cirrhosis.	Zhao N, Bai J, Li X, Xu G, Fu X, Li J, Niu L, Yao J, Zhou X.	Front Nutr	10.3389/fnut.2025.1513973	2025
	Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China.	Chi R, Li M, Zhang M, Zhang N, Zhang G, Cui L, Ma G.	Nutrients	10.3390/nu16101460	2024
Genetics	Association between gut microbiota and diabetic nephropathy: a two-sample Mendelian randomization study.	Ye Z, So T, Zhang T, Gao X.	Front Endocrinol (Lausanne)	10.3389/fendo.2024.1361440	2024
	Effects of Sodium-Glucose Cotransporter-2 Inhibitors on Modulating Protein-Bound Uremic Toxins and Gut Microbiota in Predialysis CKD Patients: Matched Case-Control Study.	Hsu CK, Chang LC, Chen YT, Chen CY, Hsu HR, Bai S, Lee CC, Lee CC, Jangir H, Sun CY, Su SC, Wu IW.	Kidney360	10.34067/kid.0000000792	2025
Enzymology	Effect of Gut Microbiota on the Pharmacokinetics of Nifedipine in Spontaneously Hypertensive Rats.	Zhou R, Yang H, Zhu P, Liu Y, Zhang Y, Zhang W, Zhou H, Li X, Li Q.	Pharmaceutics	10.3390/pharmaceutics15082085	2023
Phylogeny	Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity.	Lin YC, Wu CC, Li YE, Chen CL, Lin CR, Ni YH.	BMC Microbiol	10.1186/s12866-025-03849-0	2025
	Correlation Between Gastroesophageal Reflux Disease and Small Intestinal Bacterial Overgrowth: Analysis of Intestinal Microbiome and Metabolic Characteristics.	Wang ZT, Tan WT, Huang JL, Zhang PF, Li Q, Wang MM, Meng MM, Su H, Guo CM, Liu H.	J Inflamm Res	10.2147/jir.s487185	2025
	Disruption and adaptation: infant gut microbiota's dynamic response to SARS-CoV-2 infection.	Zhu LT, Zhao L, Zhu Y, Xu XL, Lin JJ, Duan YF, Long L, Wu YY, Xu WJ, Chen JY, Yin YH, Obeten AU, Huang Q.	Microbiome	10.1186/s40168-025-02029-6	2025
	Emerging Novel Therapies for the Treatment of Psoriasis: A Narrative Review.	Kaye AD, Thompson N, Coreil CB, Amedio LS, Rodriguez VA, Vu JN, Ahmadzadeh S, Kallurkar A, Moss TW, Shekoohi S, Varrassi G.	Cureus	10.7759/cureus.79693	2025
Transcriptome	Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria.	Zhang T, Pei Z, Wang H, Zhao J, Chen W, Lu W.	Microorganisms	10.3390/microorganisms13020234	2025
	Gut Microbiota in T1DM-Onset Pediatric Patients: Machine-Learning Algorithms to Classify Microorganisms as Disease Linked.	Biassoni R, Di Marco E, Squillario M, Barla A, Piccolo G, Ugolotti E, Gatti C, Minuto N, Patti G, Maghnie M, d'Annunzio G.	J Clin Endocrinol Metab	10.1210/clinem/dgaa407	2020
	Gut Microbiome Correlations in Hidradenitis Suppurativa Patients.	Lelonek E, Krajewski PK, Szepietowski JC.	J Clin Med	10.3390/jcm14145074	2025
Metabolism	Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.	Park S, Li C, Wu X, Zhang T.	Int J Mol Sci	10.3390/ijms241713329	2023
	A blood-based circulating microbial metagenomic panel for early diagnosis and prognosis of oesophageal adenocarcinoma.	Zaidi AH, Pratama MY, Omstead AN, Gorbonova A, Mansoor R, Melton-Kreft R, Jobe BA, Wagner PL, Kelly RJ, Goel A.	Br J Cancer	10.1038/s41416-022-01974-5	2022
Phylogeny	Altered gut microbiome profile in patients with knee osteoarthritis.	Wang X, Wu Y, Liu Y, Chen F, Chen S, Zhang F, Li S, Wang C, Gong Y, Huang R, Hu M, Ning Y, Zhao H, Guo X.	Front Microbiol	10.3389/fmicb.2023.1153424	2023
Metabolism	Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis.	Wang Z, Guo M, Li J, Jiang C, Yang S, Zheng S, Li M, Ai X, Xu X, Zhang W, He X, Wang Y, Chen Y.	Microbiol Spectr	10.1128/spectrum.00829-23	2023
	Gut microbiota and metabolites: emerging prospects in the treatment of non-small cell lung cancer.	Jiao JM, Liu CG, Zang D, Chen J.	Front Immunol	10.3389/fimmu.2025.1638942	2025
	Exploring the Role of the Gut Microbiome Across the Lifespan: Implications for Aging and Metabolic Disorders.	Aznou A, Drenth JPH, Nieuwdorp M, Meijnikman AS.	J Endocr Soc	10.1210/jendso/bvaf130	2025
	Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study.	Zhu C, Li L-Y, Li C, Wu L, Zhang Y-Y, Yao Y, Yang J, Wang S-Y, Xing L-M, Zeng X-T, Fang C.	Microbiol Spectr	10.1128/spectrum.03376-24	2025
Genetics	Comparison of gut microbiota in male MAFLD patients with varying liver stiffness.	Zhang Y, Yan S, Sheng S, Qin Q, Chen J, Li W, Li T, Gao X, Wang L, Ang L, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.873048	2022
	Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.	Rasoulimehrabani H, Khadem S, Hodzic A, Philipp M, Gallo R, Nikolov G, Seneca J, Ramesmayer J, Sivulic P, Berry D.	Microbiome Res Rep	10.20517/mrr.2025.29	2025
	Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.	Nomura K, Ishikawa D, Okahara K, Ito S, Haga K, Takahashi M, Arakawa A, Shibuya T, Osada T, Kuwahara-Arai K, Kirikae T, Nagahara A.	J Clin Med	10.3390/jcm10081749	2021
Genetics	Association of distinct microbial signatures with premalignant colorectal adenomas.	Lee JWJ, Plichta DR, Asher S, Delsignore M, Jeong T, McGoldrick J, Staller K, Khalili H, Xavier RJ, Chung DC.	Cell Host Microbe	10.1016/j.chom.2023.04.007	2023
Genetics	Analysis of the gut microbiota in children with gastroesophageal reflux disease using metagenomics and metabolomics.	Ye X, Yu F, Zhou J, Zhao C, Wu J, Ni X.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1267192	2023
	Combination of gut microbiota, proinflammatory cytokine, and ¹⁸F-FDG PET as potential indicators for predicting breast cancer recurrence.	An J, Kim BS, Yoon HJ.	Sci Rep	10.1038/s41598-025-92233-z	2025
	Christensenella minuta interacts with multiple gut bacteria.	Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ.	Front Microbiol	10.3389/fmicb.2024.1301073	2024
Phylogeny	The role of intestinal microbiota in the humoral response to SARS-CoV-2 after mRNA-1273 vaccination.	Tarrino M, Gutierrez-Bautista JF, Duran MJO, Garcia-Diaz A, Cabrera-Serrano AJ, Sainz J, Cobo F, Rodriguez T, Reguera JA, Bernal M, Lopez-Nevot MA, Sampedro A.	Sci Rep	10.1038/s41598-025-11103-w	2025
	A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.	Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD.	Nat Commun	10.1038/s41467-025-64822-z	2025
Genetics	Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy.	Zhang L, Wang Z, Zhang X, Zhao L, Chu J, Li H, Sun W, Yang C, Wang H, Dai W, Yan S, Chen X, Xu D.	Microbiol Spectr	10.1128/spectrum.00324-22	2022
Genetics	Role of CD38 in mediating the effect of Bacillus on acute pancreatitis: a study of mediated Mendelian randomization.	Xiao J, Tao Z, Luo M, Yan Y, Ke S, Mao B, Zhan J, Wang Z, Wang B, Li Z.	Front Immunol	10.3389/fimmu.2024.1452743	2024
	Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.	Lim MY, Hong S, Nam YD.	Front Immunol	10.3389/fimmu.2024.1512683	2024
	Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy.	Bischoff SC, Nguyen NK, Seethaler B, Beisner J, Kugler P, Stefan T.	Nutrients	10.3390/nu14153182	2022
Genetics	Effect of Palmitoylethanolamide Compared to a Placebo on the Gut Microbiome and Biochemistry in an Overweight Adult Population: A Randomised, Placebo Controlled, Double-Blind Study.	Batacan R, Briskey D, Bajagai YS, Smith C, Stanley D, Rao A.	Biomedicines	10.3390/biomedicines12071620	2024
	Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.	Chen J, Siliceo SL, Ni Y, Nielsen HB, Xu A, Panagiotou G.	Microbiome	10.1186/s40168-023-01604-z	2023
	Clinical effectiveness of fecal microbial transplantation for metabolic syndrome: Advances in clinical efficacy and multi-omics research.	Wang H, Tian J, Mi J.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100415	2025
Genetics	Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.	Chen Y, Nian F, Chen J, Jiang Q, Yuan T, Feng H, Shen X, Dong L.	Biomedicines	10.3390/biomedicines13041000	2025
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
	Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.	West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ, Iwai S.	Sci Rep	10.1038/s41598-022-21327-9	2022
Enzymology	First report of metronidazole resistant, nimD-positive, Bacteroides stercoris isolated from an abdominal abscess in a 70-year-old woman.	Otte E, Nielsen HL, Hasman H, Fuglsang-Damgaard D.	Anaerobe	10.1016/j.anaerobe.2016.12.010	2017
	Pharmacomicrobiomics.	Gronich N, Geva-Zatorsky N, Herren R, Kelly L, Cohen Z, Zhou H, Chen YC, Shah K, Robinson-Catala TA, Frisby G, Karnes JH, Shoda L.	Clin Pharmacol Ther	10.1002/cpt.70066	2025
	Consumption of only wild foods induces large scale, partially persistent alterations to the gut microbiome.	Rampelli S, Pomstra D, Barone M, Fabbrini M, Turroni S, Candela M, Henry AG.	Sci Rep	10.1038/s41598-025-00319-5	2025
	Gut microbiome is associated with asthma and race in children with food allergy.	Mahdavinia M, Fyolek JP, Jiang J, Thivalapill N, Bilaver LA, Warren C, Fox S, Nimmagadda SR, Newmark PJ, Sharma H, Assa'ad A, Seed PC, Gupta RS.	J Allergy Clin Immunol	10.1016/j.jaci.2023.07.024	2023
Genetics	Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.	Qayyum H, Talib MS, Ali A, Kayani MUR.	Heliyon	10.1016/j.heliyon.2025.e41938	2025
	Utility of Diagnostic Imaging in the Early Detection and Management of the Fournier Gangrene.	Sumislawski P, Kolecki J, Piotrowska M, Kotowski M, Szemitko M, Sienko J.	Diagnostics (Basel)	10.3390/diagnostics12102320	2022
	Gut Microbial Changes Associated With Obesity in Youth With Type 1 Diabetes.	Ismail HM, Perera D, Mandal R, DiMeglio LA, Evans-Molina C, Hannon T, Petrosino J, Javornik Cregeen S, Schmidt NW.	J Clin Endocrinol Metab	10.1210/clinem/dgae529	2025
	A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits.	Sarnoff RP, Bhatt RR, Osadchiy V, Dong T, Labus JS, Kilpatrick LA, Chen Z, Subramanyam V, Zhang Y, Ellingson BM, Naliboff B, Chang L, Mayer EA, Gupta A.	Neuropharmacology	10.1016/j.neuropharm.2022.109381	2023
	A pilot study of microbial signatures of liver disease in those with HIV mono-infection in Rio de Janeiro, Brazil.	Yanavich C, Perazzo H, Li F, Tobin N, Lee D, Zabih S, Morata M, Almeida C, Veloso VG, Grinsztejn B, Aldrovandi GM.	AIDS	10.1097/qad.0000000000003084	2022
Phylogeny	Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial.	Calva-Cruz OJ, Ovando-Vazquez C, De Leon-Rodriguez A, Veana F, Espitia-Rangel E, Trevino S, Barba-de la Rosa AP.	Foods	10.3390/foods12142760	2023
Pathogenicity	Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder.	Boonchooduang N, Louthrenoo O, Likhitweerawong N, Kunasol C, Thonusin C, Sriwichaiin S, Nawara W, Chattipakorn N, Chattipakorn SC.	Sci Rep	10.1038/s41598-025-87546-y	2025
	Serotonergic and immunomodulatory properties of the psychobiotic candidate Bacteroides finegoldii UO.H1052 and its extracellular vesicles.	Yousuf B, Esmail GA, Nazemof N, Bouhlel NE, Minic Z, Hammami R.	Appl Environ Microbiol	10.1128/aem.00891-25	2025
	Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.	Guo Z, Wang X, Li Y, Zhang Y, Guo P, Zhang J, Zhang Z, Ma X.	Front Immunol	10.3389/fimmu.2025.1563225	2025
	Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver.	Katona BW, Shukla A, Hu W, Nyul T, Dudzik C, Arvanitis A, Clay D, Dungan M, Weber M, Tu V, Hao F, Gan S, Chau L, Buchner AM, Falk GW, Jaffe DL, Ginsberg G, Palmer SN, Zhan X, Patterson AD, Bittinger K, Ni J.	Gut Microbes	10.1080/19490976.2025.2474141	2025
Pathogenicity	Effect of Lacticaseibacillus casei LC2W Supplementation on Glucose Metabolism and Gut Microbiota in Subjects at High Risk of Metabolic Syndrome: A Randomized, Double-blinded, Placebo-controlled Clinical Trial.	Wang D, Wang X, Han J, You C, Liu Z, Wu Z.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10312-5	2025
Pathogenicity	Gut Microbiota and Obsessive-Compulsive Disorder: A Systematic Review of Mechanistic Links, Evidence from Human and Preclinical Studies, and Therapeutic Prospects.	Eghdami S, Saeidi M, Gunturu S, Boroon M, Shalbafan M.	Life (Basel)	10.3390/life15101585	2025
Genetics	Alterations of the Gut Microbiome in Patients With Pituitary Adenoma.	Hu J, Yang J, Chen L, Meng X, Zhang X, Li W, Li Z, Huang G.	Pathol Oncol Res	10.3389/pore.2022.1610402	2022
Phylogeny	Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor.	Granato A, Renwick S, Yau C, Kong T, Daigneault MC, Knip M, DIABIMMUNE Study Group, Allen-Vercoe E, Danska JS.	Microbiome	10.1186/s40168-024-01976-w	2024
Genetics	The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.	Zhang Y, Xue G, Wang F, Zhang J, Xu L, Yu C.	Front Microbiol	10.3389/fmicb.2024.1382332	2024
	parafac4microbiome: exploratory analysis of longitudinal microbiome data using parallel factor analysis.	van der Ploeg GR, Westerhuis JA, Heintz-Buschart A, Smilde AK.	mSystems	10.1128/msystems.00472-25	2025
	Thymol-Modified Oleic and Linoleic Acids Encapsulated in Polymeric Nanoparticles: Enhanced Bioactivity, Stability, and Biomedical Potential.	Sokol MB, Sokhraneva VA, Groza NV, Mollaeva MR, Yabbarov NG, Chirkina MV, Trufanova AA, Popenko VI, Nikolskaya ED.	Polymers (Basel)	10.3390/polym16010072	2023
	In-depth investigation of the mechanism in rats with alcoholic acute pancreatitis via DNA methylation, intestinal flora, and fecal metabolomics.	Dong H, Ying W, Zhu S.	J Inflamm (Lond)	10.1186/s12950-025-00463-9	2025
	Distribution of anaerobic bacteria and their sensitivity pattern to several antibiotics at the clinical microbiology laboratory of school of medicine, universitas Indonesia, Jakarta in 2019-2020.	Tjampakasari CR, Prasetyo DS, Ningsih I, Kiranasari A.	Iran J Microbiol	10.18502/ijm.v14i1.8797	2022
	Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome.	Chang B, Zhang W, Wang Y, Zhang Y, Zhong S, Gao P, Wang L, Zhao Z.	BMC Microbiol	10.1186/s12866-024-03211-w	2024
	Bacterial and Fungal Adaptations in Cecum and Distal Colon of Piglets Fed With Dairy-Based Milk Formula in Comparison With Human Milk.	Elolimy A, Rosa F, Tripp P, Zeineldin M, Bowlin AK, Randolph C, Robeson MS, Yeruva L.	Front Microbiol	10.3389/fmicb.2022.801854	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
	Fecal and soil microbiota composition of gardening and non-gardening families.	Brown MD, Shinn LM, Reeser G, Browning M, Schwingel A, Khan NA, Holscher HD.	Sci Rep	10.1038/s41598-022-05387-5	2022
Genetics	Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries.	Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.11.047	2024
Pathogenicity	Inflammation, Gut Microbiota, and Metabolomic Shifts in Colorectal Cancer: Insights from Human and Mouse Models.	Yang C, Wusigale, You L, Li X, Kwok LY, Chen Y.	Int J Mol Sci	10.3390/ijms252011189	2024
Genetics	Investigating gut microbiota-blood and urine metabolite correlations in early sepsis-induced acute kidney injury: insights from targeted KEGG analyses.	Xu Y, Xu J, Zhu Y, Mao H, Li J, Kong X, Zhu X, Zhang J.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1375874	2024
Phylogeny	Discovering Potential Taxonomic Biomarkers of Type 2 Diabetes From Human Gut Microbiota via Different Feature Selection Methods.	Bakir-Gungor B, Bulut O, Jabeer A, Nalbantoglu OU, Yousef M.	Front Microbiol	10.3389/fmicb.2021.628426	2021
	Gut and Urinary Microbiota in Cats with Kidney Stones.	Joubran P, Roux FA, Serino M, Deschamps JY.	Microorganisms	10.3390/microorganisms12061098	2024
	Identification and Biochemical Characterization of a Surfactant-Tolerant Chondroitinase VhChlABC from Vibrio hyugaensis LWW-1.	Su J, Wang X, Yin C, Li Y, Wu H, Yu W, Han F.	Mar Drugs	10.3390/md19070399	2021
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
	Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.	Drevland OM, de Muinck EJ, Trosvik P, Hammerstad M, Kvitne KE, Midtvedt K, Asberg A, Robertsen I.	Microbiome	10.1186/s40168-025-02142-6	2025
	Fecal microbiota transplantation treatment for type 1 diabetes mellitus with malnutrition: a case report.	Xie YC, Jing XB, Chen X, Chen LZ, Zhang SH, Cai XB.	Ther Adv Chronic Dis	10.1177/20406223221117449	2022
Phylogeny	Successful secukinumab therapy in plaque psoriasis is associated with altered gut microbiota and related functional changes.	Du X, Yan C, Kong S, Che D, Peng B, Zhu L, Geng S, Guo K.	Front Microbiol	10.3389/fmicb.2023.1227309	2023
	Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism.	Liu H, Feng S, Tang M, Tian R, Zhang S.	Rev Cardiovasc Med	10.31083/j.rcm2511395	2024
	Gut microbes on the risk of advanced adenomas.	Jing Z, Zheng W, Jianwen S, Hong S, Xiaojian Y, Qiang W, Yunfeng Y, Xinyue W, Shuwen H, Feimin Z.	BMC Microbiol	10.1186/s12866-024-03416-z	2024
Metabolism	Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.	Guan Y, Zhao S, Li J, Zhang W, Guo Z, Luo Y, Jiang X, Li J, Liu J, Chen X, Zhao Z, Zhang Z.	Front Microbiol	10.3389/fmicb.2024.1369478	2024
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
	Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles.	Yousuf B, Mottawea W, Esmail GA, Nazemof N, Bouhlel NE, Njoku E, Li Y, Zhang X, Minic Z, Hammami R.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100358	2025
	Microbial metabolite ammonia disrupts TGF-beta signaling to promote colon cancer.	Bhowmick K, Yang X, Mohammad T, Xiang X, Molmenti CL, Mishra B, Dasarathy S, Krainer AR, Hassan MI, Crandall KA, Mishra L.	J Biol Chem	10.1016/j.jbc.2025.108559	2025
	Taxonomic and functional shifts of gut microbiome in immunoglobulin A vasculitis children and their mothers.	Liang Y, Zhao C, Zhao L, Sheng D, Chen B, Zhao G, Wang Q, Zhang L.	Front Pediatr	10.3389/fped.2024.1356529	2024
Pathogenicity	Lactobacilli in COVID-19: A Systematic Review Based on Next-Generation Sequencing Studies.	Taufer CR, Rampelotto PH.	Microorganisms	10.3390/microorganisms12020284	2024
	Enhancing pediatric attention-deficit hyperactivity disorder treatment: exploring the gut microbiota effects of French maritime pine bark extract and methylphenidate intervention.	Weyns AS, Ahannach S, Van Rillaer T, De Bruyne T, Lebeer S, Hermans N.	Front Nutr	10.3389/fnut.2024.1422253	2024
	Gut microbiota diversity and composition in predicting immunotherapy response and immunotherapy-related colitis in melanoma patients: A systematic review.	Oey O, Liu YY, Sunjaya AF, Simadibrata DM, Khattak MA, Gray E.	World J Clin Oncol	10.5306/wjco.v13.i11.929	2022
	Human-gut bacterial protein-protein interactions: understudied but impactful to human health.	Balint D, Brito IL.	Trends Microbiol	10.1016/j.tim.2023.09.009	2024
Transcriptome	The altered TBI fecal microbiome is stable and functionally distinct.	Pyles RB, Miller AL, Urban RJ, Sheffield-Moore M, Wright TJ, Maxwell CA, Randolph KM, Danesi CP, McGovern KA, Vargas J, Armstrong P, Kreber L, Cumpa G, Randall K, Morrison M, Masel BE.	Front Mol Neurosci	10.3389/fnmol.2024.1341808	2024
	Gut microbiota links to serum ferritin and cognition.	Rosell-Diaz M, Santos-Gonzalez E, Motger-Alberti A, Ramio-Torrenta L, Garre-Olmo J, Perez-Brocal V, Moya A, Jove M, Pamplona R, Puig J, Ramos R, Fernandez-Real JM, Mayneris-Perxachs J.	Gut Microbes	10.1080/19490976.2023.2290318	2023
Genetics	Integration analysis of tumor metagenome and peripheral immunity data of diffuse large-B cell lymphoma.	Zhang Y, Han S, Xiao X, Zheng L, Chen Y, Zhang Z, Gao X, Zhou S, Yu K, Huang L, Fu J, Hong Y, Jiang J, Qian W, Yang H, Shen J.	Front Immunol	10.3389/fimmu.2023.1146861	2023
	Ecological dynamics of the gut microbiome in response to dietary fiber.	Liu H, Liao C, Wu L, Tang J, Chen J, Lei C, Zheng L, Zhang C, Liu YY, Xavier J, Dai L.	ISME J	10.1038/s41396-022-01253-4	2022
	Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota.	Li S, Yang S, Zhou Y, Disoma C, Dong Z, Du A, Zhang Y, Chen Y, Huang W, Chen J, Song D, Chen Z, Liu P, Li S, Zheng R, Liu S, Razzaq A, Chen X, Tao S, Yu C, Feng T, Liao W, Peng Y, Jiang T, Huang J, Wu W, Hu L, Wang L, Li S, Xia Z.	Front Microbiol	10.3389/fmicb.2021.712081	2021
	Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances.	Lindell AE, Griesshammer A, Michaelis L, Papagiannidis D, Ochner H, Kamrad S, Guan R, Blasche S, Ventimiglia LN, Ramachandran B, Ozgur H, Zelezniak A, Beristain-Covarrubias N, Yam-Puc JC, Roux I, Barron LP, Richardson AK, Martin MG, Benes V, Morone N, Thaventhiran JED, Bharat TAM, Savitski MM, Maier L, Patil KR.	Nat Microbiol	10.1038/s41564-025-02032-5	2025
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
Enzymology	A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.	Welsh C, Cabotaje PR, Marcelino VR, Watts TD, Kountz DJ, Jespersen M, Gould JA, Doan NQ, Lingford JP, Koralegedara T, Solari J, D'Adamo GL, Huang P, Bong N, Gulliver EL, Young RB, Land H, Walter K, Cann I, Pereira GV, Martens EC, Wolf PG, Ridlon JM, Gaskins HR, Giles EM, Lyras D, Lappan R, Berggren G, Forster SC, Greening C.	Nat Microbiol	10.1038/s41564-025-02154-w	2025
Genetics	Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed.	Allsing N, Kelley ST, Fox AN, Sant KE.	Int J Environ Res Public Health	10.3390/ijerph20010600	2022
	Uric acid, high density lipoprotein cholesterol levels and their ratio are related to microbial enterotypes and serum metabolites in females with a blood stasis constitution.	Sun C, Liu Y, Huang W, Chen Y, Deng Y, Yuan J, Deng L, Xu N, Shang X, Wang C, Yang Z, Huang L, Qiu Q.	Lipids Health Dis	10.1186/s12944-024-02066-4	2024
Genetics	F. prausnitzii potentially modulates the association between citrus intake and depression.	Samuthpongtorn C, Chan AA, Ma W, Wang F, Nguyen LH, Wang DD, Okereke OI, Huttenhower C, Chan AT, Mehta RS.	Microbiome	10.1186/s40168-024-01961-3	2024
Pathogenicity	Gut microbiota interacting with vitamin D but not anandamide might contribute to the pathogenesis of preeclampsia: a preliminary study.	Han XQ, Jiang HH, Chen ML, Han DY, Zhou SF, Wang JW, Ji SS, Wang LY, Lou JW, Li MQ.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1469054	2024
	Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.	Mah JC, Lohmueller KE, Garud NR.	Mol Biol Evol	10.1093/molbev/msaf010	2025
Phylogeny	Lower Genital Tract Microbiome in Early Pregnancy in the Eastern European Population.	Gryaznova M, Lebedeva O, Kozarenko O, Smirnova Y, Burakova I, Syromyatnikov M, Maslov A, Popov V.	Microorganisms	10.3390/microorganisms10122368	2022
	Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.	Zhang L, Jonscher KR, Zhang Z, Xiong Y, Mueller RS, Friedman JE, Pan C.	Nat Commun	10.1038/s41467-022-31227-1	2022
Genetics	Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors.	Matsukawa H, Iida N, Kitamura K, Terashima T, Seishima J, Makino I, Kannon T, Hosomichi K, Yamashita T, Sakai Y, Honda M, Yamashita T, Mizukoshi E, Kaneko S.	Am J Cancer Res		2021
Genetics	Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.	Gruninger RJ, McCormack ML, Chomistek NC, Zaheer R, McAllister TA.	Microbiol Spectr	10.1128/spectrum.00423-25	2025
Phylogeny	Fecal Microbiota Characteristics in Constipation-Predominant and Mixed-Type Irritable Bowel Syndrome.	Gryaznova M, Smirnova Y, Burakova I, Morozova P, Lagutina S, Chizhkov P, Korneeva O, Syromyatnikov M.	Microorganisms	10.3390/microorganisms12071414	2024
	Human Fecal Microbiota Transplantation Reduces the Susceptibility to Dextran Sulfate Sodium-Induced Germ-Free Mouse Colitis.	Yang Y, Zheng X, Wang Y, Tan X, Zou H, Feng S, Zhang H, Zhang Z, He J, Cui B, Zhang X, Wu Z, Dong M, Cheng W, Tao S, Wei H.	Front Immunol	10.3389/fimmu.2022.836542	2022
Genetics	Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness.	Torma F, Kerepesi C, Jokai M, Babszki G, Koltai E, Ligeti B, Kalcsevszki R, McGreevy KM, Horvath S, Radak Z.	Aging Cell	10.1111/acel.14101	2024
	Designing function-specific minimal microbiomes from large microbial communities.	Raghu AK, Palanikumar I, Raman K.	NPJ Syst Biol Appl	10.1038/s41540-024-00373-1	2024
	Microbiota, metabolic profiles and immune biomarkers in infants receiving formula with added bovine milk fat globule membrane: a randomized, controlled trial.	Christensen C, Kok CR, Harris CL, Moore N, Wampler JL, Zhuang W, Wu SS, Hutkins R, Izard J, Auchtung JM.	Front Nutr	10.3389/fnut.2024.1465174	2024
	Temporal Dynamics of the Intestinal Microbiome Following Short-Term Dietary Restriction.	Anderson EM, Rozowsky JM, Fazzone BJ, Schmidt EA, Stevens BR, O'Malley KA, Scali ST, Berceli SA.	Nutrients	10.3390/nu14142785	2022
	Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.	Clasen F, Yildirim S, Arikan M, Garcia-Guevara F, Hanoglu L, Yilmaz NH, Sen A, Celik HK, Neslihan AA, Demir TK, Temel Z, Mardinoglu A, Moyes DL, Uhlen M, Shoaie S.	Gut Microbes	10.1080/19490976.2025.2506843	2025
	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
	Eco-evolutionary feedbacks in the human gut microbiome.	Good BH, Rosenfeld LB.	Nat Commun	10.1038/s41467-023-42769-3	2023
	Gram-positive probiotics improves acetaminophen-induced hepatotoxicity by inhibiting leucine and Hippo-YAP pathway.	Gao W, Wang G, Yuan H, Chen Y, Che J, Cheng Z, Chen L, Zhang L, Zhu Y, Liu X, Liu A, Yang Q, Cao P, Qian W, Huang W, Schnabl B, Yang L, Chu H.	Cell Biosci	10.1186/s13578-025-01370-5	2025
	Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor.	Chen TH, Cheng CY, Huang CK, Ho YH, Lin JC.	Microbiol Spectr	10.1128/spectrum.02805-22	2023
	Extraction optimization of total triterpenoids from Jatropha curcas leaves using response surface methodology and evaluations of their antimicrobial and antioxidant capacities	Wei L, Zhang W, Yin L, Yan F, Xu Y, Chen F.	Electron J Biotechnol	10.1016/j.ejbt.2014.12.005	2015
	Epilactose as a Promising Butyrate-Promoter Prebiotic via Microbiota Modulation.	Cardoso BB, Amorim C, Franco-Duarte R, Alves JI, Barbosa SG, Silverio SC, Rodrigues LR.	Life (Basel)	10.3390/life14050643	2024
	Global research trend and hotspot in the low FODMAP diet: a bibliometric analysis.	Xu C, Song Z, Hu JY, Li CC, Shen H.	J Health Popul Nutr	10.1186/s41043-024-00567-7	2024
	Revealing In Silico that Bacteria's Outer Membrane Proteins may Help our Bodies Replicate and Carry Severe Acute Respiratory Syndrome Coronavirus 2.	Aktas E, Ozdemir Ozgenturk N.	Bioinform Biol Insights	10.1177/11779322221116320	2022
Genetics	Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.	Luo Y, Sheikh TMM, Li X, Yuan Y, Yao F, Wang M, Guo X, Wu J, Shafiq M, Xie Q, Jiao X.	Virulence	10.1080/21505594.2024.2428843	2024
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
	Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.	Bauchinger F, Seki D, Berry D.	Front Microbiol	10.3389/fmicb.2024.1454634	2024
Pathogenicity	Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease.	Xie J, Zhang X, Cheng L, Deng Y, Ren H, Mu M, Zhao L, Mu C, Chen J, Liu K, Ma R.	Microbiol Spectr	10.1128/spectrum.01808-24	2024
Enzymology	Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods.	Weaver AA, Hasan NA, Klaassen M, Karathia H, Colwell RR, Shrout JD.	J Med Microbiol	10.1099/jmm.0.001068	2019
	Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome.	Peng X, Gao R, Ren J, Lu J, Ma X, Li P.	Brief Bioinform	10.1093/bib/bbad465	2023
	A Long-Chain Dextran Produced by Weissella cibaria Boosts the Diversity of Health-Related Gut Microbes Ex Vivo.	Tintore M, Cune J, Vu LD, Poppe J, Van den Abbeele P, Baudot A, de Lecea C.	Biology (Basel)	10.3390/biology13010051	2024
Metabolism	Expression of heparinase I of Bacteroides stercoris HJ-15 and its degradation tendency toward heparin-like glycosaminoglycans.	Hyun YJ, Jung IH, Kim DH.	Carbohydr Res	10.1016/j.carres.2012.05.023	2012
Metabolism	Microbiota modulation by teriflunomide therapy in people with multiple sclerosis: An observational case-control study.	Moles L, Otaegui-Chivite A, Gorostidi-Aicua M, Romarate L, Mendiburu I, Crespillo-Velasco H, Alvarez de Arcaya A, Ferreira E, Arruti M, Castillo-Trivino T, Otaegui D.	Neurotherapeutics	10.1016/j.neurot.2024.e00457	2024
Metabolism	Changes in Plasma Choline and the Betaine-to-Choline Ratio in Response to 6-Month Lifestyle Intervention Are Associated with the Changes of Lipid Profiles and Intestinal Microbiota: The ICAAN Study.	Jang H, Lim H, Park KH, Park S, Lee HJ.	Nutrients	10.3390/nu13114006	2021
	Aging-induced Alternation in the Gut Microbiota Impairs Host Antibacterial Defense.	Gu P, Wei R, Liu R, Yang Q, He Y, Guan J, He W, Li J, Zhao Y, Xie L, He J, Guo Q, Hu J, Bao J, Wang W, Guo J, Zeng Z, Chen Z, Jiang Y, Liu Z, Chen P.	Adv Sci (Weinh)	10.1002/advs.202411008	2025
Pathogenicity	Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19.	Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK, Ng SC.	Gut	10.1136/gutjnl-2020-322294	2021
	Probiotics as Adjunctive Treatment for Patients Contracted COVID-19: Current Understanding and Future Needs.	Peng J, Zhang M, Yao G, Kwok LY, Zhang W.	Front Nutr	10.3389/fnut.2021.669808	2021
	Meta-analysis of the microbial biomarkers in the gut-lung crosstalk in COVID-19, community-acquired pneumonia and Clostridium difficile infections.	Aishwarya S, Gunasekaran K.	Lett Appl Microbiol	10.1111/lam.13798	2022
	Differential effects of Bacillus subtilis- and Bacillus licheniformis-fermented products on growth performance, intestinal morphology, intestinal antioxidant and barrier function gene expression, cecal microbiota community, and microbial carbohydrate-active enzyme composition in broilers.	Chen YW, Yu YH.	Poult Sci	10.1016/j.psj.2023.102670	2023
Enzymology	Cloning, Expression, and Characterization of a New Glycosaminoglycan Lyase from Microbacterium sp. H14.	Sun J, Han X, Song G, Gong Q, Yu W.	Mar Drugs	10.3390/md17120681	2019
	Compositional Alteration of Gut Microbiota in Psoriasis Treated with IL-23 and IL-17 Inhibitors.	Huang YH, Chang LC, Chang YC, Chung WH, Yang SF, Su SC.	Int J Mol Sci	10.3390/ijms24054568	2023
	Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.	Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E.	Microbiol Spectr	10.1128/spectrum.00336-23	2023
	The inconsistent pathogenesis of endometriosis and adenomyosis: insights from endometrial metabolome and microbiome.	Li C, Xu X, Zhao X, Du B.	mSystems	10.1128/msystems.00202-25	2025
	Identification and characterization of a novel heparinase PCHepII from marine bacterium Puteibacter caeruleilacunae.	Lu D, Wang L, Ning Z, Li Z, Li M, Jia Y, Zhang Q.	Sci Rep	10.1038/s41598-023-47493-y	2023
	Gut microbiota and psoriasis: pathogenesis, targeted therapy, and future directions.	Zou X, Zou X, Gao L, Zhao H.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1430586	2024
Genetics	The human gut microbiome of athletes: metagenomic and metabolic insights.	Fontana F, Longhi G, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Turroni F, Milani C, Ventura M.	Microbiome	10.1186/s40168-023-01470-9	2023
	Intestinal microbiota reduces genotoxic endpoints induced by high-energy protons.	Maier I, Berry DM, Schiestl RH.	Radiat Res	10.1667/rr13352.1	2014
	The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children.	Heston SM, Young RR, Jenkins K, Martin PL, Stokhuyzen A, Ward DV, Bhattarai SK, Bucci V, Arshad M, Chao NJ, Seed PC, Kelly MS.	Gut Microbes	10.1080/19490976.2024.2333748	2024
	A Comprehensive Self-Management Program With Diet Education Does Not Alter Microbiome Characteristics in Women With Irritable Bowel Syndrome.	Kamp KJ, Plantinga AM, Cain KC, Burr RL, Barney P, Jarrett M, Luna RA, Savidge T, Shulman R, Heitkemper MM.	Biol Res Nurs	10.1177/1099800420984543	2021
	Lubiprostone in chronic kidney disease: Insights into mitochondrial function and polyamines from a randomized phase 2 clinical trial	Watanabe S, Nakayama M, Yokoo T, Sanada S, Ubara Y, Komatsuda A, Asanuma K, Suzuki Y, Konta T, Kazama J, Suzuki T, Fukuda S, Soga T, Yamada T, Mizutani S, Matsumoto M, Naito Y, Taguchi K, Fukami K, Kashiwagi H, Kikuchi K, Suzuki C, Tokuno H, Urasato M, Kujirai R, Matsumoto Y, Akiyama Y, Tomioka Y, Itai S, Tongu Y, Mishima E, Kawabe C, Kasahara T, Ogata Y, Toyohara T, Sato T, Tanaka T, Abe T.	Sci Adv		2025
Genetics	The gut microbiome as a potential source of non-invasive biomarkers of chronic obstructive pulmonary disease.	Li N, Yi X, Chen C, Dai Z, Deng Z, Pu J, Zhou Y, Li B, Wang Z, Ran P.	Front Microbiol	10.3389/fmicb.2023.1173614	2023
Genetics	Metagenomics Study Reveals Changes in Gut Microbiota in Centenarians: A Cohort Study of Hainan Centenarians.	Luan Z, Sun G, Huang Y, Yang Y, Yang R, Li C, Wang T, Tan D, Qi S, Jun C, Wang C, Wang S, Zhao Y, Jing Y.	Front Microbiol	10.3389/fmicb.2020.01474	2020
Enzymology	Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.	Kabiri L, Alum A, Rock C, McLain JE, Abbaszadegan M.	Can J Microbiol	10.1139/cjm-2013-0518	2013
	Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study.	Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1181328	2023
	Gut microbiome metabolites, molecular mimicry, and species-level variation drive long-term efficacy and adverse event outcomes in lung cancer survivors.	Liu X, Lu B, Tang H, Jia X, Zhou Q, Zeng Y, Gao X, Chen M, Xu Y, Wang M, Tan B, Li J.	EBioMedicine	10.1016/j.ebiom.2024.105427	2024
	Faecal Microbial Markers and Psychobiological Disorders in Subjects with Morbid Obesity. A Cross-Sectional Study.	Farup PG, Valeur J.	Behav Sci (Basel)	10.3390/bs8100089	2018
