Parabacteroides merdae (DSM 19495, ATCC 43184, CCUG 38734)

Name: Parabacteroides merdae (DSM 19495, ATCC 43184, CCUG 38734)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12499

Type strain

Strain Designation T4-1

Culture col. no. DSM 19495 ATCC 43184 CCUG 38734 CIP 104202 JCM 9497 3 more

NCBI tax ID(s) 411477 46503

Special Collections DSMZ CCUG JCM CIP

History <- JCM <- ATCC <- L. V. Moore; VPI T4-1 <- W. E. C. Moore ATCC 43184 <-- L. V. Moore VPI T4-1 <-- W. E. C. Moore. CIP <- 1994, ATCC <- L.V. Moore, VPI: strain T4-1 <- W.E.C. Moore

Links

Parabacteroides merdae T4-1 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from human faeces.

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41698

ATCC 43184,CIP 104202,JCM 9497,CCUG 38734,NCTC 13052,DSM 19495,VTT E-062953

@ref 20215

Last LPSN update 2026-02-09 11:20:51

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Tannerellaceae

Genus Parabacteroides

Species Parabacteroides merdae

Full scientific name Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006

Synonyms (1)

Bacteroides merdae

BacDive ID	Other strains from **Parabacteroides merdae** (4)	Type strain
142675	P. merdae CCUG 13713
143047	P. merdae CCUG 16520
158149	P. merdae H4_9, DSM 108227
161356	P. merdae JCM 13405

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120896	negative	rod-shaped
125439	negative		99.1
125438	negative		93.856

Colony morphology

8118

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8118	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
8118	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
34044	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)
120896	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8118	positive	growth	37	mesophilic
34044	positive	growth	37	mesophilic
54425	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8118	anaerobe
54425	anaerobe
125439	anaerobe	97.8

Spore formation

@ref	Spore formation	Confidence
125439		98.5
125438		93.833

Observation

67770

Observationquinones: MK-9, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
120896	17632 ChEBI	nitrate	-	reduction
120896	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
120896	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

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
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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120896	catalase	-	1.11.1.6
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
68380	glutamyl-glutamate 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
120896	oxidase	-
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
120896	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

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
120896	-	+	-	-	-	+	-	-	-	-	-	+	-	+	-	-	-	+	-	-

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
8118	-	-	+	+	-	+	+	+	+/-	+	+	+	-	-	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-
8118	-	-	+	+	-	+	+/-	+/-	-	+	+	+	+	-	-	-	+	+	-	+	+	+	-	+/-	+	+/-	+	+	-

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
8118	human faeces		USA	USA	North America
54425	Human feces	Texas	USA	USA	North America
67770	Human feces
120896	Human, Feces	Texas	United States of America	USA	North America	1972

Taxonmaps

69479

Global distribution of 16S sequence EU136685 (>99% sequence identity) for Parabacteroides merdae subclade from Microbeatlas

Aquatic Samples	11747
Soil Samples	3196
Animal Samples	284785
Plant Samples	969
Total Samples	300697

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
8118	yes, in single cases	1	Risk group (German classification) According to TRBA 466
120896		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	ASM2515121v1 assembly for Parabacteroides merdae ATCC 43184	complete	GCA_025151215	411477.87	8119252353	411477	96.86
66792	52683_B04 assembly for Parabacteroides merdae NCTC13052	contig	GCA_900445495	46503.89	2811995281	46503	77.57
66792	ASM15410v1 assembly for Parabacteroides merdae ATCC 43184	scaffold	GCA_000154105	411477.4	640963016	411477	54.46

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Parabacteroides merdae gene for 16S ribosomal RNA, partial sequence, strain: JCM 9497	AB238928	1492	46503
20218	Bacteroides merdae 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AY153427	431	411477
20218	Parabacteroides merdae strain JCM9497 16S ribosomal RNA gene, partial sequence	EU136685	2023	46503
20218	Bacteroides merdae 16S ribosomal RNA gene, partial sequence	U50416	62	411477
8118	B.merdae 16S rRNA (ATCC 43184T)	X83954	1405	411477
8118	Parabacteroides merdae ATCC 43184 16S ribosomal RNA, partial sequence	NR_119166	1405	411477

GC content

@ref	GC-content (mol%)	Method
8118	44
8118	45.3	sequence analysis
67770	44	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parabacteroides merdae ATCC 43184
NCBI: GCA_025151215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	68.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parabacteroides merdae ATCC 43184 ATCC 43184
NCBI: GCA_025151215.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.86	no
125438	anaerobic	anaerobicⓘ	yes	88.37	no
125438	aerobic	aerobicⓘ	no	94.21	no
125438	spore-forming	spore-formingⓘ	no	93.83	no
125438	thermophilic	thermophileⓘ	no	92.37	no
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Atlas of mRNA translation and decay for bacteria.	Huch S, Nersisyan L, Ropat M, Barrett D, Wu M, Wang J, Valeriano VD, Vardazaryan N, Huerta-Cepas J, Wei W, Du J, Steinmetz LM, Engstrand L, Pelechano V.	Nat Microbiol	10.1038/s41564-023-01393-z	2023
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
Phylogeny	Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.	Allen HK, Bayles DO, Looft T, Trachsel J, Bass BE, Alt DP, Bearson SM, Nicholson T, Casey TA.	BMC Res Notes	10.1186/s13104-016-2172-6	2016
	Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.	El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crepin A.	Front Microbiol	10.3389/fmicb.2022.828359	2022
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
	Formononetin derived from Parabacteroides merdae alleviates MPTP-induced Parkinson's disease in mice by inhibiting ferroptosis via the PI3K-AKT-ferritinophagy axis.	Dong X, Yang T, Jin Z.	Commun Biol	10.1038/s42003-025-09067-8	2025
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
	A Porphyromonas gingivalis hypothetical protein controlled by the type I-C CRISPR-Cas system is a novel adhesin important in virulence.	Irfan M, Solbiati J, Duran-Pinedo A, Rocha FG, Gibson FC, Frias-Lopez J.	mSystems	10.1128/msystems.01231-23	2024
Genetics	Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis.	Zhu J, Yin J, Chen J, Hu M, Lu W, Wang H, Zhang H, Chen W.	Gut Microbes	10.1080/19490976.2024.2336877	2024
	CryoEM structure and small-angle X-ray scattering analyses of porcine retinol-binding protein 3.	Kaushik V, Gessa L, Kumar N, Pinkas M, Czarnocki-Cieciura M, Palczewski K, Novacek J, Fernandes H.	Open Biol	10.1098/rsob.240180	2025
Metabolism	A bacterial bile acid metabolite modulates T_reg activity through the nuclear hormone receptor NR4A1.	Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR.	Cell Host Microbe	10.1016/j.chom.2021.07.013	2021
	Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.	Ortanez J, Degnan PH.	Front Microbiol	10.3389/fmicb.2024.1241582	2024
	Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales.	Bao H, Coyne MJ, Garcia-Bayona L, Comstock LE.	J Bacteriol	10.1128/jb.00122-22	2022
	Parabacteroides distasonis promotes liver regeneration by increasing beta-hydroxybutyric acid (BHB) production and BHB-driven STAT3 signals.	Guo M, Jiang X, Ouyang H, Zhang X, Zhang S, Wang P, Bi G, Wu T, Zhou W, Liang F, Yang X, Fan S, Fang JH, Chen P, Bi H.	Acta Pharm Sin B	10.1016/j.apsb.2025.01.024	2025
	A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria.	Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS.	Nat Microbiol	10.1038/s41564-022-01176-y	2022
Metabolism	Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.	Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S.	Cell	10.1016/j.cell.2022.01.002	2022
Pathogenicity	The gut-immune-brain axis in neurodevelopment and neurological disorders.	Park JC, Im SH.	Microbiome Res Rep	10.20517/mrr.2022.11	2022
	The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet.	Olson CA, Vuong HE, Yano JM, Liang QY, Nusbaum DJ, Hsiao EY.	Cell	10.1016/j.cell.2018.04.027	2018
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
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	Glucuronides in the gut: Sugar-driven symbioses between microbe and host.	Pellock SJ, Redinbo MR.	J Biol Chem	10.1074/jbc.r116.767434	2017
	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
Metabolism	A metagenomic beta-glucuronidase uncovers a core adaptive function of the human intestinal microbiome.	Gloux K, Berteau O, El Oumami H, Beguet F, Leclerc M, Dore J.	Proc Natl Acad Sci U S A	10.1073/pnas.1000066107	2011
	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
Metabolism	Dps and DpsL Mediate Survival In Vitro and In Vivo during the Prolonged Oxidative Stress Response in Bacteroides fragilis.	Betteken MI, Rocha ER, Smith CJ.	J Bacteriol	10.1128/jb.00342-15	2015
	Evidence of extensive DNA transfer between bacteroidales species within the human gut.	Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE.	mBio	10.1128/mbio.01305-14	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
	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
Genetics	In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota.	Kim BS, Kim JN, Cerniglia CE.	J Biomed Biotechnol	10.1155/2011/838040	2011
Metabolism	Proteomic analysis of a noninvasive human model of acute inflammation and its resolution: the twenty-one day gingivitis model.	Grant MM, Creese AJ, Barr G, Ling MR, Scott AE, Matthews JB, Griffiths HR, Cooper HJ, Chapple IL.	J Proteome Res	10.1021/pr100446f	2010
	The Glutaminase-Dependent Acid Resistance System: Qualitative and Quantitative Assays and Analysis of Its Distribution in Enteric Bacteria.	Pennacchietti E, D'Alonzo C, Freddi L, Occhialini A, De Biase D.	Front Microbiol	10.3389/fmicb.2018.02869	2018
	Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.	Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jimenez-Garcia B, Moal IH, Fernandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.	Proteins	10.1002/prot.25007	2016
Metabolism	A selective gut bacterial bile salt hydrolase alters host metabolism.	Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS.	Elife	10.7554/elife.37182	2018
Phylogeny	Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.	Sheridan PP, Miteva VI, Brenchley JE.	Appl Environ Microbiol	10.1128/aem.69.4.2153-2160.2003	2003
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
	Resistance of Capnocytophaga canimorsus to killing by human complement and polymorphonuclear leukocytes.	Shin H, Mally M, Meyer S, Fiechter C, Paroz C, Zaehringer U, Cornelis GR.	Infect Immun	10.1128/iai.01324-08	2009
Metabolism	Evolutionary primacy of sodium bioenergetics.	Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV.	Biol Direct	10.1186/1745-6150-3-13	2008
	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
	Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.	Peer A, Smith SP, Bayer EA, Lamed R, Borovok I.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01420.x	2009
	Evolution of the oligopeptide transporter family.	Gomolplitinant KM, Saier MH.	J Membr Biol	10.1007/s00232-011-9347-9	2011
	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	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
	Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro.	Roux I, Lindell AE, Griesshammer A, Smith T, Krishna S, Guan R, Rad D, Faria L, Blasche S, Patil KR, Kleinstreuer NC, Maier L, Kamrad S, Patil KR.	Nat Microbiol	10.1038/s41564-025-02182-6	2025
	The Role of Plasma Metabolites in Mediating the Effect of Gut Microbiota on Obstructive Sleep Apnea: A Two-Step, Two-Sample Mendelian Randomization Study.	Wang X, Zhao R, Guo J, Yang K, Xu B.	Nat Sci Sleep	10.2147/nss.s527778	2025
	Novel plant-derived compounds modulate gut microbiome dysbiosis in colitis mice: A potential therapeutic avenue for inflammatory bowel disease.	Rahaman MM, Yeshi K, Bappi MH, Islam MZ, Wangchuk P, Sarker S.	Microbiol Res	10.1016/j.micres.2025.128343	2026
	Association of the gut microbiome with diabetic nephropathy and the mediated effect of metabolites: friend or enemy?	Yu Y, Yang X, Deng J, Yin Y, Wu Y, Yu R.	Int Urol Nephrol	10.1007/s11255-025-04519-w	2025
Phylogeny	Multi-omics analysis reveals gut microbial and metabolic signatures in metabolic dysfunction-associated steatotic liver disease.	Maimaitiyiming M, Maihemuti S, Aierken T, Abulimiti G, Aibaidula T, Guan Y, Simayi A, Aimaiti M, Wang X, Abuduaini A, Aishan Y.	Front Microbiol	10.3389/fmicb.2025.1666110	2025
Genetics	Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.	Garcia-Perez P, Tomas M, Giuberti G, Capanoglu E, Callegari ML, Lucini L, Patrone V.	Microbiol Res	10.1016/j.micres.2025.128226	2025
	Effects of Traditional Asian Diet on dietary fibre requirement, gut microbiome composition, and faecal and urine metabolomes in healthy Asian women: a pilot study.	Sahran NF, Chong CW, Ismail IH, Taib F, Hoo PS, Palanisamy UD, Sundralingam U, Teh CSJ, Kong ZX, Ayub Q, Yoke Ling F, Hazlan SNH, Azlan M, Abdul Razak S, Tengku Din TADA, Abdullah N, Tagiling N, Tee V, Ehab Ayad M, Zheng FM, El-Omar E, Lee YY.	Benef Microbes	10.1163/18762891-bja00074	2025
	Yeast mannans promote laxation and specifically modulate microbiota composition in older adults: An open-label pilot study.	Moreno ML, Abbeele PVD, Baudot A, Tompkins TA, Taft DH, Yao R, Auger J, Colee J, Dahl WJ.	Nutr Res	10.1016/j.nutres.2025.02.004	2025
	Role of Gut Microbes in Hypertension: A Systematic Review of Literature.	Garde SS, Garde S.	Ann Vasc Dis	10.3400/avd.ra.24-00121	2025
Metabolism	Lactiplantibacillus plantarum P101 Alleviated Alcohol-Induced Hepatic Lipid Accumulation in Mice via AMPK Signaling Pathway: Gut Microbiota and Metabolomics Analysis.	Feng X, Wang M, Wen S, Hu L, Lan Y, Xu H.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10373-6	2025
	Structural characterization of a novel polysaccharide from Tremella fuciformis and its interaction with gut microbiota	Song H, Tianxiaguiyuan, Chu Q, Deng R, Shen X.	Journal of the Science of Food and Agriculture.		2024
	Gut Microbiota in Adults with Chronic Widespread Pain: A Systematic Review.	Leong PY, Shi LH.	Diseases	10.3390/diseases13090299	2025
	Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC-MS/MS metabolite profiling.	Fernandez-Cantos MV, Babu AF, Hanhineva K, Kuipers OP.	Microbiol Res	10.1016/j.micres.2024.127700	2024
Pathogenicity	Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets.	Haque S, Bantun F, Jalal NA, Faidah H, Babalghith AO, Alobaidy MA, Aldairi AF, Ahmad F.	Gut Pathog	10.1186/s13099-025-00712-5	2025
Phylogeny	Preliminary study of biliary microbiota and identification of bacterial species associated with pigmented gallstone formation.	Zhang R, Chen C, Zheng S, Zhang J, Chen W, Chen Z.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1532512	2025
Genetics	Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing.	Hosoda T, Suzuki M, Matsuno T, Matsui K, Ohyama K, Doi Y.	Microbiol Spectr	10.1128/spectrum.01014-25	2025
	Structural characterization of a novel polysaccharide from Tremella fuciformis and its interaction with gut microbiota.	Song H, Lu J, Chu Q, Deng R, Shen X.	J Sci Food Agric	10.1002/jsfa.13479	2024
Metabolism	Gut microbiota metabolism of branched-chain amino acids and their metabolites can improve the physiological function of aging mice.	Wang H, Feng L, Pei Z, Zhao J, Lu S, Lu W.	Aging Cell	10.1111/acel.14434	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
Genetics	A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.	Yuan J, Sun Z, Sun R, Wang J, Wu C, Liu B, Zhao X, Li Q, Zhao J, Cai K.	Biology (Basel)	10.3390/biology14080980	2025
	Fecal microbiota transplantation for hypertension: an exploratory, multicenter, randomized, blinded, placebo-controlled trial.	Fan L, Chen J, Zhang Q, Ren J, Chen Y, Yang J, Wang L, Guo Z, Bu P, Zhu B, Zhao Y, Wang Y, Liu X, Wang W, Chen Z, Gao Q, Zheng L, Cai J.	Microbiome	10.1186/s40168-025-02118-6	2025
	LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data.	Qi X, Zhang M, Wei T, Lin J, Zhao X, Yao Y, Hu Y, Zheng Y.	Microbiol Spectr	10.1128/spectrum.01542-25	2025
	Mapping the Gut Microbiota Composition in the Context of Raltegravir, Dolutegravir, and Bictegravir-A Scoping Review.	Gaspar Z, Lakatos B.	Int J Mol Sci	10.3390/ijms26136366	2025
Genetics	Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.	Li J, Zhu Y, Chang Q, Gong Y, Wan J, Xu S.	Pol J Microbiol	10.33073/pjm-2025-006	2025
	Exploring the causal relationship between gut microbiota and atopic dermatitis: A Mendelian randomization study.	Li W, Li A.	Medicine (Baltimore)	10.1097/md.0000000000040193	2024
Genetics	Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.	Cai X, Dai J, Xie Y, Xu S, Liu M.	Sci Rep	10.1038/s41598-024-71740-5	2024
	Lactobacillus gasseri CKCC1913 mediated modulation of the gut-liver axis alleviated insulin resistance and liver damage induced by type 2 diabetes.	Jiang S, Liu A, Ma W, Liu X, Luo P, Zhan M, Zhou X, Chen L, Zhang J.	Food Funct	10.1039/d3fo01701j	2023
	Gut Parabacteroides merdae protects against cardiovascular damage by enhancing branched-chain amino acid catabolism.	Qiao S, Liu C, Sun L, Wang T, Dai H, Wang K, Bao L, Li H, Wang W, Liu SJ, Liu H.	Nat Metab	10.1038/s42255-022-00649-y	2022
	Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial.	Nechalova L, Bielik V, Hric I, Babicova M, Baranovicova E, Grendar M, Koska J, Penesova A.	BMC Sports Sci Med Rehabil	10.1186/s13102-024-01029-7	2024