	Determinants of resistance and response to melanoma therapy.	Robertson BM, Fane ME, Weeraratna AT, Rebecca VW.	Nat Cancer	10.1038/s43018-024-00794-1	2024
Metabolism	Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels.	Zysset-Burri DC, Keller I, Berger LE, Neyer PJ, Steuer C, Wolf S, Zinkernagel MS.	Sci Rep	10.1038/s41598-019-51698-5	2019
Genetics	Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort.	Koponen K, Kambur O, Joseph B, Ruuskanen MO, Jousilahti P, Salido R, Brennan C, Jain M, Meric G, Inouye M, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V.	Arterioscler Thromb Vasc Biol	10.1161/atvbaha.123.319458	2024
	A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy.	Stein-Thoeringer CK, Saini NY, Zamir E, Blumenberg V, Schubert ML, Mor U, Fante MA, Schmidt S, Hayase E, Hayase T, Rohrbach R, Chang CC, McDaniel L, Flores I, Gaiser R, Edinger M, Wolff D, Heidenreich M, Strati P, Nair R, Chihara D, Fayad LE, Ahmed S, Iyer SP, Steiner RE, Jain P, Nastoupil LJ, Westin J, Arora R, Wang ML, Turner J, Menges M, Hidalgo-Vargas M, Reid K, Dreger P, Schmitt A, Muller-Tidow C, Locke FL, Davila ML, Champlin RE, Flowers CR, Shpall EJ, Poeck H, Neelapu SS, Schmitt M, Subklewe M, Jain MD, Jenq RR, Elinav E.	Nat Med	10.1038/s41591-023-02234-6	2023
	Insights into the Relationship Between the Gut Microbiome and Immune Checkpoint Inhibitors in Solid Tumors.	Ciernikova S, Sevcikova A, Novisedlakova M, Mego M.	Cancers (Basel)	10.3390/cancers16244271	2024
Genetics	Correlation of the gut microbiome and immune-related adverse events in gastrointestinal cancer patients treated with immune checkpoint inhibitors.	Zhang Y, Cheng S, Zou H, Han Z, Xie T, Zhang B, Dai D, Yin X, Liang Y, Kou Y, Tan Y, Shen L, Peng Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1099063	2023
	Alteration of the fecal microbiome in patients with cholecystectomy: potential relationship with postcholecystectomy diarrhea - before and after study.	Noh CK, Jung W, Yang MJ, Kim WH, Hwang JC.	Int J Surg	10.1097/js9.0000000000000518	2023
Genetics	Gut microbiome of helminth-infected indigenous Malaysians is context dependent.	Tee MZ, Er YX, Easton AV, Yap NJ, Lee IL, Devlin J, Chen Z, Ng KS, Subramanian P, Angelova A, Oyesola O, Sargsian S, Ngui R, Beiting DP, Boey CCM, Chua KH, Cadwell K, Lim YAL, Loke P, Lee SC.	Microbiome	10.1186/s40168-022-01385-x	2022
	Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer.	Fellows RC, Chun SK, Larson N, Fortin BM, Mahieu AL, Song WA, Seldin MM, Pannunzio NR, Masri S.	Sci Adv	10.1126/sciadv.ado1458	2024
	Improving the Hydrophobicity of Plasticized Polyvinyl Chloride for Use in an Endotracheal Tube	Marcut L, Mohan A, Corneschi I, Grosu E, Paltanea G, Avram I, Badaluta A, Vasilievici G, Nicolae C, Ditu L.	Materials (Basel)		2023
	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
	Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study.	Huminska-Lisowska K, Zielinska K, Mieszkowski J, Michalowska-Sawczyn M, Cieszczyk P, Labaj PP, Wasag B, Fraczek B, Grzywacz A, Kochanowicz A, Kosciolek T.	PLoS One	10.1371/journal.pone.0297858	2024
Enzymology	A metagenome-wide association study of gut microbiota in asthma in UK adults.	Wang Q, Li F, Liang B, Liang Y, Chen S, Mo X, Ju Y, Zhao H, Jia H, Spector TD, Xie H, Guo R.	BMC Microbiol	10.1186/s12866-018-1257-x	2018
	Association Between Adult Antibiotic Use, Microbial Dysbiosis and Atopic Conditions - A Systematic Review.	Ng WZJ, van Hasselt J, Aggarwal B, Manoharan A.	J Asthma Allergy	10.2147/jaa.s401755	2023
	Gut microbiota, angiotensin-converting enzyme, celiac disease, and risk of COVID-19 infection: a review.	Gholam-Mostafaei FS, Didari T, Ramandi M, Vafaee R, Rostami-Nejad M.	Gastroenterol Hepatol Bed Bench		2021
	Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions.	Gnanasekaran T, Sarathi A, Fang Q, Azarm A, Assis Geraldo J, Nigro E, Arumugam M.	mSystems	10.1128/msystems.01249-22	2023
Phylogeny	IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.	Brown EL, Essigmann HT, Hoffman KL, Alexander AS, Newmark M, Jiang ZD, Suescun J, Schiess MC, Hanis CL, DuPont HL.	J Parkinsons Dis	10.3233/jpd-230066	2023
	Bridging preclinical and clinical gut microbiota research using the ex vivo SIFR^® technology.	Van den Abbeele P, Deyaert S, Thabuis C, Perreau C, Bajic D, Wintergerst E, Joossens M, Firrman J, Walsh D, Baudot A.	Front Microbiol	10.3389/fmicb.2023.1131662	2023
	Depletion of core microbiome forms the shared background against diverging dysbiosis patterns in Crohn's disease and intestinal tuberculosis: insights from an integrated multi-cohort analysis.	Bajaj A, Markandey M, Samal A, Goswami S, Vuyyuru SK, Mohta S, Kante B, Kumar P, Makharia G, Kedia S, Ghosh TS, Ahuja V.	Gut Pathog	10.1186/s13099-024-00654-4	2024
	Traditional Chinese medicine improved diabetic kidney disease through targeting gut microbiota.	Wu XQ, Zhao L, Zhao YL, He XY, Zou L, Zhao YY, Li X.	Pharm Biol	10.1080/13880209.2024.2351946	2024
	Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens.	McDonald AG, Lisacek F.	Sci Rep	10.1038/s41598-023-51012-4	2024
	Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis.	Dalal R, Sadhu S, Batra A, Goswami S, Dandotiya J, K V V, Yadav R, Singh V, Chaturvedi K, Kannan R, Kumar S, Kumar Y, Rathore DK, Salunke DB, Ahuja V, Awasthi A.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00672-3	2025
	Nutrition and Chronobiology as Key Components of Multidisciplinary Therapeutic Interventions for Fibromyalgia and Associated Chronic Fatigue Syndrome: A Narrative and Critical Review.	Carrasco-Querol N, Cabricano-Canga L, Bueno Hernandez N, Goncalves AQ, Caballol Angelats R, Pozo Ariza M, Martin-Borras C, Monteso-Curto P, Castro Blanco E, Dalmau Llorca MR, Aguilar Martin C.	Nutrients	10.3390/nu16020182	2024
	A Highly Active Chondroitin Sulfate Lyase ABC for Enzymatic Depolymerization of Chondroitin Sulfate.	Fan XM, Huang JY, Ling XM, Wei W, Su WB, Zhang YW.	Polymers (Basel)	10.3390/polym14091770	2022
Genetics	Prediction of BMI traits in the Chinese population based on the gut metagenome.	Liang Y, Dou S, Zhao G, Shen J, Fu G, Fu L, Li S, Cong B, Dong C.	Microb Cell Fact	10.1186/s12934-023-02255-3	2023
	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
Enzymology	Cloning, overexpression, and characterization of recombinant heparinase III from Bacteroides stercoris HJ-15.	Hyun YJ, Lee JH, Kim DH.	Appl Microbiol Biotechnol	10.1007/s00253-009-2327-7	2010
Enzymology	Cloning, expression and characterization of acharan sulfate-degrading heparin lyase II from Bacteroides stercoris HJ-15.	Hyun YJ, Lee KS, Kim DH.	J Appl Microbiol	10.1111/j.1365-2672.2009.04418.x	2010
	The gut microbiome affects response of treatments in HER2-negative advanced gastric cancer.	Han Z, Cheng S, Dai D, Kou Y, Zhang X, Li F, Yin X, Ji J, Zhang Z, Wang X, Zhu N, Zhang Q, Tan Y, Guo X, Shen L, Peng Z.	Clin Transl Med	10.1002/ctm2.1312	2023
	Microbiota as a state-of-the-art approach in precision medicine for pancreatic cancer management: A comprehensive systematic review.	Hesami Z, Sabzehali F, Khorsand B, Alipour S, Sadeghi A, Asri N, Pazienza V, Houri H.	iScience	10.1016/j.isci.2025.112314	2025
	Do Children With Constipation Have Increased Risk of Asthma? Real-World Data From a Nationwide Population-Based Cohort Study.	Huang YC, Wu MC, Wang YH, Wei JC.	Front Pediatr	10.3389/fped.2021.714406	2021
	Delivery mode and maternal gestational diabetes are important factors in shaping the neonatal initial gut microbiota.	Shi X, Liu Y, Ma T, Jin H, Zhao F, Sun Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1397675	2024
	Ketoanalogs' Effects on Intestinal Microbiota Modulation and Uremic Toxins Serum Levels in Chronic Kidney Disease (Medika2 Study).	Rocchetti MT, Di Iorio BR, Vacca M, Cosola C, Marzocco S, di Bari I, Calabrese FM, Ciarcia R, De Angelis M, Gesualdo L.	J Clin Med	10.3390/jcm10040840	2021
Pathogenicity	Fecal microbiota transplantation in hematopoietic cell transplant and cellular therapy recipients: lessons learned and the path forward.	Habibi S, Rashidi A.	Gut Microbes	10.1080/19490976.2023.2229567	2023
	The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease.	Wiredu Ocansey DK, Hang S, Yuan X, Qian H, Zhou M, Valerie Olovo C, Zhang X, Mao F.	Gut Microbes	10.1080/19490976.2023.2176118	2023
	Dietary intervention with functional foods modulating gut microbiota for improving the efficacy of COVID-19 vaccines.	Oh S, Seo H.	Heliyon	10.1016/j.heliyon.2023.e15668	2023
	Investigating volatile compounds in the Bacteroides secretome.	Shagaleeva OY, Kashatnikova DA, Kardonsky DA, Konanov DN, Efimov BA, Bagrov DV, Evtushenko EG, Chaplin AV, Silantiev AS, Filatova JV, Kolesnikova IV, Vanyushkina AA, Stimpson J, Zakharzhevskaya NB.	Front Microbiol	10.3389/fmicb.2023.1164877	2023
	The gut microbial diversity of colon cancer patients and the clinical significance.	He T, Cheng X, Xing C.	Bioengineered	10.1080/21655979.2021.1972077	2021
	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
	Commensal Intestinal Protozoa-Underestimated Members of the Gut Microbial Community.	Dubik M, Pilecki B, Moeller JB.	Biology (Basel)	10.3390/biology11121742	2022
	A systematic review on the impact of gastrointestinal microbiota composition and function on cognition in healthy infants and children.	McMath AL, Aguilar-Lopez M, Cannavale CN, Khan NA, Donovan SM.	Front Neurosci	10.3389/fnins.2023.1171970	2023
Pathogenicity	Intestinal flora characteristics of advanced non-small cell lung cancer in China and their role in chemotherapy based on metagenomics: A prospective exploratory cohort study.	Zhang M, Liu D, Zhou H, Liu X, Li X, Cheng Y, Gao B, Chen J.	Thorac Cancer	10.1111/1759-7714.14199	2021
Phylogeny	Application of quantitative real-time PCR for rapid identification of Bacteroides fragilis group and related organisms in human wound samples.	Tong J, Liu C, Summanen P, Xu H, Finegold SM.	Anaerobe	10.1016/j.anaerobe.2011.03.004	2011
Metabolism	Isolation, Purification, and Characterization of Heparinase from Streptomyces variabilis MTCC 12266.	Singh V, Haque S, Kumari V, El-Enshasy HA, Mishra BN, Somvanshi P, Tripathi CKM.	Sci Rep	10.1038/s41598-019-42740-7	2019
	Evaluation of Systemic Treatment Options for Gastrointestinal Stromal Tumours.	Golcic M, Jones RL, Huang P, Napolitano A.	Cancers (Basel)	10.3390/cancers15164081	2023
	Evaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis.	Li Y, Jiang X, Chen J, Hu Y, Bai Y, Xu W, He L, Wang Y, Chen C, Chen J.	Front Microbiol	10.3389/fmicb.2023.1119959	2023
Metabolism	Xylitol does not inhibit xylose fermentation by engineered Saccharomyces cerevisiae expressing xylA as severely as it inhibits xylose isomerase reaction in vitro.	Ha SJ, Kim SR, Choi JH, Park MS, Jin YS.	Appl Microbiol Biotechnol	10.1007/s00253-011-3345-9	2011
Enzymology	Cloning and expression of chondroitinase AC from Bacteroides stercoris HJ-15.	Shim KW, Kim DH.	Protein Expr Purif	10.1016/j.pep.2007.11.014	2008