Genetics	A relationship between body size and the gut microbiome suggests a conservation strategy.	Xin T, Ye Q, Hu D.	Microbiol Spectr	10.1128/spectrum.00294-25	2025
	Causal relationships between gut microbiome and obstructive sleep apnea: a bi-directional Mendelian randomization.	Liu L, He G, Yu R, Lin B, Lin L, Wei R, Zhu Z, Xu Y.	Front Microbiol	10.3389/fmicb.2024.1410624	2024
	Investigation of ED4 supplementation on cardiovascular parameters in rats with elevated systemic TMAO.	Qiu YT, Huang PH, Chen YW, Shih MK, Lee BH, Sun PP, Hou CY, Chen SY.	NPJ Sci Food	10.1038/s41538-025-00552-2	2025
	Fecal microbiome composition in neonates with or without urinary tract infection.	Bahat H, Paret M, Uzan A, Klainer H, Sharon E, Turjeman S, Koren O, Goldman M, Youngster I.	Pediatr Nephrol	10.1007/s00467-024-06612-1	2025
Pathogenicity	Adverse childhood experiences and reoccurrence of illness impact the gut microbiome, which affects suicidal behaviours and the phenome of major depression: towards enterotypic phenotypes.	Maes M, Vasupanrajit A, Jirakran K, Klomkliew P, Chanchaem P, Tunvirachaisakul C, Plaimas K, Suratanee A, Payungporn S.	Acta Neuropsychiatr	10.1017/neu.2023.21	2023
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
	The immune system's mediation of the protective effect of Parabacteroides against obesity: A Mendelian randomization study.	Ouyang Y, Liao Y, Lei B, Liu L, Gao Y, Chen B, Liu H.	Medicine (Baltimore)	10.1097/md.0000000000044671	2025
	Fecal microbiome analysis in patients with metabolic syndrome and type 2 diabetes.	Sinisterra Loaiza LI, Fernandez-Edreira D, Linares-Blanco J, Cepeda A, Cardelle-Cobas A, Fernandez-Lozano C.	PeerJ	10.7717/peerj.19108	2025
	Koji amazake produced by double saccharification contains more isomaltose and modifies the gut microbiota in mice.	Murakami A, Saito A, Namai F, Fujii T, Tochio T, Toida J, Shimosato T.	Front Nutr	10.3389/fnut.2024.1489912	2024
	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
	Pregnancy-induced changes to the gut microbiota drive macrophage pyroptosis and exacerbate septic inflammation.	Chen X, Wu R, Li L, Zeng Y, Chen J, Wei M, Feng Y, Chen G, Wang Y, Lin L, Luo H, Chen A, Zeng Z, He F, Bai Y, Zhang S, Han Y, Wang Z, Zhao X, Xiao W, Jiang Y, Gong S.	Immunity	10.1016/j.immuni.2023.01.015	2023
	Roles of intestinal Parabacteroides in human health and diseases.	Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lu X.	FEMS Microbiol Lett	10.1093/femsle/fnac072	2022
	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
	Microbial Dysbiosis as an Emerging Pathology of Suicidal Behaviour? A Critical Review, Passing Through Depression to Chronic Pain.	Costanza A, Alexander J, Amerio A, Aguglia A, Magnani L, Parise A, Saverino D, Serafini G, Amore M, Nguyen KD.	Ann Neurosci	10.1177/09727531251349024	2025
Phylogeny	Culture-based characterization of gut microbiota in inflammatory bowel disease.	Park H, Yeo S, Lee T, Han Y, Ryu CB, Huh CS.	Front Microbiol	10.3389/fmicb.2025.1538620	2025
	Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.	Liu Y, Qiu Q, Chen Y, Deng Y, Huang W, Sun C, Shang X, Chen X, Wang C, Han L, Chen S, Yuan J, Xu F, Yang Z, Fang X, Huang L.	Microbiol Spectr	10.1128/spectrum.01459-24	2025
	Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands.	Boiten KE, Notermans DW, Rentenaar RJ, van Prehn J, Bode LGM, Maat I, van der Zwet W, Jansz A, Siebers TJH, Rossen JWA, de Greeff SC, Hendrickx APA, Kuijper EJ, Veloo ACM.	J Antimicrob Chemother	10.1093/jac/dkae043	2024
	Total flavonoids of Chrysanthemum indicum L inhibit colonic barrier injury induced by acute pancreatitis by affecting gut microorganisms.	Yang X, Hu J, Zhong C, Xu S, Hua S, Liu P, He L.	Aging (Albany NY)	10.18632/aging.205924	2024
	Bone morphogenetic proteins, DNA methylation, and gut microbiota interaction in lumbar disc degeneration: A multi-omics Mendelian randomization study.	Li XY, Wang PY, Wang QJ, Wang DF, Wang SK, Wang Y, Zhu WG, Wang W, Kong C, Lu SB, Chen XL.	JOR Spine	10.1002/jsp2.70027	2024
	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
	Association of Mucin-Degrading Gut Microbiota and Dietary Patterns with Colonic Transit Time in Constipation: A Secondary Analysis of a Randomized Clinical Trial.	Wu X, Yang HJ, Ryu MS, Jung SJ, Ha K, Jeong DY, Park S.	Nutrients	10.3390/nu17010138	2024
Metabolism	Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation.	Olivares M, Hernandez-Calderon P, Cardenas-Brito S, Liebana-Garcia R, Sanz Y, Benitez-Paez A.	Genome Biol	10.1186/s13059-024-03325-4	2024
	The Efficacy of Cheonggukjang in Alleviating Menopausal Syndrome and Its Effects on the Gut Microbiome: A Randomized, Double-Blind Trial.	Han AL, Ryu MS, Yang HJ, Jeong DY, Choi KH.	Nutrients	10.3390/nu17030505	2025
	Physical Activity and Metabolic Disorders-What Does Gut Microbiota Have to Do with It?	Sokal-Dembowska A, Polak-Szczybylo E, Helma K, Musz P, Setlik M, Fic W, Wachowiak D, Jarmakiewicz-Czaja S.	Curr Issues Mol Biol	10.3390/cimb47080630	2025
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
	Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.	Ye X, Sahana G, Lund MS, Li B, Cai Z.	Anim Microbiome	10.1186/s42523-025-00386-z	2025
	MicroED structure of the C11 cysteine protease clostripain.	Ruma YN, Bu G, Hattne J, Gonen T.	J Struct Biol X	10.1016/j.yjsbx.2024.100107	2024
Pathogenicity	Proton Pump Inhibitor-Induced Gut Dysbiosis Increases Mortality Rates for Patients with Clostridioides difficile Infection.	Lin CY, Cheng HT, Kuo CJ, Lee YS, Sung CM, Keidan M, Rao K, Kao JY, Hsieh SY.	Microbiol Spectr	10.1128/spectrum.00486-22	2022
	Impact of active lifestyle on the primary school children saliva microbiota composition.	Mancini A, Cerulli C, Vitucci D, Lasorsa VA, Parente D, Di Credico A, Orru S, Brustio PR, Lupo C, Rainoldi A, Schena F, Capasso M, Buono P.	Front Nutr	10.3389/fnut.2023.1226891	2023
	Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM).	Carpio LE, Olivares M, Benitez-Paez A, Serrano-Candelas E, Barigye SJ, Sanz Y, Gozalbes R.	Int J Mol Sci	10.3390/ijms25115744	2024
Transcriptome	Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep.	Cheng X, Liang Y, Ji K, Feng M, Du X, Jiao D, Wu X, Zhong C, Cong H, Yang G.	Microbiome	10.1186/s40168-025-02096-9	2025
Phylogeny	The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery.	Yang Y, Zhou HY, Zhou GM, Chen J, Ming R, Zhang D, Jiang HW.	Front Microbiol	10.3389/fmicb.2024.1494049	2024
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
	An early post-birth immune-microbiota landscape predicts the development of necrotizing enterocolitis in term newborns with congenital heart defects.	Zaikova E, Kaplina A, Belozertsev D, Kostareva A, Sitkin S, Petrova N, Mashevskiy G, Pervunina T, Kudryavtsev I, Golovkin A, Kalinina O.	Sci Rep	10.1038/s41598-025-02542-6	2025
Pathogenicity	3-O-Acetyl-11-Keto-beta-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.	Xu F, Li W, Zheng XJ, Hao Y, Yang YH, Yang H, Zhang S, Cao WX, Li XX, Zhang X, Du GH, Ji TF, Wang JH.	Oncol Res	10.32604/or.2025.062386	2025
Pathogenicity	A mini-review of the relationship between intestinal microecology and acute respiratory distress syndrome.	Chen L, He H, Li C, Nie S, Liu D, Shi Q.	PeerJ	10.7717/peerj.19995	2025
	Effect of the gut microbiome, skin microbiome, plasma metabolome, white blood cells subtype, immune cells, inflammatory proteins, and inflammatory cytokines on asthma: a two-sample Mendelian randomized study and mediation analysis.	Guo W, Hong E, Ma H, Wang J, Wang Q.	Front Immunol	10.3389/fimmu.2025.1436888	2025
	Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach.	Zund JN, Caflisch M, Mujezinovic D, Pluss S, Lacroix C, Pugin B.	FEMS Microbiol Ecol	10.1093/femsec/fiaf054	2025
	Nasal Microbiota Profiling as a Predictive Secondary Tool for COVID-19 Diagnosis: The Critical Role of Taxonomic Resolution.	De Jaegher S, D'Aguanno M, Pinzauti D, Biazzo M.	Microorganisms	10.3390/microorganisms13030501	2025
Genetics	Comparison Of The Gut Microbiota In Different Age Groups In China.	Yan H, Qin Q, Yan S, Chen J, Yang Y, Li T, Gao X, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.877914	2022
Biotechnology	Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.	Jamaluddin NF, Brovkina O, Nor Rashid N, Al-Maleki AR, Lim YA, Tan MP, Lee SC, Duvallet C, Corzett CH, Alm E, Groussin M, Poyet M, Ibrahim F.	Sci Rep	10.1038/s41598-025-07117-z	2025
Phylogeny	Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis.	Budzinski L, Sempert T, Lietz L, Maier R, Kang GU, von Stuckrad ASL, Goetzke CC, Roth M, Shah A, Abbas A, Lehman K, Necke K, Bartsch S, Hoffmann U, Mashreghi MF, Biesen R, Kallinich T, Chang HD.	Mol Cell Pediatr	10.1186/s40348-024-00186-6	2024
Pathogenicity	Comparative Protective Effects of Static Magnetic Field-Treated and Untreated Corn Sprouts on DSS-Induced Ulcerative Colitis in Mice: Inflammation Modulation and Gut Microbiota Regulation.	Zhao J, Gu Y, Sun S, Guo A, Zheng M, Cai D, Lin K, Liu H.	Foods	10.3390/foods14183248	2025
Phylogeny	Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing.	Welham Z, Li J, Engel AF, Molloy MP.	Cancers (Basel)	10.3390/cancers15205045	2023
Metabolism	Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.	Dirks B, Davis TL, Carnero EA, Corbin KD, Smith SR, Rittmann BE, Krajmalnik-Brown R.	ISME J	10.1093/ismejo/wraf103	2025
	Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome.	Jones SJ, Bell DJ, McFarlane JS.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x25000482	2025
	Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.	Keskey R, Bluiminck S, Sangwan N, Meltzer R, Lam A, Thewissen R, Zaborin A, van Goor H, Zaborina O, Alverdy J.	Microbiol Spectr	10.1128/spectrum.02766-24	2025
Genetics	Metagenomics Analysis of Altered Gut Microbiome in Psoriasis and the Mediation Analysis: A Case-Control Study.	Xiao Y, Jing D, Xiao H, Mao M, Kuang Y, Shen M, Lv C, Jian X, Peng C, Chen X.	Psoriasis (Auckl)	10.2147/ptt.s505283	2025
Phylogeny	Impact of a Lifestyle Intervention on Gut Microbiome Composition: A Quasi-Controlled Before-and-After Analysis.	Shehata F, Dwyer KM, Axtens M, McGee SL, Rivera LR.	Metabolites	10.3390/metabo15110692	2025
	Synthesis and antimicrobial activity of aminoalkyl resveratrol derivatives inspired by cationic peptides.	Cebrian R, Lucas R, Fernandez-Cantos MV, Slot K, Penalver P, Martinez-Garcia M, Parraga-Leo A, de Paz MV, Garcia F, Kuipers OP, Morales JC.	J Enzyme Inhib Med Chem	10.1080/14756366.2022.2146685	2023
	Effects of a 217-km mountain ultramarathon on the gut microbiota of an obese runner: A case report.	Saragiotto GK, de Oliveira LFV, Scharlack NK, de Oliveira MM, Freire FC, Simabuco FM, Sivieri K, Sartoratto A, Belli T, Antunes AEC.	Physiol Rep	10.14814/phy2.70017	2024
	Role of gut microbiota and derived metabolites in cardiovascular diseases.	Yu J, Yang YN, Chen W, Hu J, Jin Z, Wu C, Li Y.	iScience	10.1016/j.isci.2025.113247	2025
	Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.	Junca H, Steube A, Mrowietz S, Stallhofer J, Vital M, Dos Anjos Borges LG, Pieper DH, Stallmach A.	ISME Commun	10.1093/ismeco/ycae167	2025
	Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.	Hai C, Hao Z, Bu L, Lei J, Liu X, Zhao Y, Bai C, Su G, Yang L, Li G.	Commun Biol	10.1038/s42003-024-07252-9	2024
	Gut Microbiome Correlations in Hidradenitis Suppurativa Patients.	Lelonek E, Krajewski PK, Szepietowski JC.	J Clin Med	10.3390/jcm14145074	2025
Genetics	Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.	Chen J, Luo Y, Hao Y, Wang Q, Wang Q.	Front Nutr	10.3389/fnut.2025.1676238	2025
	Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults.	Deng L, Xu J, Xue Q, Wei Y, Wang J.	Microorganisms	10.3390/microorganisms13071657	2025
	Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.	Naspolini NF, Schuroff PA, Vanzele PAR, Pereira-Santos D, Valim TA, Bonham KS, Fujita A, Passos-Bueno MR, Beltrao-Braga PCB, Carvalho ACPLF, Klepac-Ceraj V, Polanczyk GV, Campos AC, Taddei CR.	Gut Microbes	10.1080/19490976.2025.2493900	2025
	Gut microbiota may affect Alzheimer's disease through synaptic function mediated by CAMs pathway: A study combining Mendelian randomization and bioinformatics.	Liu JY, Tan CY, Luo L, Yin X.	J Alzheimers Dis Rep	10.1177/25424823241310719	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
	An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson's disease participants.	Hall DA, Voigt RM, Cantu-Jungles TM, Hamaker B, Engen PA, Shaikh M, Raeisi S, Green SJ, Naqib A, Forsyth CB, Chen T, Manfready R, Ouyang B, Rasmussen HE, Sedghi S, Goetz CG, Keshavarzian A.	Nat Commun	10.1038/s41467-023-36497-x	2023
	Causal Associations Between the Gut Microbiota and Hypertension-Related Traits Through Mendelian Randomization: A Cross-Sectional Cohort Study.	Tian Y, Gu M, Chen D, Dong Q, Wang Y, Sun W, Kong X.	J Clin Hypertens (Greenwich)	10.1111/jch.14925	2025
	Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome.	Chu W, Han Q, Xu J, Wang J, Sun Y, Li W, Chen ZJ, Du Y.	Fertil Steril	10.1016/j.fertnstert.2020.01.027	2020
	Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects.	Benitez-Paez A, Hartstra AV, Nieuwdorp M, Sanz Y.	Gut Microbes	10.1080/19490976.2022.2078621	2022
Genetics	Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing.	Correa F, Luise D, Palladino G, Estelle J, Turroni S, Scicchitano D, Babbi G, Rampelli S, Candela M, Martelli PL, Stefanelli C, Perez-Calvo E, Trevisi P.	Anim Microbiome	10.1186/s42523-025-00477-x	2025
Genetics	Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case-control study.	Oh S, Kim J, Shin CM, Lee HJ, Lee HS, Park KU.	J Transl Med	10.1186/s12967-024-05989-9	2025
	Bifidobacterium longum subsp. infantis CCFM1426 enhances the anti-colitic effect of vitamin A via retinoic acid restoration and gut microbiota modulation in ulcerative colitis mice.	Yu X, Huang L, Wang Y, Li L, Lu W, Zhang Z, Wang H.	Front Nutr	10.3389/fnut.2025.1644649	2025
	Fecal Microbiome in Women With Fibromyalgia: Functional Composition and Symptom Correlations.	Erdrich S, Gelissen IC, Toma R, Vuyisich M, Harnett JE.	ACR Open Rheumatol	10.1002/acr2.70115	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
	Gut microbiota links to histological damage in chronic HBV infection patients and aggravates fibrosis via fecal microbiota transplantation in mice.	Wang F, Wu Y, Ni J, Xie Q, Shen J, Chen H, Ma C, Yao Y, Wang J, Xu L, Xiang Q, Zhao Y, Chen Y, Li L.	Microbiol Spectr	10.1128/spectrum.00764-25	2025
Pathogenicity	Unraveling the gut microbiota's role in obesity: key metabolites, microbial species, and therapeutic insights.	Iqbal M, Yu Q, Tang J, Xiang J.	J Bacteriol	10.1128/jb.00479-24	2025
Pathogenicity	Potential roles of the interactions between gut microbiota and metabolites in LPS-induced intrauterine inflammation (IUI) and associated preterm birth (PTB).	Jia B, Tang L, Liu H, Chen W, Chen Q, Zhong M, Yin A.	J Transl Med	10.1186/s12967-023-04603-8	2024
	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
	cAMP-independent Crp homolog adds to the multi-layer regulatory network in Porphyromonas gingivalis.	Smiga M, Roszkiewicz E, Slezak P, Tracz M, Olczak T.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1535009	2025
Pathogenicity	Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome.	Hu X, Li H, Zhao X, Zhou R, Liu H, Sun Y, Fan Y, Shi Y, Qiao S, Liu S, Liu H, Zhang S.	Theranostics	10.7150/thno.55946	2021
	The gut microbiota modulates responses to anti-PD-1 and chemotherapy combination therapy and related adverse events in patients with advanced solid tumors.	Wu Z, Zhang S, Li L, Huang Z, Huang D, Hu Y.	Front Oncol	10.3389/fonc.2022.887383	2022
	Targeted Gut Microbiota Modulation Enhances Levodopa Bioavailability and Motor Recovery in MPTP Parkinson's Disease Models.	Ai P, Xu S, Yuan Y, Xu Z, He X, Mo C, Zhang Y, Yang X, Xiao Q.	Int J Mol Sci	10.3390/ijms26115282	2025
	Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study.	Zeng Q, Zhao M, Wang F, Li Y, Li H, Zheng J, Chen X, Zhao X, Ji L, Gao X, Liu C, Wang Y, Cheng S, Xu J, Pan B, Sun J, Li Y, Li D, He Y, Zheng L.	Front Endocrinol (Lausanne)	10.3389/fendo.2022.906310	2022
Phylogeny	Cellulase activity and age-based variation of intestinal microbiota in Hezuo pigs.	Liang Y, Wang F, Jia R, Li J, Wang L, Li Y, Li Y, Gun S, Yang Q.	Front Microbiol	10.3389/fmicb.2025.1599847	2025
Genetics	beta-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics.	Candeliere F, Raimondi S, Ranieri R, Musmeci E, Zambon A, Amaretti A, Rossi M.	Front Microbiol	10.3389/fmicb.2022.826994	2022
	Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study.	Zapala B, Stefura T, Wojcik-Pedziwiatr M, Kabut R, Balajewicz-Nowak M, Milewicz T, Dudek A, Stoj A, Rudzinska-Bar M.	J Clin Med	10.3390/jcm10235698	2021
Phylogeny	Exploring gut microbiota alterations in Parkinson's disease: insights from a 16S amplicon sequencing Eastern European pilot study.	Ilie OD, Vacarean-Trandafir IC, Amarandi RM, Nita IB, Dobrin PR, Doroftei M, Ivanov IC, Savuta G, Kirov B, Doroftei B.	Front Neurosci	10.3389/fnins.2025.1654995	2025
	Metabolomic Signatures Highlight Fiber-Degrading Bacteroides Species in Mediterranean Diet Response Among Ulcerative Colitis.	Haskey N, Ye J, Josephson J, Raman M, Ghosh S, Gibson DL.	Gastro Hep Adv	10.1016/j.gastha.2024.100606	2025
	Impact of Edible Insect Polysaccharides on Mouse Gut Microbiota: A Study on White-Spotted Flower Chafer Larva (Protaetia brevitarsis seulensis) and Silkworm Pupa (Bombyx mori).	Lee JH, Son H, Subramaniyam S, Lim HJ, Park S, Choi RY, Kim IW, Seo M, Kweon HY, Kim Y, Kim SW, Choi JS, Shin Y.	Foods	10.3390/foods14010006	2024
	Assembly archetypes in ecological communities.	Flores-Arguedas H, Antolin-Camarena O, Saavedra S, Angulo MT.	J R Soc Interface	10.1098/rsif.2023.0349	2023
	The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults.	Osuna-Prieto FJ, Xu H, Ortiz-Alvarez L, Di X, Kohler I, Jurado-Fasoli L, Rubio-Lopez J, Plaza-Diaz J, Vilchez-Vargas R, Link A, Gil A, Ruiz JR, Rensen PCN, Martinez-Tellez B.	Metabolomics	10.1007/s11306-023-02016-8	2023
	Enterotype-stratified gut microbial signatures in MASLD and cirrhosis based on integrated microbiome data.	Yuan H, Zhou J, Wu X, Wang S, Park S.	Front Microbiol	10.3389/fmicb.2025.1568672	2025
	Both viable Bifidobacterium longum subsp. infantis B8762 and heat-killed cells alleviate the intestinal inflammation of DSS-induced IBD rats.	Li Z, Peng C, Sun Y, Zhang T, Feng C, Zhang W, Huang T, Yao G, Zhang H, He Q.	Microbiol Spectr	10.1128/spectrum.03509-23	2024
	Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.	Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE, Alzheimer Gut Microbiome Project Consortium, Kaddurah-Daouk R, Knight R, Bendlin BB.	Alzheimers Dement	10.1002/alz.70417	2025
Pathogenicity	Association of gut microbiota and inflammatory markers in obese patients with type 2 diabetes mellitus: post hoc analysis of a synbiotic interventional study.	Sugawara Y, Kanazawa A, Aida M, Yoshida Y, Yamashiro Y, Watada H.	Biosci Microbiota Food Health	10.12938/bmfh.2021-081	2022
	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
	Dissecting the molecular interactions between botanical extracts and the human gut microbiota.	Mancabelli L, Tarracchini C, Longhi G, Alessandri G, Ventura M, Turroni F.	Front Microbiol	10.3389/fmicb.2025.1610170	2025
	MicroRNA-Enriched Plant-Derived Exosomes Alleviate Colitis by Modulating Systemic Immunity, Metabolic Homeostasis, and Gut Microbiota.	Shi R, Tan W, Jin H, Chan SI, Li W, Lei SS, Cui G, Wang Y, Yang DH, Zhong Z.	Adv Sci (Weinh)	10.1002/advs.202505921	2025
	Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives.	Neiroukh D, Hajdarpasic A, Ayhan C, Sultan S, Soliman O.	J Clin Med	10.3390/jcm13226938	2024
	Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.	Chen CC, Chiu JY, Tan AH, Toh TS, Lim SY, Tan EK, Pettersson S, Hsu CC, Liou JM, Wu MS, Hsu CL, Lin CH.	Neurology	10.1212/wnl.0000000000213592	2025
	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
Phylogeny	Catalpol-a compound from Rehmannia glutinosa can improve hyperlipidemia by modulating gut microbiota and endogenous metabolic pathways.	Pei X, Dong W, Yu Y, Wang Y, Wang S, Dai L.	Front Microbiol	10.3389/fmicb.2025.1689778	2025
	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
	Exercise and microbiome: From big data to therapy.	Meng D, Ai S, Spanos M, Shi X, Li G, Cretoiu D, Zhou Q, Xiao J.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.10.034	2023
	Potential application of pig (Sus scrofa domestica) skin peptide-iron chelates in the treatment of iron deficiency anemia and regulation of intestinal flora metabolism.	Huang S, Deng H, Liang K, Zhao X, Zhang J.	Front Nutr	10.3389/fnut.2025.1553668	2025
Genetics	Investigating the association between gut microbiome and aortic aneurysm diseases: a bidirectional two-sample Mendelian randomization analysis.	Sun Y, Dong H, Sun C, Du D, Gao R, Voevoda M, Knyazev R, Wu N.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1406845	2024
	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
	Gut Microbiota and Bile Acids Mediate the Clinical Benefits of YH1 in Male Patients with Type 2 Diabetes Mellitus: A Pilot Observational Study.	Huang YH, Wu YH, Tang HY, Chen ST, Wang CC, Ho WJ, Lin YH, Liu GH, Lin PY, Lo CJ, Yeh YM, Cheng ML.	Pharmaceutics	10.3390/pharmaceutics14091857	2022
	Effect of herbal medicine Bojungikgi-tang on gut microbiome and symptoms in anorexic patients with atopic dermatitis: a randomized controlled trial.	Lee B, Ko MM, Ahn YM, Park HJ, Jung SY, Jung HA, Lee H, Kim PW, Choi Y, Han K, Shin S, Jung J.	Front Pharmacol	10.3389/fphar.2025.1593477	2025
Genetics	A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.	Kim S, Thapa I, Ali H.	BMC Microbiol	10.1186/s12866-024-03633-6	2024
	Gut microbiome for predicting immune checkpoint blockade-associated adverse events.	Hu M, Lin X, Sun T, Shao X, Huang X, Du W, Guo M, Zhu X, Zhou Y, Tong T, Guo F, Han T, Wu X, Shi Y, Xiao X, Zhang Y, Hong J, Chen H.	Genome Med	10.1186/s13073-024-01285-9	2024
	Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria.	Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E, Mangalam AK.	Sci Rep	10.1038/s41598-023-27436-3	2023
	Prebiotic-Engineered Oral Nanoplatform against Ulcerative Colitis via Photodynamic Remodeling of Gut Microbiota and Macrophage Polarization.	He N, Jiang H, Dai T, Kim GS, Liu P, Zhao Y, Li S, Cao J, Li Z.	Biomater Res	10.34133/bmr.0283	2025
	Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets.	Pu G, Hou L, Du T, Zhou W, Liu C, Niu P, Wu C, Bao W, Huang R, Li P.	mSystems	10.1128/msystems.00937-22	2023
Genetics	Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system.	Royseth V, Hurysz BM, Kaczorowska AK, Dorawa S, Fedoy AE, Arsin H, Serafim MSM, Myers SA, Werbowy O, Kaczorowski T, Stokke R, O'Donoghue AJ, Steen IH.	Front Microbiol	10.3389/fmicb.2023.1199085	2023
	Epigenetics and Gut Microbiota in the Pathogenesis and Treatment of Bipolar Disorder (BD).	Nohesara S, Mostafavi Abdolmaleky H, Pirani A, Thiagalingam S.	Cells	10.3390/cells14141104	2025
Genetics	Characteristics of the gut microbiome in esports players compared with those in physical education students and professional athletes.	Kulecka M, Fraczek B, Balabas A, Czarnowski P, Zeber-Lubecka N, Zapala B, Baginska K, Glowienka M, Szot M, Skorko M, Kluska A, Piatkowska M, Mikula M, Ostrowski J.	Front Nutr	10.3389/fnut.2022.1092846	2022
Pathogenicity	Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy.	Ishizaka A, Koga M, Mizutani T, Suzuki Y, Matano T, Yotsuyanagi H.	BMC Microbiol	10.1186/s12866-024-03431-0	2024
Phylogeny	Gut microbiota as prognosis markers for patients with HBV-related acute-on-chronic liver failure.	Wang K, Zhang Z, Mo ZS, Yang XH, Lin BL, Peng L, Xu Y, Lei CY, Zhuang XD, Lu L, Yang RF, Chen T, Gao ZL.	Gut Microbes	10.1080/19490976.2021.1921925	2021
	Effects of GLP-1 Analogues and Agonists on the Gut Microbiota: A Systematic Review.	Gofron KK, Wasilewski A, Malgorzewicz S.	Nutrients	10.3390/nu17081303	2025
	Gut microbial features may influence antiviral IgG levels after vaccination against viral respiratory infectious diseases: the evidence from two-sample bidirectional mendelian randomization.	Tu J, Wang Y, Ye X, Wang Y, Zou Y, Jia L, Yang S, Yu R, Liu W, Huang P.	BMC Infect Dis	10.1186/s12879-024-09189-0	2024
	Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains.	Koo H, Morrow CD.	PLoS One	10.1371/journal.pone.0274633	2022
Genetics	Mode of Action of Psyllium in Reducing Gas Production from Inulin and its Interaction with Colonic Microbiota: A 24-hour, Randomized, Placebo-Controlled Trial in Healthy Human Volunteers.	Alhasani AT, Modasia AA, Anodiyil M, Corsetti M, Aliyu AI, Crooks C, Marciani L, Reid J, Yakubov GE, Taylor M, Avery A, Harris H, Warren FJ, Spiller RC.	J Nutr	10.1016/j.tjnut.2024.12.017	2025
	Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.	Wong MK, Boukhaled GM, Armstrong E, Liu R, Heirali AA, Yee NR, Tsang J, Spiliopoulou P, Schneeberger PHH, Wang BX, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	J Immunother Cancer	10.1136/jitc-2024-010681	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
	Gut Bacteria Seize Control of the Brain to Prevent Epilepsy.	Dooling SW, Costa-Mattioli M.	Cell Host Microbe	10.1016/j.chom.2018.06.014	2018
	A comprehensive narrative review on precision medicine approach to hypertension: exploring the role of genetics, epigenetics, microbiome, and artificial intelligence.	Sami A, Ashraf R, Nisar S, Mustehsan ZH, Javed MA, Ozsahin DU, Waheed Y.	J Health Popul Nutr	10.1186/s41043-025-01058-z	2025
Phylogeny	Fecal Microbial Dysbiosis Is Associated with Colorectal Cancer Risk in a Korean Population.	Kim J, Gunathilake M, Yeo HY, Oh JH, Kim BC, Han N, Kim B, Pyun H, Lim MY, Nam YD, Chang HJ.	Cancer Res Treat	10.4143/crt.2024.382	2025
	Design and pharmacodynamic study of live biotherapeutic products with efficient degradation of branched-chain amino acids.	Chen Z, Xu J, Zhang H, Wang Y, Li M, Wu Y, Zhu Y, Liu Y, Xia H, Zheng H.	Bioeng Transl Med	10.1002/btm2.70075	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
Metabolism	Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria.	McCoubrey LE, Elbadawi M, Orlu M, Gaisford S, Basit AW.	Pharmaceutics	10.3390/pharmaceutics13071026	2021
Pathogenicity	Network analysis and experimental validation to investigate chenpi against functional dyspepsia through TLR4/MyD88 by regulating the gut microbial structure.	Hu J, Wang X, Guo X, Wen W, Xue J, Liao Z, Chen L.	Front Pharmacol	10.3389/fphar.2025.1495799	2025
	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
	A low-cost, easy-to-use prototype bioreactor model for the investigation of human gut microbiota: validation using a prebiotic treatment.	Agrinier AL, Pilon G, Marette A.	Front Microbiol	10.3389/fmicb.2024.1250366	2024
	Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo.	Deyaert S, Poppe J, Dai Vu L, Baudot A, Bubeck S, Bayne T, Krishnan K, Giusto M, Moltz S, Van den Abbeele P.	Metabolites	10.3390/metabo14090497	2024
	Associations of Plastic Bottle Exposure with Infant Growth, Fecal Microbiota, and Short-Chain Fatty Acids.	Tilves C, Zhao HJ, Differding MK, Zhang M, Liu T, Hoyo C, Ostbye T, Benjamin-Neelon SE, Mueller NT.	Microorganisms	10.3390/microorganisms11122924	2023
	Maturation of the gut metabolome during the first year of life in humans.	Ouyang R, Ding J, Huang Y, Zheng F, Zheng S, Ye Y, Li Q, Wang X, Ma X, Zou Y, Chen R, Zhuo Z, Li Z, Xin Q, Zhou L, Lu X, Ren Z, Liu X, Kovatcheva-Datchary P, Xu G.	Gut Microbes	10.1080/19490976.2023.2231596	2023
Genetics	Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.	Cunningham-Oakes E, Bronowski C, Chinyama E, Jere KC, Sindhu KNC, Kang G, Iturriza-Gomara M, Darby AC, Parker EPK.	BMC Microbiol	10.1186/s12866-023-03098-z	2023
Pathogenicity	Lactobacilli in COVID-19: A Systematic Review Based on Next-Generation Sequencing Studies.	Taufer CR, Rampelotto PH.	Microorganisms	10.3390/microorganisms12020284	2024
	The Probiotic Parabacteroides johnsonii Ameliorates Metabolic Disorders Through Promoting BCAAs to BSCFAs Conversion.	Chen Y, Jiang S, Wang H, Si M, Wu H, Liang X, Yao S, Zhang Y, Wen X, Yang J.	Adv Sci (Weinh)	10.1002/advs.202502624	2025
	Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase.	Dadi P, Pauling CW, Shrivastava A, Shah DD.	iScience	10.1016/j.isci.2025.112289	2025
	Causal links between gut microbiomes, cytokines and risk of different subtypes of epilepsy: a Mendelian randomization study.	Qiu Y, Song B, Xie M, Tao Y, Yin Z, Wang M, Ma C, Chen Z, Wang Z.	Front Neurosci	10.3389/fnins.2024.1397430	2024
Phylogeny	In Search of Healthy Ageing: A Microbiome-Based Precision Nutrition Approach for Type 2 Diabetes Prevention.	Gonzalez A, Fullaondo A, Odriozola A.	Nutrients	10.3390/nu17111877	2025
	The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Kim EH, Choi J, Choi Y, Yoon H, Lee SM, Seok YJ.	Gut Liver	10.5009/gnl230385	2024
	Association between post-stroke cognitive impairment and gut microbiota: A PRISMA-compliant systematic review and meta-analysis.	Hu X, Mao Y, Luo F, Wang X.	Medicine (Baltimore)	10.1097/md.0000000000034764	2023
	Chinese Sausage Simulates High Calorie-Induced Obesity In Vivo, Identifying the Potential Benefits of Weight Loss and Metabolic Syndrome of Resveratrol Butyrate Monomer Derivatives.	Huang PH, Chen YW, Shie CK, Chen SY, Lee BH, Yin LJ, Hou CY, Shih MK.	J Nutr Metab	10.1155/jnme/8414627	2025
	Evaluation of Menopausal Syndrome Relief and Anti-Obesity Efficacy of the Korean Fermented Food Doenjang: A Randomized, Double-Blind Clinical Trial.	Han AL, Ryu MS, Yang HJ, Jeong DY, Choi KH.	Nutrients	10.3390/nu16081194	2024
	Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.	Li D, Li M, Gao H, Hu K, Xie R, Fan J, Huang M, Liao C, Han C, Guo Z, Chen X, Li M.	Front Microbiol	10.3389/fmicb.2024.1475984	2024
Pathogenicity	The regulation of intestinal flora on host's genes may play an essential role in the development of endometrial hyperplastic processes in yang deficiency individuals.	Zhang HX, Zhao XL, Wu HX, Luo ZQ, Wang LM, Lv SR, Huang XR, Dong N, Li DZ, Bao C, Su LD, Liu YX, Hu HQ, Bu ZX, Zhang HR, Liu Y, Chang SJ, He ZY, Sai L, Wang HW, Guo HM, Huang XH, Cao X.	Int J Clin Exp Pathol	10.62347/hbkg3920	2024
	Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.	Choi JY, Shim B, Park Y, Kang YA.	Korean J Intern Med	10.3904/kjim.2023.097	2023
	Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.	Qu Q, Dou Q, Xiang Z, Yu B, Chen L, Fan Z, Zhao X, Yang S, Zeng P.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00661-6	2025
Metabolism	Berberine Alleviates Kainic Acid-Induced Acute Epileptic Seizures in Mice via Reshaping Gut Microbiota-Associated Lipid Metabolism.	Dai WT, Zhu Y, Jiang ZM, Xiang Y, Mao XY, Liu ZQ.	CNS Neurosci Ther	10.1111/cns.70253	2025
	Increased abundance of Ruminococcus gnavus in gut microbiota is associated with moyamoya disease and non-moyamoya intracranial large artery disease.	Mineharu Y, Nakamura Y, Sato N, Kamata T, Oichi Y, Fujitani T, Funaki T, Okuno Y, Miyamoto S, Koizumi A, Harada KH.	Sci Rep	10.1038/s41598-022-24496-9	2022
Phylogeny	Gut Microbiota Profile Changes in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease: A Metagenomic Study.	De Caro C, Spagnuolo R, Quirino A, Mazza E, Carrabetta F, Maurotti S, Cosco C, Bennardo F, Roberti R, Russo E, Giudice A, Giudice A, Pujia A, Doldo P, Matera G, Marascio N.	Int J Mol Sci	10.3390/ijms25105453	2024
	Oral and gut dysbiosis leads to functional alterations in Parkinson's disease.	Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW, Chung SJ.	NPJ Parkinsons Dis	10.1038/s41531-022-00351-6	2022
Pathogenicity	Phenotyping of Fecal Microbiota of Winnie, a Rodent Model of Spontaneous Chronic Colitis, Reveals Specific Metabolic, Genotoxic, and Pro-inflammatory Properties.	Tala A, Guerra F, Resta SC, Calcagnile M, Barca A, Tredici SM, De Donno MD, Vacca M, Liso M, Chieppa M, De Angelis M, Verri T, Bozzetti MG, Bucci C, Alifano P.	Inflammation	10.1007/s10753-022-01706-0	2022
	Six months of different exercise type in sedentary primary schoolchildren: impact on physical fitness and saliva microbiota composition.	Mancini A, Vitucci D, Lasorsa VA, Lupo C, Brustio PR, Capasso M, Orru S, Rainoldi A, Schena F, Buono P.	Front Nutr	10.3389/fnut.2024.1465707	2024
	Distinct Plasma Metabolomic and Gut Microbiome Profiles after Gestational Diabetes Mellitus Diet Treatment: Implications for Personalized Dietary Interventions.	Sugino KY, Hernandez TL, Barbour LA, Kofonow JM, Frank DN, Friedman JE.	Microorganisms	10.3390/microorganisms12071369	2024
	Modulation of intestinal metabolites by calorie restriction and its association with gut microbiota in a xenograft model of colorectal cancer.	Zhang Y, Dong L, Dai X, Huang Y, Gao Y, Wang F.	Discov Oncol	10.1007/s12672-024-00897-2	2024
	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
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
Metabolism	The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine.	Mousa S, Sarfraz M, Mousa WK.	Metabolites	10.3390/metabo13050674	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
	Impact of the gut microbiome on atherosclerosis.	Mao Y, Kong C, Zang T, You L, Wang LS, Shen L, Ge JB.	mLife	10.1002/mlf2.12110	2024
Phylogeny	Unraveling the gut microbiota of Mexican pinnipeds: the dominance of life histories over phylogeny.	Pacheco-Sandoval A, Schramm Y, Heckel G, Giffard-Mena I, Lago-Leston A.	Appl Environ Microbiol	10.1128/aem.02030-23	2024
	Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites.	Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y, Wang Z.	Microbiol Spectr	10.1128/spectrum.01437-23	2024
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
	Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System.	Park S, Wu X.	Int J Mol Sci	10.3390/ijms232113574	2022
	Antibiotic-induced gut dysbiosis elicits gut-brain axis relevant multi-omic signatures and behavioral and neuroendocrine changes in a nonhuman primate model.	Hayer SS, Conrin M, French JA, Benson AK, Alvarez S, Cooper K, Fischer A, Alsafwani ZW, Gasper W, Suhr Van Haute MJ, Hassenstab HR, Azadmanesh S, Briardy M, Gerbers S, Jabenis A, Thompson JL, Clayton JB.	Gut Microbes	10.1080/19490976.2024.2305476	2024
	Enriched taxa were found among the gut microbiota of centenarians in East China.	Wang N, Li R, Lin H, Fu C, Wang X, Zhang Y, Su M, Huang P, Qian J, Jiang F, Wang H, Jiang L, Yu X, Liu J, Chen Y, Jiang Q.	PLoS One	10.1371/journal.pone.0222763	2019
Metabolism	Low-dose valine attenuates diet-induced metabolic dysfunction-associated steatotic liver disease (MASLD) in mice by enhancing leptin sensitivity and modulating the gut microbiome.	Felicianna, Lo EKK, Chen C, Ismaiah MJ, Zhang F, Leung HKM, El-Nezami H.	Mol Metab	10.1016/j.molmet.2024.102059	2024
	Evaluation of Body Changes and the Anti-Obesity Effect after Consumption of Korean Fermented Food, Cheonggukjang: Randomized, Double-Blind Clinical Trial.	Han AL, Jeong SJ, Ryu MS, Yang HJ, Jeong DY, Seo YB.	Foods	10.3390/foods12112190	2023
	Gut microbiota profile in CDKL5 deficiency disorder patients.	Borghi E, Xynomilakis O, Ottaviano E, Ceccarani C, Vigano I, Tognini P, Vignoli A.	Sci Rep	10.1038/s41598-024-56989-0	2024
	Gut microbial characteristics in poor appetite and undernutrition: a cohort of older adults and microbiota transfer in germ-free mice.	Fluitman KS, Davids M, Olofsson LE, Wijdeveld M, Tremaroli V, Keijser BJF, Visser M, Backhed F, Nieuwdorp M, IJzerman RG.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13002	2022
	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
	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
Phylogeny	Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study	Issilbayeva A, Sergazy S, Zhashkeyev A, Gulyayev A, Kozhakhmetov S, Shulgau Z, Nurgaziyev M, Nurgaziyeva A, Zhetkenev S, Mukhanbetzhanov N, Jarmukhanov Z, Mukhanbetzhanova Z, Vinogradova E, Zhumadilov Z, Kushugulova A, Aljofan M.	Front Med (Lausanne)		2025
	Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition.	Lin YY, Chang PE, Shen SY, Wang SD.	Poult Sci	10.1016/j.psj.2023.102731	2023
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
	Genetically predicted immune cells mediate the association between gut microbiota and neuropathy pain.	Lan Z, Wei Y, Yue K, He R, Jiang Z.	Inflammopharmacology	10.1007/s10787-024-01514-y	2024
	Antibiotics-induced dysbiosis impacts dendritic morphology of adult mouse cortical interneurons.	Nakhal MM, Mydeen AB, Yassin LK, Almazrouei R, Alkamali R, Alsulaimi M, Elsaleh RI, BaniYas S, Al Houqani S, Al-Marzooq F, Hassane M, Voitetskii R, Statsenko Y, Allam M, Akour A, Hamad MIK.	Front Neuroanat	10.3389/fnana.2025.1557961	2025
Genetics	Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome.	Lemons JMS, Narrowe AB, Liu L, Firrman J, Mahalak KK, Van den Abbeele P, Baudot A, Deyaert S, Li Y, Yu LL.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1298392	2023
	Bifico relieves irritable bowel syndrome by regulating gut microbiota dysbiosis and inflammatory cytokines.	Zhou Y, Zhang F, Mao L, Feng T, Wang K, Xu M, Lv B, Wang X.	Eur J Nutr	10.1007/s00394-022-02958-0	2023
	Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort.	Shen Y, Laue HE, Shrubsole MJ, Wu H, Bloomquist TR, Larouche A, Zhao K, Gao F, Boivin A, Prada D, Hunting DJ, Gillet V, Takser L, Baccarelli AA.	Environ Health Perspect	10.1289/ehp9674	2022
	Differences in gut microbes in captive pangolins and the effects of captive breeding.	Jiao W, Liu L, Zeng Z, Li L, Chen J.	Front Microbiol	10.3389/fmicb.2022.1053925	2022
	Impact of broad-spectrum antibiotics on the gut-microbiota-spleen-brain axis.	Wan X, Eguchi A, Sakamoto A, Fujita Y, Yang Y, Qu Y, Hatano M, Mori C, Hashimoto K.	Brain Behav Immun Health	10.1016/j.bbih.2022.100573	2023
Phylogeny	Gut microbiota changes associated with low-carbohydrate diet intervention for obesity.	Li L, Zhao X, Abdugheni R, Yu F, Zhao Y, Ma BF, Yang Z, Li R, Li Y, Maimaitiyiming Y, Maimaiti M.	Open Life Sci	10.1515/biol-2022-0803	2024
Genetics	Gut virome alterations in patients with chronic obstructive pulmonary disease.	Liu Y, Huang Q, Zhuang Z, Yang H, Gou X, Xu T, Liu K, Wang J, Liu B, Gao P, Cao F, Yang B, Zhang C, Chen M, Fan G.	Microbiol Spectr	10.1128/spectrum.04287-23	2024
	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
Metabolism	[Bioconversion of cellulose to methane by a consortium consisting of four microbial strains].	Wu JM, Ma AZ, Cui MM, Yu Q, Qi HY, Zhuang XL, Zhuang GQ.	Huan Jing Ke Xue		2014
	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
	Causal relationship between the gut microbiome and basal cell carcinoma, melanoma skin cancer, ease of skin tanning: evidence from three two-sample mendelian randomisation studies.	Lou J, Cui S, Li J, Jin G, Fan Y, Huang N.	Front Immunol	10.3389/fimmu.2024.1279680	2024
	Performance evaluation and bacteria analysis of AFB-MFC enriched with high-strength synthetic wastewater.	Huang JS, Guo Y, Yang P, Li CM, Gao H, Feng L, Zhang Y.	Water Sci Technol	10.2166/wst.2013.390	2014
Metabolism	Branched-chain amino acids induce hyperammonemia via gut-liver axis-mediated ammonia overproduction in laying hens.	Jian H, Xu M, Liu F, Zhang L, Huang Q, Ma J, Zou X, Dong X.	Anim Nutr	10.1016/j.aninu.2025.03.012	2025