	Detection of Intestinal Dysbiosis in Post-COVID-19 Patients One to Eight Months after Acute Disease Resolution.	Ferreira-Junior AS, Borgonovi TF, De Salis LVV, Leite AZ, Dantas AS, De Salis GVV, Cruz GNF, De Oliveira LFV, Gomes E, Penna ALB, De Oliveira GLV.	Int J Environ Res Public Health	10.3390/ijerph191610189	2022
Metabolism	Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism.	Xu T, Wang X, Chen Y, Li H, Zhao L, Ding X, Zhang C.	mBio	10.1128/mbio.03487-22	2023
	Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation.	Elkrief A, Waters NR, Smith N, Dai A, Slingerland J, Aleynick N, Febles B, Gogia P, Socci ND, Lumish M, Giardina PA, Chaft JE, Eng J, Motzer RJ, Mendelsohn RB, Markey KA, Zhuang M, Li Y, Yang Z, Hollmann TJ, Rudin CM, van den Brink MRM, Shia J, DeWolf S, Schoenfeld AJ, Hellmann MD, Babady NE, Faleck DM, Peled JU.	Cancer Immunol Res	10.1158/2326-6066.cir-23-0498	2024
	Gut microbiota and COVID-19: A systematic review.	SeyedAlinaghi S, Afzalian A, Pashaei Z, Varshochi S, Karimi A, Mojdeganlou H, Mojdeganlou P, Razi A, Ghanadinezhad F, Shojaei A, Amiri A, Dashti M, Ghasemzadeh A, Dadras O, Mehraeen E, Afsahi AM.	Health Sci Rep	10.1002/hsr2.1080	2023
	Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors.	Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M.	Nat Commun	10.1038/s41467-023-38558-7	2023
Genetics	Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.	Holman DB, Kommadath A, Tingley JP, Abbott DW.	Microbiol Spectr	10.1128/spectrum.02380-22	2022
	Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study.	Chen L, Sun M, Xu D, Gao Z, Shi Y, Wang S, Zhou Y.	Front Microbiol	10.3389/fmicb.2022.1027188	2022
	A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases.	Liu X, Tang S, Zhong H, Tong X, Jie Z, Ding Q, Wang D, Guo R, Xiao L, Xu X, Yang H, Wang J, Zong Y, Liu W, Liu X, Zhang Y, Brix S, Kristiansen K, Hou Y, Jia H, Zhang T.	Cell Discov	10.1038/s41421-020-00239-w	2021
	Our experience with 80 cases of SARS-CoV-2-Clostridioides difficile co-infection: An observational study.	Birlutiu V, Dobritoiu ES, Lupu CD, Herteliu C, Birlutiu RM, Dragomirescu D, Vorovenci A.	Medicine (Baltimore)	10.1097/md.0000000000029823	2022
Genetics	Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows.	Fu H, He M, Wu J, Zhou Y, Ke S, Chen Z, Liu Q, Liu M, Jiang H, Huang L, Chen C.	Front Microbiol	10.3389/fmicb.2021.729039	2021
	Gut metagenome-derived signature predicts hepatic decompensation and mortality in NAFLD-related cirrhosis.	Sharpton SR, Oh TG, Madamba E, Wang C, Yu RT, Atkins AR, Huan T, Downes M, Evans RM, Loomba R.	Aliment Pharmacol Ther	10.1111/apt.17236	2022
	Dysbiosis in the Development of Type I Diabetes and Associated Complications: From Mechanisms to Targeted Gut Microbes Manipulation Therapies.	Gradisteanu Pircalabioru G, Corcionivoschi N, Gundogdu O, Chifiriuc MC, Marutescu LG, Ispas B, Savu O.	Int J Mol Sci	10.3390/ijms22052763	2021
Genetics	Revealing antimicrobial resistance in stormwater with MinION.	Bialasek M, Milobedzka A.	Chemosphere	10.1016/j.chemosphere.2020.127392	2020
	Photodynamic Therapy for the Treatment of Infected Leg Ulcers-A Pilot Study.	Krupka M, Bozek A, Bartusik-Aebisher D, Cieslar G, Kawczyk-Krupka A.	Antibiotics (Basel)	10.3390/antibiotics10050506	2021
Metabolism	A highly active heparinase I from Bacteroides cellulosilyticus: Cloning, high level expression, and molecular characterization.	Gao LW, Zhu HT, Liu CY, Lv ZX, Fan XM, Zhang YW.	PLoS One	10.1371/journal.pone.0240920	2020
	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
	Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China.	Baker M, Zhang X, Maciel-Guerra A, Dong Y, Wang W, Hu Y, Renney D, Hu Y, Liu L, Li H, Tong Z, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T.	Nat Food	10.1038/s43016-023-00814-w	2023
	Microbial dysbiosis in irritable bowel syndrome: A single-center metagenomic study in Saudi Arabia.	Masoodi I, Alshanqeeti AS, Alyamani EJ, AlLehibi AA, Alqutub AN, Alsayari KN, Alomair AO.	JGH Open	10.1002/jgh3.12313	2020
	COVID-19 and Gut Microbiota: A Potential Connection.	Rajput S, Paliwal D, Naithani M, Kothari A, Meena K, Rana S.	Indian J Clin Biochem	10.1007/s12291-020-00948-9	2021
	Immunomodulatory Effects of Probiotics on COVID-19 Infection by Targeting the Gut-Lung Axis Microbial Cross-Talk.	Synodinou KD, Nikolaki MD, Triantafyllou K, Kasti AN.	Microorganisms	10.3390/microorganisms10091764	2022
Phylogeny	Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.	Kumar H, Jang YN, Kim K, Park J, Jung MW, Park JE.	Animals (Basel)	10.3390/ani10081372	2020
	Pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data.	Zhang M, Zhang M, Zhang C, Du H, Wei G, Pang X, Zhou H, Liu B, Zhao L.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2009.00694.x	2009
	The first case of hand infection caused by Dermabacter jinjuensis in a symmetrical peripheral gangrene patient.	Cho SH, Park JS, Lee WK, Shin MK, Jung M, Lee KM, Hwang KJ, Moon DK.	Ann Med Surg (Lond)	10.1016/j.amsu.2018.10.008	2018
	The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).	Li-Gao R, Grubbs K, Bertoni AG, Hoffman KL, Petrosino JF, Ramesh G, Wu M, Rotter JI, Chen YI, Evans AM, Robinson RJ, Sommerville L, Mook-Kanamori D, Goodarzi MO, Michelotti GA, Sheridan PA.	Metabolites	10.3390/metabo12090787	2022
	Impact of Mediterranean Diet on Disease Activity and Gut Microbiota Composition of Rheumatoid Arthritis Patients.	Picchianti Diamanti A, Panebianco C, Salerno G, Di Rosa R, Salemi S, Sorgi ML, Meneguzzi G, Mariani MB, Rai A, Iacono D, Sesti G, Pazienza V, Lagana B.	Microorganisms	10.3390/microorganisms8121989	2020
	Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance.	Zhou Y, Fu H, Yang H, Wu J, Chen Z, Jiang H, Liu M, Liu Q, Huang L, Gao J, Chen C.	Microbiome	10.1186/s40168-022-01241-y	2022
	Host metabolic benefits of prebiotic exopolysaccharides produced by Leuconostoc mesenteroides.	Miyamoto J, Shimizu H, Hisa K, Matsuzaki C, Inuki S, Ando Y, Nishida A, Izumi A, Yamano M, Ushiroda C, Irie J, Katayama T, Ohno H, Itoh H, Yamamoto K, Kimura I.	Gut Microbes	10.1080/19490976.2022.2161271	2023
	Changes in the Intestinal Microbiota of Patients with Inflammatory Bowel Disease with Clinical Remission during an 8-Week Infliximab Infusion Cycle.	Seong G, Kim N, Joung JG, Kim ER, Chang DK, Chun J, Hong SN, Kim YH.	Microorganisms	10.3390/microorganisms8060874	2020
Genetics	Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts.	Abed JY, Godon T, Mehdaoui F, Plante PL, Boissinot M, Bergeron MG, Belanger RE, Muckle G, Poliakova N, Ayotte P, Corbeil J, Rousseau E.	Commun Biol	10.1038/s42003-022-04372-y	2022
	Successful Dietary Therapy in Paediatric Crohn's Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls.	Verburgt CM, Dunn KA, Ghiboub M, Lewis JD, Wine E, Sigall Boneh R, Gerasimidis K, Shamir R, Penny S, Pinto DM, Cohen A, Bjorndahl P, Svolos V, Bielawski JP, Benninga MA, de Jonge WJ, Van Limbergen JE.	J Crohns Colitis	10.1093/ecco-jcc/jjac105	2023
Genetics	Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.	Branck T, Hu Z, Nickols WA, Walsh AM, Bhosle A, Short MI, Nearing JT, Asnicar F, McIver LJ, Maharjan S, Rahnavard A, Louyakis AS, Badri DV, Brockel C, Thompson KN, Huttenhower C.	ISME J	10.1093/ismejo/wrae201	2024
Enzymology	A novel D-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae.	Silva PC, Ceja-Navarro JA, Azevedo F, Karaoz U, Brodie EL, Johansson B.	Sci Rep	10.1038/s41598-021-83937-z	2021
Enzymology	Purification and characterization of heparin lyase I from Bacteroides stercoris HJ-15.	Kim WS, Kim BT, Kim DH, Kim YS.	J Biochem Mol Biol	10.5483/bmbrep.2004.37.6.684	2004
	Targeting gut microbiota: new therapeutic opportunities in multiple sclerosis.	Kujawa D, Laczmanski L, Budrewicz S, Pokryszko-Dragan A, Podbielska M.	Gut Microbes	10.1080/19490976.2023.2274126	2023
Metabolism	Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis.	van der Lelie D, Oka A, Taghavi S, Umeno J, Fan TJ, Merrell KE, Watson SD, Ouellette L, Liu B, Awoniyi M, Lai Y, Chi L, Lu K, Henry CS, Sartor RB.	Nat Commun	10.1038/s41467-021-23460-x	2021
	The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia.	Rettedal EA, Ilesanmi-Oyelere BL, Roy NC, Coad J, Kruger MC.	JBMR Plus	10.1002/jbm4.10452	2021
	The rheumatoid arthritis gut microbial biobank reveals core microbial species that associate and effect on host inflammation and autoimmune responses.	Huang HJ, Liu C, Sun XW, Wei RQ, Liu LW, Chen HY, Abdugheni R, Wang CY, Wang XM, Jiang H, Niu HY, Feng LJ, He JH, Jiang Y, Zhao Y, Wang YL, Shu Q, Bi MX, Zhang L, Liu B, Liu SJ.	Imeta	10.1002/imt2.242	2024
	Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.	Theis BF, Park JS, Kim JSA, Zeydabadinejad S, Vijay-Kumar M, Yeoh BS, Saha P.	Biomedicines	10.3390/biomedicines13061357	2025
	Predicting Neurodegenerative Disease Using Prepathology Gut Microbiota Composition: a Longitudinal Study in Mice Modeling Alzheimer's Disease Pathologies.	Borsom EM, Conn K, Keefe CR, Herman C, Orsini GM, Hirsch AH, Palma Avila M, Testo G, Jaramillo SA, Bolyen E, Lee K, Caporaso JG, Cope EK.	Microbiol Spectr	10.1128/spectrum.03458-22	2023
	Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity.	Wilson BC, Vatanen T, Jayasinghe TN, Leong KSW, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Holland DJ, Cutfield WS, O'Sullivan JM.	Microbiome	10.1186/s40168-021-01060-7	2021
Metabolism	Dietary Fiber, Gut Microbiota, and Metabolic Regulation-Current Status in Human Randomized Trials.	Myhrstad MCW, Tunsjo H, Charnock C, Telle-Hansen VH.	Nutrients	10.3390/nu12030859	2020
	Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review.	Imade EE, Obayagbona NO.	Gut Microbiome (Camb)	10.1017/gmb.2024.3	2024
Phylogeny	Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese.	Nizigiyimana P, Xu B, Liu L, Luo L, Liu T, Jiang M, Liu Z, Li C, Luo X, Lei M.	Front Endocrinol (Lausanne)	10.3389/fendo.2022.942383	2022
	Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth.	Testerman T, Li Z, Galuppo B, Graf J, Santoro N.	Hepatol Commun	10.1002/hep4.1944	2022
	Cerebellar abscess in a cynomolgus macaque (Macaca fascicularis).	Villano JS, Ogden B, Goh A, Hui LS, Chow PK.	J Med Primatol	10.1111/j.1600-0684.2007.00254.x	2008
	Alterations in the gut microbiota of patients with acquired immune deficiency syndrome.	Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang X, Li K, He J, Du Y, Wang H, Chen Y, Nie Y.	J Cell Mol Med	10.1111/jcmm.13508	2018
Metabolism	Gut microbiota determines the fate of dietary fiber-targeted interventions in host health.	Wang W, Fan Z, Yan Q, Pan T, Luo J, Wei Y, Li B, Fang Z, Lu W.	Gut Microbes	10.1080/19490976.2024.2416915	2024
Genetics	Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.	Serrano-Gomez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, Machiels K, Guarner F, Vermeire S, Manichanh C.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.11.037	2021