	Oral exposure to Staphylococcus aureus enterotoxin B could promote the Ovalbumin-induced food allergy by enhancing the activation of DCs and T cells.	Yuan J, Tong P, Meng X, Wu Y, Li X, Gao J, Chen H.	Front Immunol	10.3389/fimmu.2023.1250458	2023
	Spontaneous cholecystopleural fistula leading to biliothorax and sepsis in a cat.	VanDeventer GM, Cuq BY.	JFMS Open Rep	10.1177/2055116919830206	2019
	The Gut Microbiome Is Associated With Therapeutic Responses and Toxicities of Neoadjuvant Chemoradiotherapy in Rectal Cancer Patients-A Pilot Study.	Shi W, Shen L, Zou W, Wang J, Yang J, Wang Y, Liu B, Liu B, Xie L, Zhu J, Zhang Z.	Front Cell Infect Microbiol	10.3389/fcimb.2020.562463	2020
Pathogenicity	Gut microbiota composition is associated with disease severity and host immune responses in COVID-19.	Fan R, Liu S, Sun N, Yang Y, Deng X, Hu B, Sun C, Wen C, Li H, Cheng D, Huang C, Hou P, Zhang T.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1274690	2023
	Gut Microbiota and Host Cometabolism Are Altered by Patiromer-Induced Changes in Serum and Stool Potassium.	Gao B, Friedman ES, Regunathan R, Shrivastava A, Barrows IR, Amdur RL, Andrews SC, Barrows ED, Raj DS.	Kidney Int Rep	10.1016/j.ekir.2020.12.026	2021
	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
Genetics	Study protocol for FIBROKIT: a new tool for fibromyalgia diagnosis and patient follow-up.	Del Amo LL, Duran-Gonzalez E, Ramirez-Tejero JA, Martinez-Lara A, Cotan D.	Front Neurol	10.3389/fneur.2023.1286539	2023
Enzymology	Active site flexibility revealed in crystal structures of Parabacteroides merdae beta-glucuronidase from the human gut microbiome.	Little MS, Ervin SM, Walton WG, Tripathy A, Xu Y, Liu J, Redinbo MR.	Protein Sci	10.1002/pro.3507	2018
	Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages.	Shridhar SV, Beghini F, Alexander M, Singh A, Juarez RM, Brito IL, Christakis NA.	Cell Rep	10.1016/j.celrep.2024.114442	2024
	Targeting the Gut Microbiota in Coronavirus Disease 2019: Hype or Hope?	Lau HC, Ng SC, Yu J.	Gastroenterology	10.1053/j.gastro.2021.09.009	2022
	Features of combined gut bacteria and fungi from a Chinese cohort of colorectal cancer, colorectal adenoma, and post-operative patients.	Li X, Feng J, Wang Z, Liu G, Wang F.	Front Microbiol	10.3389/fmicb.2023.1236583	2023
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 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
Pathogenicity	The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.	Chandrasekaran P, Krausz M, Han Y, Mitsuiki N, Gabrysch A, Noltner C, Proietti M, Heller T, Grou C, Calderon V, Subramanian P, Jones DR, Siu Y, Deming C, Conlan S, Holland SM, Segre JA, Uzel G, Grimbacher B, Falcone EL.	Microbiome	10.1186/s40168-025-02028-7	2025
	Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.	White MG, Damania A, Alshenaifi J, Sahasrabhojane P, Peacock O, Losh J, Wong MC, Lutter-Berkova Z, Chang GJ, Futreal A, Wargo JA, Ajami NJ, Kopetz S, You YN.	Ann Surg	10.1097/sla.0000000000006015	2023
	Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism.	Hu X, Xia K, Dai M, Han X, Yuan P, Liu J, Liu S, Jia F, Chen J, Jiang F, Yu J, Yang H, Wang J, Xu X, Jin X, Kristiansen K, Xiao L, Chen W, Han M, Duan S.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00386-4	2023
	Gut microbiota-metabolite interactions meditate the effect of dietary patterns on precocious puberty.	Wang Y, Jin C, Li H, Liang X, Zhao C, Wu N, Yue M, Zhao L, Yu H, Wang Q, Ge Y, Huo M, Lv X, Zhang L, Zhao G, Gai Z.	iScience	10.1016/j.isci.2024.109887	2024
Pathogenicity	Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression.	Zhao SS, Chen L, Yang J, Wu ZH, Wang XY, Zhang Q, Liu WJ, Liu HX.	Microbiol Spectr	10.1128/spectrum.02612-22	2022
	The effect of intestinal flora on immune checkpoint inhibitors in tumor treatment: a narrative review.	Wang D, Hao H, Li X, Wang Z.	Ann Transl Med	10.21037/atm-20-4535	2020
Genetics	Involvement of Gut Microbiota in Schizophrenia and Treatment Resistance to Antipsychotics.	Manchia M, Fontana A, Panebianco C, Paribello P, Arzedi C, Cossu E, Garzilli M, Montis MA, Mura A, Pisanu C, Congiu D, Copetti M, Pinna F, Pazienza V, Squassina A, Carpiniello B.	Biomedicines	10.3390/biomedicines9080875	2021
	The key players of inflammasomes and pyroptosis in sepsis-induced pathogenesis and organ dysfunction	Zhu L, Hu M, Xu H, Xu H, Ren B, Xu R, Guo M, Chen H, Zhang D, Fang H.	Front Pharmacol		2025
Genetics	Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.	Park S, Zhang T, Kang S.	Int J Mol Sci	10.3390/ijms24119533	2023
	Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense.	Dunn KA, MacDonald T, Rodrigues GJ, Forbrigger Z, Bielawski JP, Langille MGI, Van Limbergen J, Kulkarni K.	Front Cell Infect Microbiol	10.3389/fcimb.2022.924707	2022
	Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator.	Salazar J, Duran P, Diaz MP, Chacin M, Santeliz R, Mengual E, Gutierrez E, Leon X, Diaz A, Bernal M, Escalona D, Hernandez LAP, Bermudez V.	Int J Environ Res Public Health	10.3390/ijerph20105845	2023
	Ketogenic Diet and Epilepsy.	Ulamek-Koziol M, Czuczwar SJ, Januszewski S, Pluta R.	Nutrients	10.3390/nu11102510	2019
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
	Exploring the interaction between the gut microbiota and cyclic adenosine monophosphate-protein kinase A signaling pathway: a potential therapeutic approach for neurodegenerative diseases.	Deng F, Yang D, Qing L, Chen Y, Zou J, Jia M, Wang Q, Jiang R, Huang L.	Neural Regen Res	10.4103/nrr.nrr-d-24-00607	2025
	A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage.	Li T, Ding N, Guo H, Hua R, Lin Z, Tian H, Yu Y, Fan D, Yuan Z, Gonzalez FJ, Wu Y.	Cell Host Microbe	10.1016/j.chom.2023.12.015	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
	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
Phylogeny	Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder.	Xu Y, Wang Y, Xu J, Song Y, Liu B, Xiong Z.	Microbiol Spectr	10.1128/spectrum.00331-22	2022
	Anti-Obesity Effects of Traditional and Commercial Kochujang in Overweight and Obese Adults: A Randomized Controlled Trial.	Han AL, Jeong SJ, Ryu MS, Yang HJ, Jeong DY, Park DS, Lee HK.	Nutrients	10.3390/nu14142783	2022
	The Local Microbiome in Esophageal Cancer and Treatment Response: A Review of Emerging Data and Future Directions.	Pandey A, Lieu CH, Kim SS.	Cancers (Basel)	10.3390/cancers15143562	2023
	Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing.	Mankowska-Wierzbicka D, Zuraszek J, Wierzbicka A, Gabryel M, Mahadea D, Baturo A, Zakerska-Banaszak O, Slomski R, Skrzypczak-Zielinska M, Dobrowolska A.	Biomedicines	10.3390/biomedicines11020367	2023
Phylogeny	Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.	Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE.	Cell Host Microbe	10.1016/j.chom.2024.08.016	2024
	Association of Gut Microbial Dysbiosis and Hypertension: A Systematic Review.	Naik SS, Ramphall S, Rijal S, Prakash V, Ekladios H, Mulayamkuzhiyil Saju J, Mandal N, Kham NI, Shahid R, Venugopal S.	Cureus	10.7759/cureus.29927	2022
Metabolism	Gut microbiota dysbiosis in Chinese children with type 1 diabetes mellitus: An observational study.	Liu X, Cheng YW, Shao L, Sun SH, Wu J, Song QH, Zou HS, Ling ZX.	World J Gastroenterol	10.3748/wjg.v27.i19.2394	2021
	Gut Metagenome as a Potential Diagnostic and Predictive Biomarker in Slow Transit Constipation.	Tian H, Ye C, Yang B, Cui J, Zheng Z, Wu C, Zhou S, Lv X, Qin N, Qin H, Li N, Chen Q.	Front Med (Lausanne)	10.3389/fmed.2021.777961	2021
Phylogeny	Maternal microbiota and gestational diabetes: impact on infant health.	Singh P, Elhaj DAI, Ibrahim I, Abdullahi H, Al Khodor S.	J Transl Med	10.1186/s12967-023-04230-3	2023
	Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities.	Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M.	Microb Biotechnol	10.1111/1751-7915.14509	2024
	The gut microbiome regulates the clinical efficacy of sulfasalazine therapy for IBD-associated spondyloarthritis.	Lima SF, Pires S, Rupert A, Oguntunmibi S, Jin WB, Marderstein A, Funez-dePagnier G, Maldarelli G, Viladomiu M, Putzel G, Yang W, Tran N, Xiang G, Grier A, Guo CJ, Lukin D, Mandl LA, Scherl EJ, Longman RS.	Cell Rep Med	10.1016/j.xcrm.2024.101431	2024
	Evaluating Effects of Antibiotics Across Preclinical Models of the Human Gastrointestinal Microbiota.	Auchtung TA, Lerma AI, Schuchart K, Auchtung JM.	Microbiologyopen	10.1002/mbo3.70030	2025
	Regulatory Effects of Combined Dietary Supplementation With Essential Oils and Organic Acids on Microbial Communities of Cobb Broilers.	Qiao J, Shang Z, Liu X, Wang K, Wu Z, Wei Q, Li H.	Front Microbiol	10.3389/fmicb.2021.814626	2021
	The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection.	Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1335450	2024
	Carrot RG-I Reduces Interindividual Differences between 24 Adults through Consistent Effects on Gut Microbiota Composition and Function Ex Vivo.	Van den Abbeele P, Deyaert S, Albers R, Baudot A, Mercenier A.	Nutrients	10.3390/nu15092090	2023
	Microbial colonization programs are structured by breastfeeding and guide healthy respiratory development.	Shenhav L, Fehr K, Reyna ME, Petersen C, Dai DLY, Dai R, Breton V, Rossi L, Smieja M, Simons E, Silverman MA, Levy M, Bode L, Field CJ, Marshall JS, Moraes TJ, Mandhane PJ, Turvey SE, Subbarao P, Surette MG, Azad MB.	Cell	10.1016/j.cell.2024.07.022	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
	Gut Microbiome as Potential Therapeutics in Multiple Sclerosis.	Zhu W, Dykstra K, Zhang L, Xia Z.	Curr Treat Options Neurol	10.1007/s11940-021-00693-1	2021
Enzymology	First report of Parabacteroides goldsteinii bacteraemia in a patient with complicated intra-abdominal infection.	Awadel-Kariem FM, Patel P, Kapoor J, Brazier JS, Goldstein EJ.	Anaerobe	10.1016/j.anaerobe.2010.01.001	2010
	The impact of gut microbiome enterotypes on ulcerative colitis: identifying key bacterial species and revealing species co-occurrence networks using machine learning.	Wu X, Zhang T, Zhang T, Park S.	Gut Microbes	10.1080/19490976.2023.2292254	2024
	Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients - A recent literature survey.	Ziegler S, Bereswill S, Heimesaat MM.	Eur J Microbiol Immunol (Bp)	10.1556/1886.2022.00017	2022
	A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers.	Xu J, Zheng Z, Yang L, Li R, Ma X, Zhang J, Yin F, Liu L, Xu Q, Shen Q, Shen X, Wu C, Liu J, Qin N, Sheng J, Jin P, Jin P.	Cell Biosci	10.1186/s13578-022-00940-1	2022
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
	Yoyo Dieting, Post-Obesity Weight Loss, and Their Relationship with Gut Health.	Phuong-Nguyen K, McGee SL, Aston-Mourney K, Mcneill BA, Mahmood MQ, Rivera LR.	Nutrients	10.3390/nu16183170	2024
Pathogenicity	A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study.	Ahrens AP, Culpepper T, Saldivar B, Anton S, Stoll S, Handberg EM, Xu K, Pepine C, Triplett EW, Aggarwal M.	Nutrients	10.3390/nu13103459	2021
	Effects of wearing personal protective equipment during COVID-19 pandemic on composition and diversity of skin bacteria and fungi of medical workers.	Lin X, Li YZ, Chen T, Min SH, Wang DF, Ding MM, Jiang G.	J Eur Acad Dermatol Venereol	10.1111/jdv.18216	2022
	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
Genetics	Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands.	Quaiser A, Dufresne A, Ballaud F, Roux S, Zivanovic Y, Colombet J, Sime-Ngando T, Francez AJ.	Front Microbiol	10.3389/fmicb.2015.00375	2015
	The Effect of Multiprobiotics on Memory and Attention in Fibromyalgia: A Pilot Randomized Controlled Trial.	Cardona D, Roman P, Canadas F, Sanchez-Labraca N.	Int J Environ Res Public Health	10.3390/ijerph18073543	2021
	Changes in the Gut Microbiota are Associated with Hypertension, Hyperlipidemia, and Type 2 Diabetes Mellitus in Japanese Subjects.	Takagi T, Naito Y, Kashiwagi S, Uchiyama K, Mizushima K, Kamada K, Ishikawa T, Inoue R, Okuda K, Tsujimoto Y, Ohnogi H, Itoh Y.	Nutrients	10.3390/nu12102996	2020
	Active bacterial communities of pig fecal microbiota transplantation suspension prepared and preserved under different conditions.	Lin C, Wan J, Lu Y, Zhang H, Chen X, Su Y, Zhu W.	AMB Express	10.1186/s13568-019-0787-4	2019
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
	Obesity, Gut Microbiota, and Metabolome: From Pathophysiology to Nutritional Interventions.	Puljiz Z, Kumric M, Vrdoljak J, Martinovic D, Ticinovic Kurir T, Krnic MO, Urlic H, Puljiz Z, Zucko J, Dumanic P, Mikolasevic I, Bozic J.	Nutrients	10.3390/nu15102236	2023
	Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota.	Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L.	iScience	10.1016/j.isci.2024.110093	2024
	Protective Effect of Vegan Microbiota on Liver Steatosis Is Conveyed by Dietary Fiber: Implications for Fecal Microbiota Transfer Therapy.	Daskova N, Heczkova M, Modos I, Hradecky J, Hudcovic T, Kuzma M, Pelantova H, Buskova I, Sticova E, Funda D, Golias J, Drabonova B, Jarkovska J, Kralova M, Cibulkova I, Gojda J, Cahova M.	Nutrients	10.3390/nu15020454	2023
	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