	Gut Microbiota in Neurological Disorders.	Grochowska M, Laskus T, Radkowski M.	Arch Immunol Ther Exp (Warsz)	10.1007/s00005-019-00561-6	2019
Metabolism	Expression, Purification and Characterization of Chondroitinase AC II from Marine Bacterium Arthrobacter sp. CS01.	Fang Y, Yang S, Fu X, Xie W, Li L, Liu Z, Mou H, Zhu C.	Mar Drugs	10.3390/md17030185	2019
	Influence of grape consumption on the human microbiome.	Dave A, Beyoglu D, Park EJ, Idle JR, Pezzuto JM.	Sci Rep	10.1038/s41598-023-34813-5	2023
	Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function.	Proctor A, Parvinroo S, Richie T, Jia X, Lee STM, Karp PD, Paley S, Kostic AD, Pierre JF, Wannemuehler MJ, Phillips GJ.	mSystems	10.1128/msystems.00293-22	2022
	Respiratory tract infections and gut microbiome modifications: A systematic review.	Woodall CA, McGeoch LJ, Hay AD, Hammond A.	PLoS One	10.1371/journal.pone.0262057	2022
Genetics	Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children.	Li H, Zhao L, Zhang M.	Front Microbiol	10.3389/fmicb.2021.683714	2021
Enzymology	Purification and characterization of novel salt-active acharan sulfate lyase from Bacteroides stercoris HJ-15.	Hong SW, Shin HY, Kim YS, Kim DH.	Eur J Biochem	10.1046/j.1432-1033.2003.03696.x	2003
	Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows' feces, colostrum, milk, and suckling piglets' feces.	Llaurado-Calero E, Climent E, Chenoll E, Ballester M, Badiola I, Lizardo R, Torrallardona D, Esteve-Garcia E, Tous N.	Front Microbiol	10.3389/fmicb.2022.982712	2022
Metabolism	Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine.	Chen J, Wang Q, Wang A, Lin Z.	Front Cell Infect Microbiol	10.3389/fcimb.2019.00470	2019
Pathogenicity	Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp.	Ahmad S, Gordon IJ, Tsang KK, Alexei AG, Sychantha D, Colautti J, Trilesky SL, Kim Y, Wang B, Whitney JC.	Proc Natl Acad Sci U S A	10.1073/pnas.2213771120	2023
Phylogeny	Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment.	Verburg I, van Veelen HPJ, Waar K, Rossen JWA, Friedrich AW, Hernandez Leal L, Garcia-Cobos S, Schmitt H.	Microorganisms	10.3390/microorganisms9040718	2021
Metabolism	Intestinal bacterial indicator phylotypes associate with impaired DNA double-stranded break sensors but augmented skeletal bone micro-structure.	Maier I, Liu J, Ruegger PM, Deutschmann J, Patsch JM, Helbich TH, Borneman J, Schiestl RH.	Carcinogenesis	10.1093/carcin/bgz204	2020
Metabolism	The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights.	McCann JR, Bihlmeyer NA, Roche K, Catherine C, Jawahar J, Kwee LC, Younge NE, Silverman J, Ilkayeva O, Sarria C, Zizzi A, Wootton J, Poppe L, Anderson P, Arlotto M, Wei Z, Granek JA, Valdivia RH, David LA, Dressman HK, Newgard CB, Shah SH, Seed PC, Rawls JF, Armstrong SC.	Obesity (Silver Spring)	10.1002/oby.23081	2021
Enzymology	Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia.	Maas RM, Deng Y, Dersjant-Li Y, Petit J, Verdegem MCJ, Schrama JW, Kokou F.	Sci Rep	10.1038/s41598-021-87408-3	2021
Transcriptome	Spatial transcriptomes and microbiota reveal immune mechanism that respond to pathogen infection in the posterior intestine of Sebastes schlegelii.	Cao M, Xue T, Huo H, Zhang X, Wang NN, Yan X, Li C.	Open Biol	10.1098/rsob.220302	2023
	Preliminary evidence for an influence of exposure to polycyclic aromatic hydrocarbons on the composition of the gut microbiota and neurodevelopment in three-year-old healthy children.	Zhang W, Sun Z, Zhang Q, Sun Z, Su Y, Song J, Wang B, Gao R.	BMC Pediatr	10.1186/s12887-021-02539-w	2021
	Islet-reactive CD8⁺ T cell frequencies in the pancreas, but not in blood, distinguish type 1 diabetic patients from healthy donors.	Culina S, Lalanne AI, Afonso G, Cerosaletti K, Pinto S, Sebastiani G, Kuranda K, Nigi L, Eugster A, Osterbye T, Maugein A, McLaren JE, Ladell K, Larger E, Beressi JP, Lissina A, Appay V, Davidson HW, Buus S, Price DA, Kuhn M, Bonifacio E, Battaglia M, Caillat-Zucman S, Dotta F, Scharfmann R, Kyewski B, Mallone R, ImMaDiab Study Group.	Sci Immunol	10.1126/sciimmunol.aao4013	2018
	Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity.	Hazan S, Stollman N, Bozkurt HS, Dave S, Papoutsis AJ, Daniels J, Barrows BD, Quigley EM, Borody TJ.	BMJ Open Gastroenterol	10.1136/bmjgast-2022-000871	2022
	Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation.	Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.	Sci Rep	10.1038/s41598-024-56242-8	2024
Metabolism	Are Nonnutritive Sweeteners Obesogenic? Associations between Diet, Faecal Microbiota, and Short-Chain Fatty Acids in Morbidly Obese Subjects.	Farup PG, Lydersen S, Valeur J.	J Obes	10.1155/2019/4608315	2019
	Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women.	Tian B, Yao JH, Lin X, Lv WQ, Jiang LD, Wang ZQ, Shen J, Xiao HM, Xu H, Xu LL, Cheng X, Shen H, Qiu C, Luo Z, Zhao LJ, Yan Q, Deng HW, Zhang LS.	Front Microbiol	10.3389/fmicb.2022.957885	2022
Metabolism	Purification and characterization of novel chondroitin ABC and AC lyases from Bacteroides stercoris HJ-15, a human intestinal anaerobic bacterium.	Hong SW, Kim BT, Shin HY, Kim WS, Lee KS, Kim YS, Kim DH.	Eur J Biochem	10.1046/j.1432-1033.2002.02967.x	2002
	Amaranth and buckwheat grains: Nutritional profile, development of functional foods, their pre-clinical cum clinical aspects and enrichment in feed.	Kumar H, Guleria S, Kimta N, Dhalaria R, Nepovimova E, Dhanjal DS, Alomar SY, Kuca K.	Curr Res Food Sci	10.1016/j.crfs.2024.100836	2024
Pathogenicity	Anaerobic bacteria growth in the presence of cathelicidin LL-37 and selected ceragenins delivered as magnetic nanoparticles cargo.	Durnas B, Piktel E, Watek M, Wollny T, Gozdz S, Smok-Kalwat J, Niemirowicz K, Savage PB, Bucki R.	BMC Microbiol	10.1186/s12866-017-1075-6	2017
Genetics	SARS-CoV-2 triggered oxidative stress and abnormal energy metabolism in gut microbiota.	Zhou T, Wu J, Zeng Y, Li J, Yan J, Meng W, Han H, Feng F, He J, Zhao S, Zhou P, Wu Y, Yang Y, Han R, Jin W, Li X, Yang Y, Li X.	MedComm (2020)	10.1002/mco2.112	2022
Pathogenicity	Renal Health Improvement in Diabetes through Microbiome Modulation of the Gut-Kidney Axis with Biotics: A Systematic and Narrative Review of Randomized Controlled Trials.	Paul P, Kaul R, Chaari A.	Int J Mol Sci	10.3390/ijms232314838	2022
Metabolism	Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD.	Jiao N, Loomba R, Yang ZH, Wu D, Fang S, Bettencourt R, Lan P, Zhu R, Zhu L.	Physiol Genomics	10.1152/physiolgenomics.00011.2021	2021
	A Surface Loop in the N-Terminal Domain of Pedobacter heparinus Heparin Lyase II is Important for Activity.	Mori M, Ichikawa M, Kiguchi Y, Miyazaki T, Hattori M, Nishikawa A, Tonozuka T.	J Appl Glycosci (1999)	10.5458/jag.jag.jag-2015_019	2016
	Modeling spatial interaction networks of the gut microbiota.	Cao X, Dong A, Kang G, Wang X, Duan L, Hou H, Zhao T, Wu S, Liu X, Huang H, Wu R.	Gut Microbes	10.1080/19490976.2022.2106103	2022
	Gut microbiota facilitate chronic spontaneous urticaria.	Zhu L, Jian X, Zhou B, Liu R, Munoz M, Sun W, Xie L, Chen X, Peng C, Maurer M, Li J.	Nat Commun	10.1038/s41467-023-44373-x	2024
Enzymology	Purification and characterization of acharan sulfate lyases, two novel heparinases, from Bacteroides stercoris HJ-15.	Kim BT, Hong SW, Kim WS, Kim YS, Kim DH.	Eur J Biochem	10.1046/j.1432-1327.2001.02156.x	2001
Enzymology	Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease.	Onyango SO, Juma J, De Paepe K, Van de Wiele T.	Front Microbiol	10.3389/fmicb.2021.653448	2021
	MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.	Li Y, Gu B, Liu G, Xia W, Fan K, Mei Y, Huang P, Pan S.	J Thorac Dis	10.3978/j.issn.2072-1439.2014.02.15	2014
Pathogenicity	First national survey of antibiotic susceptibility of the Bacteroides fragilis group: emerging resistance to carbapenems in Argentina.	Fernandez-Canigia L, Litterio M, Legaria MC, Castello L, Predari SC, Di Martino A, Rossetti A, Rollet R, Carloni G, Bianchini H, Cejas D, Radice M, Gutkind G, Anaerobe Surveillance Team.	Antimicrob Agents Chemother	10.1128/aac.05622-11	2012
Metabolism	Microbiota-derived short-chain fatty acids do not interfere with SARS-CoV-2 infection of human colonic samples.	Pascoal LB, Rodrigues PB, Genaro LM, Gomes ABDSP, Toledo-Teixeira DA, Parise PL, Bispo-Dos-Santos K, Simeoni CL, Guimaraes PV, Buscaratti LI, Elston JGA, Marques-Souza H, Martins-de-Souza D, Ayrizono MLS, Velloso LA, Proenca-Modena JL, Moraes-Vieira PMM, Mori MAS, Farias AS, Vinolo MAR, Leal RF.	Gut Microbes	10.1080/19490976.2021.1874740	2021
Metabolism	Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China.	Wang X, Ning Y, Li C, Gong Y, Huang R, Hu M, Poulet B, Xu K, Zhao G, Zhou R, Lammi MJ, Guo X.	Cell Death Dis	10.1038/s41419-021-04322-2	2021
	Purification and characterization of a novel heparinase from Bacteroides stercoris HJ-15.	Kim BT, Kim WS, Kim YS, Linhardt RJ, Kim DH.	J Biochem	10.1093/oxfordjournals.jbchem.a022756	2000
Genetics	Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.	Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I.	Gut Microbes	10.1080/19490976.2023.2226921	2023
	Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management.	Villa F, Marchandin H, Lavigne J-P, Schuldiner S, Cellier N, Sotto A, Loubet P.	Clin Microbiol Rev	10.1128/cmr.00143-23	2024
	Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia.	Alomair AO, Masoodi I, Alyamani EJ, Allehibi AA, Qutub AN, Alsayari KN, Altammami MA, Alshanqeeti AS.	Gastroenterol Res Pract	10.1155/2018/5284754	2018
	The importance of genetic research on the dominant species of human intestinal indigenous microbiota.	Kurihara S.	Biosci Microbiota Food Health	10.12938/bmfh.2020-011	2021
Metabolism	Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses.	Wan J, Jing Y, Rao Y, Zhang S, Luo G.	Appl Environ Microbiol	10.1128/aem.02632-17	2018
Genetics	Relationship between the Gut Microbiome and Energy/Nutrient Intake in a Confined Bioregenerative Life Support System.	Chen J, Wang Q, Hao Z, Li Z, Sahu SK, Liu H, Xiao L.	Appl Environ Microbiol	10.1128/aem.02465-19	2020
Pathogenicity	Cinnamaldehyde Improves Metabolic Functions in Streptozotocin-Induced Diabetic Mice by Regulating Gut Microbiota.	Zhao H, Wu H, Duan M, Liu R, Zhu Q, Zhang K, Wang L.	Drug Des Devel Ther	10.2147/dddt.s288011	2021
Pathogenicity	Obesity-associated inflammation countered by a Mediterranean diet: the role of gut-derived metabolites.	Florkowski M, Abiona E, Frank KM, Brichacek AL.	Front Nutr	10.3389/fnut.2024.1392666	2024
Genetics	Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome.	Dhariwal A, Haugli Braten LC, Sturod K, Salvadori G, Bargheet A, Amdal H, Junges R, Berild D, Zwart JA, Storheim K, Petersen FC.	Gut Microbes	10.1080/19490976.2022.2157200	2023
Metabolism	Degradation of acharan sulfate and heparin by Bacteroides stercoris HJ-15, a human intestinal bacterium.	Kim DH, Kim BT, Park SY, Kim NY, Han MJ, Shin KH, Kim WS, Kim YS.	Arch Pharm Res	10.1007/bf02975378	1998
Pathogenicity	Microbiota Modulation of the Gut-Lung Axis in COVID-19.	de Oliveira GLV, Oliveira CNS, Pinzan CF, de Salis LVV, Cardoso CRB.	Front Immunol	10.3389/fimmu.2021.635471	2021
	Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System.	Gnanasekaran T, Assis Geraldo J, Ahrenkiel DW, Alvarez-Silva C, Saenz C, Khan A, Hanteer O, Gunalan V, Trost K, Moritz T, Arumugam M.	mSystems	10.1128/msystems.00232-21	2021
Metabolism	The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants.	Tanaka M, Sanefuji M, Morokuma S, Yoden M, Momoda R, Sonomoto K, Ogawa M, Kato K, Nakayama J.	Gut Microbes	10.1080/19490976.2019.1650997	2020
	Exploring Changes in the Host Gut Microbiota During a Controlled Human Infection Model for Campylobacter jejuni.	Stamps BW, Kuroiwa J, Isidean SD, Schilling MA, Harro C, Talaat KR, Sack DA, Tribble DR, Maue AC, Rimmer JE, Laird RM, Porter CK, Goodson MS, Poly F.	Front Cell Infect Microbiol	10.3389/fcimb.2021.702047	2021
	Global Research Trends in Irritable Bowel Syndrome: A Bibliometric and Visualized Study.	Zhang T, Ma X, Tian W, Zhang J, Wei Y, Zhang B, Wang F, Tang X.	Front Med (Lausanne)	10.3389/fmed.2022.922063	2022
	Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome.	van der Vossen EWJ, Bastos D, Stols-Goncalves D, de Goffau MC, Davids M, Pereira JPB, Li Yim AYF, Henneman P, Netea MG, de Vos WM, de Jonge W, Groen AK, Nieuwdorp M, Levin E.	Gut Microbes	10.1080/19490976.2021.1993513	2021
	Big data mining, rational modification, and ancestral sequence reconstruction inferred multiple xylose isomerases for biorefinery.	Chen S, Xu Z, Ding B, Zhang Y, Liu S, Cai C, Li M, Dale BE, Jin M.	Sci Adv	10.1126/sciadv.add8835	2023
	Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade.	Andrews MC, Duong CPM, Gopalakrishnan V, Iebba V, Chen WS, Derosa L, Khan MAW, Cogdill AP, White MG, Wong MC, Ferrere G, Fluckiger A, Roberti MP, Opolon P, Alou MT, Yonekura S, Roh W, Spencer CN, Curbelo IF, Vence L, Reuben A, Johnson S, Arora R, Morad G, Lastrapes M, Baruch EN, Little L, Gumbs C, Cooper ZA, Prieto PA, Wani K, Lazar AJ, Tetzlaff MT, Hudgens CW, Callahan MK, Adamow M, Postow MA, Ariyan CE, Gaudreau PO, Nezi L, Raoult D, Mihalcioiu C, Elkrief A, Pezo RC, Haydu LE, Simon JM, Tawbi HA, McQuade J, Hwu P, Hwu WJ, Amaria RN, Burton EM, Woodman SE, Watowich S, Diab A, Patel SP, Glitza IC, Wong MK, Zhao L, Zhang J, Ajami NJ, Petrosino J, Jenq RR, Davies MA, Gershenwald JE, Futreal PA, Sharma P, Allison JP, Routy B, Zitvogel L, Wargo JA.	Nat Med	10.1038/s41591-021-01406-6	2021
Genetics	Variation and transmission of the human gut microbiota across multiple familial generations.	Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G.	Nat Microbiol	10.1038/s41564-021-01021-8	2022
Pathogenicity	Review of the in vitro activity of gemifloxacin against gram-positive and gram-negative anaerobic pathogens.	Goldstein EJ.	J Antimicrob Chemother	10.1093/jac/45.suppl_3.55	2000
	Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.	De Paepe K, Verspreet J, Courtin CM, Van de Wiele T.	ISME J	10.1038/s41396-019-0550-5	2020
	Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease.	Zhang Y, Xu J, Wang X, Ren X, Liu Y.	BMC Genomics	10.1186/s12864-019-6251-7	2019
Pathogenicity	Role of the Microbiome in the Pathogenesis of COVID-19.	De R, Dutta S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.736397	2022
	The Influence of Essential Oils on Gut Microbial Profiles in Pigs.	Ruzauskas M, Bartkiene E, Stankevicius A, Bernatoniene J, Zadeike D, Lele V, Starkute V, Zavistanaviciute P, Grigas J, Zokaityte E, Pautienius A, Juodeikiene G, Jakstas V.	Animals (Basel)	10.3390/ani10101734	2020
Metabolism	Comparative microbial analysis of paired amniotic fluid and cord blood from pregnancies complicated by preterm birth and early-onset neonatal sepsis.	Wang X, Buhimschi CS, Temoin S, Bhandari V, Han YW, Buhimschi IA.	PLoS One	10.1371/journal.pone.0056131	2013
Metabolism	Engineering dual-glycan responsive expression systems for tunable production of heterologous proteins in Bacteroides thetaiotaomicron.	Jones DR, Smith MB, McLean R, Grondin JM, Amundsen CR, Inglis GD, Selinger B, Abbott DW.	Sci Rep	10.1038/s41598-019-53726-w	2019
Genetics	Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.	Zeybel M, Arif M, Li X, Altay O, Yang H, Shi M, Akyildiz M, Saglam B, Gonenli MG, Yigit B, Ulukan B, Ural D, Shoaie S, Turkez H, Nielsen J, Zhang C, Uhlen M, Boren J, Mardinoglu A.	Adv Sci (Weinh)	10.1002/advs.202104373	2022
	Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis.	Zhang J, Sun Z, Jiang S, Bai X, Ma C, Peng Q, Chen K, Chang H, Fang T, Zhang H.	mSystems	10.1128/msystems.00017-19	2019
	Fecal multi-omics analysis reveals diverse molecular alterations of gut ecosystem in COVID-19 patients.	He F, Zhang T, Xue K, Fang Z, Jiang G, Huang S, Li K, Gu Z, Shi H, Zhang Z, Zhu H, Lin L, Li J, Xiao F, Shan H, Yan R, Li X, Yan Z.	Anal Chim Acta	10.1016/j.aca.2021.338881	2021
Pathogenicity	Prebiotic UG1601 mitigates constipation-related events in association with gut microbiota: A randomized placebo-controlled intervention study.	Chu JR, Kang SY, Kim SE, Lee SJ, Lee YC, Sung MK.	World J Gastroenterol	10.3748/wjg.v25.i40.6129	2019
Metabolism	Bovine intestinal bacteria inactivate and degrade ceftiofur and ceftriaxone with multiple beta-lactamases.	Wagner RD, Johnson SJ, Cerniglia CE, Erickson BD.	Antimicrob Agents Chemother	10.1128/aac.00008-11	2011
Genetics	phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.	Gruber-Vodicka HR, Seah BKB, Pruesse E.	mSystems	10.1128/msystems.00920-20	2020
	Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD.	Casen C, Vebo HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, Dzankovic S, Froyland C, Nestestog R, Engstrand L, Munkholm P, Nielsen OH, Rogler G, Simren M, Ohman L, Vatn MH, Rudi K.	Aliment Pharmacol Ther	10.1111/apt.13236	2015
Metabolism	Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder.	Dan Z, Mao X, Liu Q, Guo M, Zhuang Y, Liu Z, Chen K, Chen J, Xu R, Tang J, Qin L, Gu B, Liu K, Su C, Zhang F, Xia Y, Hu Z, Liu X.	Gut Microbes	10.1080/19490976.2020.1747329	2020
	Determination of the structure of oligosaccharides prepared from acharan sulfate.	Kim YS, Ahn MY, Wu SJ, Kim DH, Toida T, Teesch LM, Park Y, Yu G, Lin J, Linhardt RJ.	Glycobiology	10.1093/glycob/8.9.869	1998
Metabolism	Characterization of a Bacteroides species from human intestine that degrades glycosaminoglycans.	Ahn MY, Shin KH, Kim DH, Jung EA, Toida T, Linhardt RJ, Kim YS.	Can J Microbiol	10.1139/cjm-44-5-423	1998
	Preparation and structural determination of large oligosaccharides derived from acharan sulfate.	Chi L, Munoz EM, Choi HS, Ha YW, Kim YS, Toida T, Linhardt RJ.	Carbohydr Res	10.1016/j.carres.2006.02.030	2006
	Effects of Intranasal Pseudorabies Virus AH02LA Infection on Microbial Community and Immune Status in the Ileum and Colon of Piglets.	Zhang C, Liu Y, Chen S, Qiao Y, Zheng Y, Xu M, Wang Z, Hou J, Wang J, Fan H.	Viruses	10.3390/v11060518	2019
	Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status.	Mayneris-Perxachs J, Arnoriaga-Rodriguez M, Luque-Cordoba D, Priego-Capote F, Perez-Brocal V, Moya A, Burokas A, Maldonado R, Fernandez-Real JM.	Microbiome	10.1186/s40168-020-00913-x	2020
	Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China.	Li J, Hou Q, Zhang J, Xu H, Sun Z, Menghe B, Zhang H.	Front Microbiol	10.3389/fmicb.2017.00484	2017
Phylogeny	Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis.	Huh JW, Roh TY.	BMC Microbiol	10.1186/s12866-020-01887-4	2020
Pathogenicity	Prevalence of antimicrobial resistance among clinical isolates of Bacteroides fragilis group in Canada in 2010-2011: CANWARD surveillance study.	Karlowsky JA, Walkty AJ, Adam HJ, Baxter MR, Hoban DJ, Zhanel GG.	Antimicrob Agents Chemother	10.1128/aac.05823-11	2012
	Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota.	Li H, Zhang L, Li J, Wu Q, Qian L, He J, Ni Y, Kovatcheva-Datchary P, Yuan R, Liu S, Shen L, Zhang M, Sheng B, Li P, Kang K, Wu L, Fang Q, Long X, Wang X, Li Y, Ye Y, Ye J, Bao Y, Zhao Y, Xu G, Liu X, Panagiotou G, Xu A, Jia W.	Nat Metab	10.1038/s42255-024-00988-y	2024
Genetics	Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans.	Lancaster SM, Lee-McMullen B, Abbott CW, Quijada JV, Hornburg D, Park H, Perelman D, Peterson DJ, Tang M, Robinson A, Ahadi S, Contrepois K, Hung CJ, Ashland M, McLaughlin T, Boonyanit A, Horning A, Sonnenburg JL, Snyder MP.	Cell Host Microbe	10.1016/j.chom.2022.03.036	2022
	MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.	Huson DH, Beier S, Flade I, Gorska A, El-Hadidi M, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R.	PLoS Comput Biol	10.1371/journal.pcbi.1004957	2016
	Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes.	Li J, Li J, George Markowitz RH, Brooks AW, Mallott EK, Leigh BA, Olszewski T, Zare H, Bagheri M, Smith HM, Friese KA, Habibi I, Lawrence WM, Rost CL, Ledeczi A, Eeds AM, Ferguson JF, Silver HJ, Bordenstein SR.	PLoS Biol	10.1371/journal.pbio.3001758	2022
Phylogeny	Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans.	Thingholm LB, Bang C, Ruhlemann MC, Starke A, Sicks F, Kaspari V, Jandowsky A, Frolich K, Ismer G, Bernhard A, Bombis C, Struve B, Rausch P, Franke A.	BMC Microbiol	10.1186/s12866-021-02337-5	2021
Metabolism	Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions.	Tuncil YE, Thakkar RD, Marcia ADR, Hamaker BR, Lindemann SR.	Sci Rep	10.1038/s41598-018-34912-8	2018
Metabolism	The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29.	Ndeh D, Munoz Munoz J, Cartmell A, Bulmer D, Wills C, Henrissat B, Gray J.	J Biol Chem	10.1074/jbc.ra118.004510	2018
	Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis.	Cheema AK, Maier I, Dowdy T, Wang Y, Singh R, Ruegger PM, Borneman J, Fornace AJ, Schiestl RH.	PLoS One	10.1371/journal.pone.0151190	2016
	Ingestion of hyaluronans (molecular weights 800 k and 300 k) improves dry skin conditions: a randomized, double blind, controlled study.	Kawada C, Yoshida T, Yoshida H, Sakamoto W, Odanaka W, Sato T, Yamasaki T, Kanemitsu T, Masuda Y, Urushibata O.	J Clin Biochem Nutr	10.3164/jcbn.14-81	2015
Genetics	Metatranscriptome of human faecal microbial communities in a cohort of adult men.	Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C.	Nat Microbiol	10.1038/s41564-017-0084-4	2018
Genetics	CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice.	Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, Nagarkatti M.	Eur J Immunol	10.1002/eji.201646792	2017
Metabolism	Decreased Abundance of Akkermansia muciniphila Leads to the Impairment of Insulin Secretion and Glucose Homeostasis in Lean Type 2 Diabetes.	Zhang J, Ni Y, Qian L, Fang Q, Zheng T, Zhang M, Gao Q, Zhang Y, Ni J, Hou X, Bao Y, Kovatcheva-Datchary P, Xu A, Li H, Panagiotou G, Jia W.	Adv Sci (Weinh)	10.1002/advs.202100536	2021