	Gut Microbiota Perturbation in Early Life Could Influence Pediatric Blood Pressure Regulation in a Sex-Dependent Manner in Juvenile Rats.	Yang Y, Li J, Zhou Z, Wu S, Zhao J, Jia W, Liu M, Shen X, He F, Cheng R.	Nutrients	10.3390/nu15122661	2023
	A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial.	Wu X, Tjahyo AS, Volchanskaya VSB, Wong LH, Lai X, Yong YN, Osman F, Tay SL, Govindharajulu P, Ponnalagu S, Tso R, Teo HS, Khoo K, Fan H, Goh CC, Yap CPL, Leow MK, Henry CJ, Haldar S, Lim KJ.	Nat Commun	10.1038/s41467-025-56084-6	2025
	Multiple Enzymes Expressed by the Gut Microbiota Can Transform Typhaneoside and Are Associated with Improving Hyperlipidemia.	Xu H, Feng R, Ye ML, Hu JC, Lu JY, Wang JY, Zuo HT, Zhao Y, Song JY, Jiang JD, Zhou YZ, Wang Y.	Adv Sci (Weinh)	10.1002/advs.202411770	2025
	The Gut Microbiome May Help Address Mental Health Disparities in Hispanics: A Narrative Review.	Vera-Urbina F, Dos Santos-Torres MF, Godoy-Vitorino F, Torres-Hernandez BA.	Microorganisms	10.3390/microorganisms10040763	2022
	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
Pathogenicity	Influence of Short-Term Consumption of Hericium erinaceus on Serum Biochemical Markers and the Changes of the Gut Microbiota: A Pilot Study.	Xie XQ, Geng Y, Guan Q, Ren Y, Guo L, Lv Q, Lu ZM, Shi JS, Xu ZH.	Nutrients	10.3390/nu13031008	2021
Phylogeny	Alterations of the Gut Microbiome in Hypertension.	Yan Q, Gu Y, Li X, Yang W, Jia L, Chen C, Han X, Huang Y, Zhao L, Li P, Fang Z, Zhou J, Guan X, Ding Y, Wang S, Khan M, Xin Y, Li S, Ma Y.	Front Cell Infect Microbiol	10.3389/fcimb.2017.00381	2017
	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
	Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.	Zhu H, Li M, Bi D, Yang H, Gao Y, Song F, Zheng J, Xie R, Zhang Y, Liu H, Yan X, Kong C, Zhu Y, Xu Q, Wei Q, Qin H.	Nat Commun	10.1038/s41467-024-45572-w	2024
	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
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
	Microbiota from Specific Pathogen-Free Mice Reduces Campylobacter jejuni Chicken Colonization.	Almansour A, Fu Y, Alenezi T, Bansal M, Alrubaye B, Wang H, Sun X.	Pathogens	10.3390/pathogens10111387	2021
	Transcriptome and Gut Microbiota Profiling Revealed the Protective Effect of Tibetan Tea on Ulcerative Colitis in Mice.	Wang N, Wu T, Du D, Mei J, Luo H, Liu Z, Saleemi MK, Zhang R, Chang C, Mehmood MA, Zhu H.	Front Microbiol	10.3389/fmicb.2021.748594	2021
	Molecular characterization of alterations in the intestinal microbiota of patients with grade 3 hypertension.	Mushtaq N, Hussain S, Zhang S, Yuan L, Li H, Ullah S, Wang Y, Xu J.	Int J Mol Med	10.3892/ijmm.2019.4235	2019
Metabolism	Lactobacillus casei Zhang and vitamin K2 prevent intestinal tumorigenesis in mice via adiponectin-elevated different signaling pathways.	Zhang Y, Ma C, Zhao J, Xu H, Hou Q, Zhang H.	Oncotarget	10.18632/oncotarget.15791	2017
Genetics	Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages.	Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Popova A, Kulikov E, Shneider M, Ignatov A, Miroshnikov K.	Int J Mol Sci	10.3390/ijms24021586	2023
	Nutritional Therapy Modulates Intestinal Microbiota and Reduces Serum Levels of Total and Free Indoxyl Sulfate and P-Cresyl Sulfate in Chronic Kidney Disease (Medika Study).	Di Iorio BR, Rocchetti MT, De Angelis M, Cosola C, Marzocco S, Di Micco L, di Bari I, Accetturo M, Vacca M, Gobbetti M, Di Iorio M, Bellasi A, Gesualdo L.	J Clin Med	10.3390/jcm8091424	2019
	The Gut Microbiota in Parkinson Disease: Interactions with Drugs and Potential for Therapeutic Applications.	Menozzi E, Schapira AHV.	CNS Drugs	10.1007/s40263-024-01073-4	2024
	SARS-CoV-2 infection elucidates features of pregnancy-specific immunity.	Oh DS, Kim E, Normand R, Lu G, Shook LL, Lyall A, Jasset O, Demidkin S, Gilbert E, Kim J, Akinwunmi B, Tantivit J, Tirard A, Arnold BY, Slowikowski K, MGH COVID-19 Collection & Processing Team, Goldberg MB, Filbin MR, Hacohen N, Nguyen LH, Chan AT, Yu XG, Li JZ, Yonker L, Fasano A, Perlis RH, Pasternak O, Gray KJ, Choi GB, Drew DA, Sen P, Villani AC, Edlow AG, Huh JR.	Cell Rep	10.1016/j.celrep.2024.114933	2024
	How important are fatty acids in human health and can they be used in treating diseases?	Dicks LMT.	Gut Microbes	10.1080/19490976.2024.2420765	2024
	Antibiotics are associated with decreased progression-free survival of advanced melanoma patients treated with immune checkpoint inhibitors.	Elkrief A, El Raichani L, Richard C, Messaoudene M, Belkaid W, Malo J, Belanger K, Miller W, Jamal R, Letarte N, Wong P, Routy B.	Oncoimmunology	10.1080/2162402x.2019.1568812	2019
Enzymology	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.	McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC.	J Biol Chem	10.1074/jbc.m115.706143	2016
Enzymology	Markers Specific to Bacteroides fragilis Group Bacteria as Indicators of Anthropogenic Pollution of Surface Waters.	Niestepski S, Harnisz M, Korzeniewska E, Osinska A.	Int J Environ Res Public Health	10.3390/ijerph17197137	2020
	Gut microbiota profile of COVID-19 patients: Prognosis and risk stratification (MicroCOVID-19 study).	Nobre JG, Delgadinho M, Silva C, Mendes J, Mateus V, Ribeiro E, Costa DA, Lopes M, Pedroso AI, Trigueiros F, Rodrigues MI, de Sousa CL, Brito M.	Front Microbiol	10.3389/fmicb.2022.1035422	2022
Genetics	Human Gut Metagenomes Encode Diverse GH156 Sialidases.	Mann E, Shekarriz S, Surette MG.	Appl Environ Microbiol	10.1128/aem.01755-22	2022
	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
Metabolism	Dynamic Alterations of the Gut Microbial Pyrimidine and Purine Metabolism in the Development of Liver Cirrhosis.	Xiong Y, Wu L, Shao L, Wang Y, Huang Z, Huang X, Li C, Wu A, Liu Z, Fan X, Zhou P.	Front Mol Biosci	10.3389/fmolb.2021.811399	2021
Phylogeny	Far infrared radiation induces changes in gut microbiota and activates GPCRs in mice.	Khan I, Pathan S, Li XA, Leong WK, Liao WL, Wong V, Hsiao WLW.	J Adv Res	10.1016/j.jare.2019.12.003	2020
	Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients.	Marfil-Sanchez A, Seelbinder B, Ni Y, Varga J, Berta J, Hollosi V, Dome B, Megyesfalvi Z, Dulka E, Galffy G, Weiss GJ, Panagiotou G, Lohinai Z.	PLoS One	10.1371/journal.pone.0259898	2021
	Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.	Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP.	Nat Commun	10.1038/s41467-024-50124-3	2024
	Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data.	Guo M, Xu E, Ai D.	Front Genet	10.3389/fgene.2019.00213	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
Enzymology	Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria.	Roncase EJ, Moon C, Chatterjee S, Gonzalez-Paez GE, Craik CS, O'Donoghue AJ, Wolan DW.	ACS Chem Biol	10.1021/acschembio.7b00143	2017
	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
	The Antidepressant Effect of Deoiled Sunflower Seeds on Chronic Unpredictable Mild Stress in Mice Through Regulation of Microbiota-Gut-Brain Axis.	Lu X, Qi C, Zheng J, Sun M, Jin L, Sun J.	Front Nutr	10.3389/fnut.2022.908297	2022
	Human gut microbiome: Therapeutic opportunities for metabolic syndrome-Hype or hope?	Horvath A, Zukauskaite K, Hazia O, Balazs I, Stadlbauer V.	Endocrinol Diabetes Metab	10.1002/edm2.436	2024
	Evidence for the Beneficial Effects of Brazilian Native Fruits and Their By-Products on Human Intestinal Microbiota and Repercussions on Non-Communicable Chronic Diseases-A Review.	Lima MDC, do Nascimento HMA, da Silva JYP, de Brito Alves JL, de Souza EL.	Foods	10.3390/foods12183491	2023
	Longevity-Associated Core Gut Microbiota Mining and Effect of Mediated Probiotic Combinations on Aging Mice: Case Study of a Long-Lived Population in Guangxi, China.	Li RD, Zheng WX, Zhang QR, Song Y, Liao YT, Shi FC, Wei XH, Zhou F, Zheng XH, Tan KY, Li QY.	Nutrients	10.3390/nu15071609	2023
	The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease.	Zhong J, Wu D, Zeng Y, Wu G, Zheng N, Huang W, Li Y, Tao X, Zhu W, Sheng L, Shen X, Zhang W, Zhu R, Li H.	Microbiol Spectr	10.1128/spectrum.02467-22	2022
	Vaginal and neonatal microbiota in pregnant women with preterm premature rupture of membranes and consecutive early onset neonatal sepsis.	Dos Anjos Borges LG, Pastuschek J, Heimann Y, Dawczynski K, PEONS study group, Schleussner E, Pieper DH, Zollkau J.	BMC Med	10.1186/s12916-023-02805-x	2023
	Immune Checkpoint Blockade for Advanced NSCLC: A New Landscape for Elderly Patients.	Perrotta F, Rocco D, Vitiello F, De Palma R, Guerra G, De Luca A, Navani N, Bianco A.	Int J Mol Sci	10.3390/ijms20092258	2019
	Illuminating vital surface molecules of symbionts in health and disease.	Hudak JE, Alvarez D, Skelly A, von Andrian UH, Kasper DL.	Nat Microbiol	10.1038/nmicrobiol.2017.99	2017
	Clinical significance of microbiota changes under the influence of psychotropic drugs. An updated narrative review.	Misera A, Loniewski I, Palma J, Kulaszynska M, Czarnecka W, Kaczmarczyk M, Liskiewicz P, Samochowiec J, Skonieczna-Zydecka K.	Front Microbiol	10.3389/fmicb.2023.1125022	2023
	Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection.	Xie G, Zhao B, Wang X, Bao L, Xu Y, Ren X, Ji J, He T, Zhao H.	Infect Dis Ther	10.1007/s40121-021-00476-w	2021
Metabolism	A Soluble Fiber Diet Increases Bacteroides fragilis Group Abundance and Immunoglobulin A Production in the Gut.	Nakajima A, Sasaki T, Itoh K, Kitahara T, Takema Y, Hiramatsu K, Ishikawa D, Shibuya T, Kobayashi O, Osada T, Watanabe S, Nagahara A.	Appl Environ Microbiol	10.1128/aem.00405-20	2020
	Short- and Branched-Chain Fatty Acids as Fecal Markers for Microbiota Activity in Vegans and Omnivores.	Trefflich I, Dietrich S, Braune A, Abraham K, Weikert C.	Nutrients	10.3390/nu13061808	2021
	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
	Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens.	Borrelli L, Coretti L, Dipineto L, Bovera F, Menna F, Chiariotti L, Nizza A, Lembo F, Fioretti A.	Sci Rep	10.1038/s41598-017-16560-6	2017
	Dietary fibre supplementation enhances radiotherapy tumour control and alleviates intestinal radiation toxicity.	Then CK, Paillas S, Moomin A, Misheva MD, Moir RA, Hay SM, Bremner D, Roberts Nee Nellany KS, Smith EE, Heidari Z, Sescu D, Wang X, Suarez-Bonnet A, Hay N, Murdoch SL, Saito R, Collie-Duguid ESR, Richardson S, Priestnall SL, Wilson JM, Gurumurthy M, Royle JS, Samuel LM, Ramsay G, Vallis KA, Foster KR, McCullagh JSO, Kiltie AE.	Microbiome	10.1186/s40168-024-01804-1	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
	2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids.	Vigsnaes LK, Ghyselinck J, Van den Abbeele P, McConnell B, Moens F, Marzorati M, Bajic D.	Pathogens	10.3390/pathogens10080927	2021
Pathogenicity	A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis.	Panah FM, Nielsen KD, Simpson GL, Schonherz A, Schramm A, Lauridsen C, Nielsen TS, Hojberg O, Fredborg M, Purup S, Canibe N.	Front Microbiol	10.3389/fmicb.2023.1018242	2023
	Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis.	Damman CJ, Brittnacher MJ, Westerhoff M, Hayden HS, Radey M, Hager KR, Marquis SR, Miller SI, Zisman TL.	PLoS One	10.1371/journal.pone.0133925	2015
	Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.	Li C, Strazar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ.	Cell	10.1016/j.cell.2024.03.014	2024
Pathogenicity	Analysis of Gut Microbiota in Rheumatoid Arthritis Patients: Disease-Related Dysbiosis and Modifications Induced by Etanercept.	Picchianti-Diamanti A, Panebianco C, Salemi S, Sorgi ML, Di Rosa R, Tropea A, Sgrulletti M, Salerno G, Terracciano F, D'Amelio R, Lagana B, Pazienza V.	Int J Mol Sci	10.3390/ijms19102938	2018
Genetics	Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome.	Yang Z, Fu H, Su H, Cai X, Wang Y, Hong Y, Hu J, Xie Z, Wang X.	Front Microbiol	10.3389/fmicb.2022.1017147	2022
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
	The efficacy of Lacticaseibacillus paracasei MSMC39-1 and Bifidobacterium animalis TA-1 probiotics in modulating gut microbiota and reducing the risk of the characteristics of metabolic syndrome: A randomized, double-blinded, placebo-controlled study.	Luangphiphat W, Prombutara P, Jamjuree P, Chantarangkul C, Vitheejongjaroen P, Muennarong C, Fukfon K, Onwan M, Taweechotipatr M.	PLoS One	10.1371/journal.pone.0317202	2025
Phylogeny	Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children.	Desai C, Handley SA, Rodgers R, Rodriguez C, Ordiz MI, Manary MJ, Holtz LR.	PLoS Negl Trop Dis	10.1371/journal.pntd.0008387	2020
Pathogenicity	Dried yeast cell walls high in beta-glucan and mannan-oligosaccharides positively affect microbial composition and activity in the canine gastrointestinal tract in vitro.	Van den Abbeele P, Duysburgh C, Rakebrandt M, Marzorati M.	J Anim Sci	10.1093/jas/skaa173	2020
	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
Pathogenicity	Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.	Islam SMS, Ryu HM, Sayeed HM, Byun HO, Jung JY, Kim HA, Suh CH, Sohn S.	Front Immunol	10.3389/fimmu.2021.712312	2021
	PNT1 Is a C11 Cysteine Peptidase Essential for Replication of the Trypanosome Kinetoplast.	Grewal JS, McLuskey K, Das D, Myburgh E, Wilkes J, Brown E, Lemgruber L, Gould MK, Burchmore RJ, Coombs GH, Schnaufer A, Mottram JC.	J Biol Chem	10.1074/jbc.m116.714972	2016