Metabolism	Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire.	Zhang C, Bjorkman A, Cai K, Liu G, Wang C, Li Y, Xia H, Sun L, Kristiansen K, Wang J, Han J, Hammarstrom L, Pan-Hammarstrom Q.	Front Immunol	10.3389/fimmu.2018.00908	2018
	A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans.	Benitez-Paez A, Kjolbaek L, Gomez Del Pulgar EM, Brahe LK, Astrup A, Matysik S, Schott HF, Krautbauer S, Liebisch G, Boberska J, Claus S, Rampelli S, Brigidi P, Larsen LH, Sanz Y.	mSystems	10.1128/msystems.00209-19	2019
	Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.	Ianiro G, Puncochar M, Karcher N, Porcari S, Armanini F, Asnicar F, Beghini F, Blanco-Miguez A, Cumbo F, Manghi P, Pinto F, Pinto F, Masucci L, Quaranta G, De Giorgi S, Sciume GD, Bibbo S, Del Chierico F, Putignani L, Sanguinetti M, Gasbarrini A, Valles-Colomer M, Cammarota G, Segata N.	Nat Med	10.1038/s41591-022-01964-3	2022
Phylogeny	The underlying microbial mechanism of epizootic rabbit enteropathy triggered by a low fiber diet.	Jin DX, Zou HW, Liu SQ, Wang LZ, Xue B, Wu, Tian G, Cai J, Yan TH, Wang ZS, Peng QH.	Sci Rep	10.1038/s41598-018-30178-2	2018
Metabolism	Uncovering the Catalytic Direction of Chondroitin AC Exolyase: FROM THE REDUCING END TOWARDS THE NON-REDUCING END.	Yin FX, Wang FS, Sheng JZ.	J Biol Chem	10.1074/jbc.c115.708396	2016
	The Potential of Pectins to Modulate the Human Gut Microbiota Evaluated by In Vitro Fermentation: A Systematic Review.	Pascale N, Gu F, Larsen N, Jespersen L, Respondek F.	Nutrients	10.3390/nu14173629	2022
	Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.	iMSMS Consortium. Electronic address: sergio.baranzini@ucsf.edu, iMSMS Consortium.	Cell	10.1016/j.cell.2022.08.021	2022
Pathogenicity	Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.	Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brozynska M, Zhu Q, Tripathi A, Vazquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Meric G.	Nat Genet	10.1038/s41588-021-00991-z	2022
Pathogenicity	Ingested hyaluronan moisturizes dry skin.	Kawada C, Yoshida T, Yoshida H, Matsuoka R, Sakamoto W, Odanaka W, Sato T, Yamasaki T, Kanemitsu T, Masuda Y, Urushibata O.	Nutr J	10.1186/1475-2891-13-70	2014
Pathogenicity	Immunomodulation by the Commensal Microbiome During Immune-Targeted Interventions: Focus on Cancer Immune Checkpoint Inhibitor Therapy and Vaccination.	Reens AL, Cabral DJ, Liang X, Norton JE, Therien AG, Hazuda DJ, Swaminathan G.	Front Immunol	10.3389/fimmu.2021.643255	2021
Metabolism	Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose.	Chomvong K, Bauer S, Benjamin DI, Li X, Nomura DK, Cate JH.	PLoS One	10.1371/journal.pone.0158111	2016
Metabolism	Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis.	Verhoeven MD, Lee M, Kamoen L, van den Broek M, Janssen DB, Daran JG, van Maris AJ, Pronk JT.	Sci Rep	10.1038/srep46155	2017
Genetics	Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach.	Wei X, Yan X, Zou D, Yang Z, Wang X, Liu W, Wang S, Li X, Han J, Huang L, Yuan J.	BMC Gastroenterol	10.1186/1471-230x-13-175	2013
Genetics	Dispersal strategies shape persistence and evolution of human gut bacteria.	Hildebrand F, Gossmann TI, Frioux C, Ozkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P.	Cell Host Microbe	10.1016/j.chom.2021.05.008	2021
	Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease.	Walters SS, Quiros A, Rolston M, Grishina I, Li J, Fenton A, DeSantis TZ, Thai A, Andersen GL, Papathakis P, Nieves R, Prindiville T, Dandekar S.	SOJ Microbiol Infect Dis	10.15226/sojmid/2/3/00122	2014
Genetics	Investigating host-microbiome interactions by droplet based microfluidics.	Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Dore J, Hollfelder F, Potocki-Veronese G.	Microbiome	10.1186/s40168-020-00911-z	2020
	The Role of Dysbiosis in Critically Ill Patients With COVID-19 and Acute Respiratory Distress Syndrome.	Battaglini D, Robba C, Fedele A, Tranca S, Sukkar SG, Di Pilato V, Bassetti M, Giacobbe DR, Vena A, Patroniti N, Ball L, Brunetti I, Torres Marti A, Rocco PRM, Pelosi P.	Front Med (Lausanne)	10.3389/fmed.2021.671714	2021
Metabolism	Microbiota and body weight control: Weight watchers within?	Boscaini S, Leigh SJ, Lavelle A, Garcia-Cabrerizo R, Lipuma T, Clarke G, Schellekens H, Cryan JF.	Mol Metab	10.1016/j.molmet.2021.101427	2022
Pathogenicity	Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine.	Bescucci DM, Moote PE, Ortega Polo R, Uwiera RRE, Inglis GD.	Appl Environ Microbiol	10.1128/aem.01569-20	2020
Genetics	Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.	Ranjan R, Rani A, Metwally A, Metwally A, McGee HS, Perkins DL.	Biochem Biophys Res Commun	10.1016/j.bbrc.2015.12.083	2016
Pathogenicity	In vitro activity of gemifloxacin (SB 265805) against anaerobes.	Goldstein EJ, Citron DM, Warren Y, Tyrrell K, Merriam CV.	Antimicrob Agents Chemother	10.1128/aac.43.9.2231	1999
Metabolism	Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation.	Peng B, Huang S, Liu T, Geng A.	Microb Cell Fact	10.1186/s12934-015-0253-1	2015
Metabolism	Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha).	Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA.	J Ind Microbiol Biotechnol	10.1007/s10295-019-02242-x	2020
Metabolism	Degradation of complex arabinoxylans by human colonic Bacteroidetes.	Pereira GV, Abdel-Hamid AM, Dutta S, D'Alessandro-Gabazza CN, Wefers D, Farris JA, Bajaj S, Wawrzak Z, Atomi H, Mackie RI, Gabazza EC, Shukla D, Koropatkin NM, Cann I.	Nat Commun	10.1038/s41467-020-20737-5	2021
	Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology?	Adamczyk-Sowa M, Medrek A, Madej P, Michlicka W, Dobrakowski P.	J Immunol Res	10.1155/2017/7904821	2017
Metabolism	Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.	Nakamichi Y, Mikami B, Murata K, Hashimoto W.	J Biol Chem	10.1074/jbc.m113.522573	2014
Pathogenicity	Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity.	Mendoza JL, Fischer S, Gee MH, Lam LH, Brackenridge S, Powrie FM, Birnbaum M, McMichael AJ, Garcia KC, Gillespie GM.	Elife	10.7554/elife.58128	2020
	Effects of intrapartum penicillin prophylaxis on intestinal bacterial colonization in infants.	Jaureguy F, Carton M, Panel P, Foucaud P, Butel MJ, Doucet-Populaire F.	J Clin Microbiol	10.1128/jcm.42.11.5184-5188.2004	2004
	ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.	Gonzalez E, Pitre FE, Brereton NJB.	Environ Microbiol	10.1111/1462-2920.14632	2019
	Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut.	Zitomersky NL, Coyne MJ, Comstock LE.	Infect Immun	10.1128/iai.01348-10	2011
Enzymology	L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene.	Koivuranta KT, Ilmen M, Wiebe MG, Ruohonen L, Suominen P, Penttila M.	Microb Cell Fact	10.1186/s12934-014-0107-2	2014
Metabolism	Characterization of glycosaminoglycan (GAG) sulfatases from the human gut symbiont Bacteroides thetaiotaomicron reveals the first GAG-specific bacterial endosulfatase.	Ulmer JE, Vilen EM, Namburi RB, Benjdia A, Beneteau J, Malleron A, Bonnaffe D, Driguez PA, Descroix K, Lassalle G, Le Narvor C, Sandstrom C, Spillmann D, Berteau O.	J Biol Chem	10.1074/jbc.m114.573303	2014
Phylogeny	Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.	Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M.	Infect Immun	10.1128/iai.00862-09	2010
Phylogeny	PCR-restriction fragment length polymorphism analysis for identification of Bacteroides spp. and characterization of nitroimidazole resistance genes.	Stubbs SL, Brazier JS, Talbot PR, Duerden BI.	J Clin Microbiol	10.1128/jcm.38.9.3209-3213.2000	2000
Metabolism	Serine lipids of Porphyromonas gingivalis are human and mouse Toll-like receptor 2 ligands.	Clark RB, Cervantes JL, Maciejewski MW, Farrokhi V, Nemati R, Yao X, Anstadt E, Fujiwara M, Wright KT, Riddle C, La Vake CJ, Salazar JC, Finegold S, Nichols FC.	Infect Immun	10.1128/iai.00803-13	2013
	The Gut Microbiota in Multiple Sclerosis: An Overview of Clinical Trials.	Schepici G, Silvestro S, Bramanti P, Mazzon E.	Cell Transplant	10.1177/0963689719873890	2019
	Variation of acharan sulfate and monosaccharide composition and analysis of neutral N-glycans in African giant snail (Achatina fulica).	Park Y, Zhang Z, Laremore TN, Li B, Sim JS, Im AR, Ahn MY, Kim YS, Linhardt RJ.	Glycoconj J	10.1007/s10719-008-9149-1	2008
	Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences.	Ogilvie LA, Bowler LD, Caplin J, Dedi C, Diston D, Cheek E, Taylor H, Ebdon JE, Jones BV.	Nat Commun	10.1038/ncomms3420	2013
Phylogeny	Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.	Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J.	Appl Environ Microbiol	10.1128/aem.65.11.4799-4807.1999	1999
Pathogenicity	Multicenter study of in vitro susceptibility of the Bacteroides fragilis group, 1995 to 1996, with comparison of resistance trends from 1990 to 1996.	Snydman DR, Jacobus NV, McDermott LA, Supran S, Cuchural GJ, Finegold S, Harrell L, Hecht DW, Iannini P, Jenkins S, Pierson C, Rihs J, Gorbach SL.	Antimicrob Agents Chemother	10.1128/aac.43.10.2417	1999
Pathogenicity	Multicenter survey of the changing in vitro antimicrobial susceptibilities of clinical isolates of Bacteroides fragilis group, Prevotella, Fusobacterium, Porphyromonas, and Peptostreptococcus species.	Aldridge KE, Ashcraft D, Cambre K, Pierson CL, Jenkins SG, Rosenblatt JE.	Antimicrob Agents Chemother	10.1128/aac.45.4.1238-1243.2001	2001
Pathogenicity	Intestinal microbiota has important effect on severity of hand foot and mouth disease in children.	Shen C, Xu Y, Ji J, Wei J, Jiang Y, Yang Y, Yang M, Huang H, Zou R, Fang C, Zeng F, Yang F, Wang X, Yuan J, Li J, Wang X, Yang H, Gong S, Wang H, Xia H, Ma J, Liu Y	BMC Infect Dis	10.1186/s12879-021-06748-7	2021
Metabolism	Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.	Mendez-Salazar EO, Vazquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Cubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martinez-Flores K, Fernandez-Torres J, Lozada-Perez C, Pineda C, Sanchez-Gonzalez A, Silveira LH, Burguete-Garcia AI, Orbe-Orihuela C, Lagunas-Martinez A, Vazquez-Gomez A, Lopez-Reyes A, Palacios-Gonzalez B, Martinez-Nava GA	Mol Med	10.1186/s10020-021-00311-5	2021
Phylogeny	Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.	Lan PTN, Sakamoto M, Sakata S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64517-0	2006

References

#8172	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19555
#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 )
#34043	; Curators of the CIP;
#54424	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38733
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#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 .
#123313	Collection of Institut Pasteur ; Curators of the CIP; CIP 104203
#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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Bacteroides stercoris (DSM 19555, ATCC 43183, CIP 104203)

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