	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
Genetics	The Implication of Mechanistic Approaches and the Role of the Microbiome in Polycystic Ovary Syndrome (PCOS): A Review.	Mukherjee AG, Wanjari UR, Kannampuzha S, Murali R, Namachivayam A, Ganesan R, Dey A, Babu A, Renu K, Vellingiri B, Ramanathan G, Priya Doss C G, Elsherbiny N, Elsherbini AM, Alsamman AM, Zayed H, Gopalakrishnan AV.	Metabolites	10.3390/metabo13010129	2023
	Microbiome in Cancer Development and Treatment.	Ciernikova S, Sevcikova A, Mladosievicova B, Mego M.	Microorganisms	10.3390/microorganisms12010024	2023
Metabolism	Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study.	Goris T, Cuadrat RRC, Braune A.	Nutrients	10.3390/nu13082688	2021
	Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.	Thomas AM, Fidelle M, Routy B, Kroemer G, Wargo JA, Segata N, Zitvogel L.	Nat Rev Clin Oncol	10.1038/s41571-023-00785-8	2023
Genetics	Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach.	Barber C, Mego M, Sabater C, Vallejo F, Bendezu RA, Masihy M, Guarner F, Espin JC, Margolles A, Azpiroz F.	Nutrients	10.3390/nu13082638	2021
Phylogeny	Bacterial ecology of abattoir wastewater treated by an anaerobic digestor.	Jabari L, Gannoun H, Khelifi E, Cayol JL, Godon JJ, Hamdi M, Fardeau ML.	Braz J Microbiol	10.1016/j.bjm.2015.11.029	2016
Metabolism	TH1 cell-inducing Escherichia coli strain identified from the small intestinal mucosa of patients with Crohn's disease.	Nagayama M, Yano T, Atarashi K, Tanoue T, Sekiya M, Kobayashi Y, Sakamoto H, Miura K, Sunada K, Kawaguchi T, Morita S, Sugita K, Narushima S, Barnich N, Isayama J, Kiridooshi Y, Shiota A, Suda W, Hattori M, Yamamoto H, Honda K.	Gut Microbes	10.1080/19490976.2020.1788898	2020
Metabolism	Activation Mechanism of the Bacteroides fragilis Cysteine Peptidase, Fragipain.	Herrou J, Choi VM, Bubeck Wardenburg J, Crosson S.	Biochemistry	10.1021/acs.biochem.6b00546	2016
	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
	Degradation of chondroitin sulfate A by a PUL-like operon in Tannerella forsythia.	Nguyen P, Eshaque R, Garland BA, Dang A, Suits MDL.	PLoS One	10.1371/journal.pone.0272904	2022
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
Phylogeny	Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.	Kintses B, Mehi O, Ari E, Szamel M, Gyorkei A, Jangir PK, Nagy I, Pal F, Fekete G, Tengolics R, Nyerges A, Liko I, Balint A, Molnar T, Balint B, Vasarhelyi BM, Bustamante M, Papp B, Pal C.	Nat Microbiol	10.1038/s41564-018-0313-5	2019
	Functional properties of miscanthus fiber and prebiotic blends in extruded canine diets.	Finet S, He F, Clark LV, de Godoy MRC.	J Anim Sci	10.1093/jas/skac078	2022
	Gut Dysbiosis and Western Diet in the Pathogenesis of Essential Arterial Hypertension: A Narrative Review.	Canale MP, Noce A, Di Lauro M, Marrone G, Cantelmo M, Cardillo C, Federici M, Di Daniele N, Tesauro M.	Nutrients	10.3390/nu13041162	2021
	Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma.	Bjork JR, Bolte LA, Maltez Thomas A, Lee KA, Rossi N, Wind TT, Smit LM, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Spector TD, Bataille V, Segata N, Hospers GAP, Weersma RK.	Nat Med	10.1038/s41591-024-02803-3	2024
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
	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
Genetics	Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.	Asnicar F, Manara S, Zolfo M, Truong DT, Scholz M, Armanini F, Ferretti P, Gorfer V, Pedrotti A, Tett A, Segata N.	mSystems	10.1128/msystems.00164-16	2017
	Effects of novel microecologics combined with traditional Chinese medicine and probiotics on growth performance and health of broilers.	Gao J, Wang R, Liu J, Wang W, Chen Y, Cai W.	Poult Sci	10.1016/j.psj.2021.101412	2022
Pathogenicity	Gut Microbiota Markers and Dietary Habits Associated with Extreme Longevity in Healthy Sardinian Centenarians.	Palmas V, Pisanu S, Madau V, Casula E, Deledda A, Cusano R, Uva P, Loviselli A, Velluzzi F, Manzin A.	Nutrients	10.3390/nu14122436	2022
Genetics	Rural environment reduces allergic inflammation by modulating the gut microbiota.	Yang Z, Chen Z, Lin X, Yao S, Xian M, Ning X, Fu W, Jiang M, Li N, Xiao X, Feng M, Lian Z, Yang W, Ren X, Zheng Z, Zhao J, Wei N, Lu W, Roponen M, Schaub B, Wong GWK, Su Z, Wang C, Li J.	Gut Microbes	10.1080/19490976.2022.2125733	2022
Phylogeny	Genotypic diversity of anaerobic isolates from bloodstream infections.	Simmon KE, Mirrett S, Reller LB, Petti CA.	J Clin Microbiol	10.1128/jcm.02469-07	2008
Genetics	Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.	Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C.	Nat Microbiol	10.1038/s41564-017-0089-z	2018
Genetics	Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages.	Jonge PA, Meijenfeldt FABV, Rooijen LEV, Brouns SJJ, Dutilh BE.	Viruses	10.3390/v11121085	2019
	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
Metabolism	Determining the association between fibromyalgia, the gut microbiome and its biomarkers: A systematic review.	Erdrich S, Hawrelak JA, Myers SP, Harnett JE.	BMC Musculoskelet Disord	10.1186/s12891-020-03201-9	2020
	Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro.	Oliphant K, Cochrane K, Schroeter K, Daigneault MC, Yen S, Verdu EF, Allen-Vercoe E.	mSystems	10.1128/msystems.00404-19	2020
	Gut microbial taxa elevated by dietary sugar disrupt memory function.	Noble EE, Olson CA, Davis E, Tsan L, Chen YW, Schade R, Liu C, Suarez A, Jones RB, de La Serre C, Yang X, Hsiao EY, Kanoski SE.	Transl Psychiatry	10.1038/s41398-021-01309-7	2021
	Gut-specific telomerase expression counteracts systemic aging in telomerase-deficient zebrafish.	El Mai M, Bird M, Allouche A, Targen S, Serifoglu N, Lopes-Bastos B, Guigonis JM, Kang D, Pourcher T, Yue JX, Ferreira MG.	Nat Aging	10.1038/s43587-023-00401-5	2023
	Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation.	Bell KJ, Saad S, Tillett BJ, McGuire HM, Bordbar S, Yap YA, Nguyen LT, Wilkins MR, Corley S, Brodie S, Duong S, Wright CJ, Twigg S, de St Groth BF, Harrison LC, Mackay CR, Gurzov EN, Hamilton-Williams EE, Marino E.	Microbiome	10.1186/s40168-021-01193-9	2022
Genetics	Massive expansion of human gut bacteriophage diversity.	Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD.	Cell	10.1016/j.cell.2021.01.029	2021
	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
Genetics	A human gut bacterial genome and culture collection for improved metagenomic analyses.	Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD.	Nat Biotechnol	10.1038/s41587-018-0009-7	2019
	Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.	Meslier V, Laiola M, Roager HM, De Filippis F, Roume H, Quinquis B, Giacco R, Mennella I, Ferracane R, Pons N, Pasolli E, Rivellese A, Dragsted LO, Vitaglione P, Ehrlich SD, Ercolini D.	Gut	10.1136/gutjnl-2019-320438	2020
Phylogeny	Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.	Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M, Lipkin WI.	Microbiome	10.1186/s40168-017-0261-y	2017
	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
Metabolism	An Atlas of beta-Glucuronidases in the Human Intestinal Microbiome.	Pollet RM, D'Agostino EH, Walton WG, Xu Y, Little MS, Biernat KA, Pellock SJ, Patterson LM, Creekmore BC, Isenberg HN, Bahethi RR, Bhatt AP, Liu J, Gharaibeh RZ, Redinbo MR.	Structure	10.1016/j.str.2017.05.003	2017
	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
	Nanomedicine to modulate immunotherapy in cutaneous melanoma (Review).	Volovat SR, Negru S, Stolniceanu CR, Volovat C, Lungulescu C, Scripcariu D, Cobzeanu BM, Stefanescu C, Grigorescu C, Augustin I, Lupascu Ursulescu C, Volovat CC.	Exp Ther Med	10.3892/etm.2021.9967	2021
Phylogeny	Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.	Jiang X, Hall AB, Xavier RJ, Alm EJ.	PLoS One	10.1371/journal.pone.0223680	2019
Metabolism	High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.	Creswell R, Tan J, Leff JW, Brooks B, Mahowald MA, Thieroff-Ekerdt R, Gerber GK.	Genome Med	10.1186/s13073-020-00758-x	2020
	Alisol B 23-acetate attenuates CKD progression by regulating the renin-angiotensin system and gut-kidney axis.	Chen H, Wang MC, Chen YY, Chen L, Wang YN, Vaziri ND, Miao H, Zhao YY.	Ther Adv Chronic Dis	10.1177/2040622320920025	2020
	Intestinal microbiota composition of interleukin-10 deficient C57BL/6J mice and susceptibility to Helicobacter hepaticus-induced colitis.	Yang I, Eibach D, Kops F, Brenneke B, Woltemate S, Schulze J, Bleich A, Gruber AD, Muthupalani S, Fox JG, Josenhans C, Suerbaum S.	PLoS One	10.1371/journal.pone.0070783	2013
Phylogeny	Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.	Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C.	Genome Med	10.1186/s13073-016-0271-6	2016
Pathogenicity	Probiotic-directed modulation of gut microbiota is basal microbiome dependent.	Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H.	Gut Microbes	10.1080/19490976.2020.1736974	2020
Genetics	Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome.	Madi N, Chen D, Wolff R, Shapiro BJ, Garud NR.	Elife	10.7554/elife.78530	2023
	SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota.	Sokol H, Contreras V, Maisonnasse P, Desmons A, Delache B, Sencio V, Machelart A, Brisebarre A, Humbert L, Deryuter L, Gauliard E, Heumel S, Rainteau D, Dereuddre-Bosquet N, Menu E, Ho Tsong Fang R, Lamaziere A, Brot L, Wahl C, Oeuvray C, Rolhion N, Van Der Werf S, Ferreira S, Le Grand R, Trottein F.	Gut Microbes	10.1080/19490976.2021.1893113	2021
	Elevated systemic antibodies towards commensal gut microbiota in autoinflammatory condition.	Manukyan GP, Ghazaryan KA, Ktsoyan ZA, Khachatryan ZA, Arakelova KA, Kelly D, Grant G, Aminov RI.	PLoS One	10.1371/journal.pone.0003172	2008
Metabolism	Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities.	Soto-Martin EC, Warnke I, Farquharson FM, Christodoulou M, Horgan G, Derrien M, Faurie JM, Flint HJ, Duncan SH, Louis P.	mBio	10.1128/mbio.00886-20	2020
	Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease.	Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, Singh N, Damman CJ, Hager KR, Nielson H, Miller SI.	Inflamm Bowel Dis	10.1097/mib.0000000000000307	2015
	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
Genetics	Dietary modulation of the gut microbiota--a randomised controlled trial in obese postmenopausal women.	Brahe LK, Le Chatelier E, Prifti E, Pons N, Kennedy S, Blaedel T, Hakansson J, Dalsgaard TK, Hansen T, Pedersen O, Astrup A, Ehrlich SD, Larsen LH.	Br J Nutr	10.1017/s0007114515001786	2015
	Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease.	Douglas GM, Hansen R, Jones CMA, Dunn KA, Comeau AM, Bielawski JP, Tayler R, El-Omar EM, Russell RK, Hold GL, Langille MGI, Van Limbergen J.	Microbiome	10.1186/s40168-018-0398-3	2018
	Current Perspectives On The Role Of The Ketogenic Diet In Epilepsy Management.	Goswami JN, Sharma S.	Neuropsychiatr Dis Treat	10.2147/ndt.s201862	2019
	Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota?	Brahe LK, Astrup A, Larsen LH.	Adv Nutr	10.3945/an.115.010587	2016
Metabolism	Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy.	Iebba V, Guerrieri F, Di Gregorio V, Levrero M, Gagliardi A, Santangelo F, Sobolev AP, Circi S, Giannelli V, Mannina L, Schippa S, Merli M.	Sci Rep	10.1038/s41598-018-26509-y	2018
	The Landscape of Nanovectors for Modulation in Cancer Immunotherapy.	Volovat SR, Ursulescu CL, Moisii LG, Volovat C, Boboc D, Scripcariu D, Amurariti F, Stefanescu C, Stolniceanu CR, Agop M, Lungulescu C, Volovat CC.	Pharmaceutics	10.3390/pharmaceutics14020397	2022
Genetics	Baseline human gut microbiota profile in healthy people and standard reporting template.	King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R.	PLoS One	10.1371/journal.pone.0206484	2019
	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
Enzymology	Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase.	Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA.	Mol Biochem Parasitol	10.1016/j.molbiopara.2014.01.003	2014
	Gut-educated IgA plasma cells defend the meningeal venous sinuses.	Fitzpatrick Z, Frazer G, Ferro A, Clare S, Bouladoux N, Ferdinand J, Tuong ZK, Negro-Demontel ML, Kumar N, Suchanek O, Tajsic T, Harcourt K, Scott K, Bashford-Rogers R, Helmy A, Reich DS, Belkaid Y, Lawley TD, McGavern DB, Clatworthy MR.	Nature	10.1038/s41586-020-2886-4	2020
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
	Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis.	Alipour M, Zaidi D, Valcheva R, Jovel J, Martinez I, Sergi C, Walter J, Mason AL, Wong GK, Dieleman LA, Carroll MW, Huynh HQ, Wine E.	J Crohns Colitis	10.1093/ecco-jcc/jjv223	2016
Metabolism	Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies.	Kitada Y, Muramatsu K, Toju H, Kibe R, Benno Y, Kurihara S, Matsumoto M.	Sci Adv	10.1126/sciadv.aat0062	2018
Metabolism	Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases.	Biernat KA, Pellock SJ, Bhatt AP, Bivins MM, Walton WG, Tran BNT, Wei L, Snider MC, Cesmat AP, Tripathy A, Erie DA, Redinbo MR.	Sci Rep	10.1038/s41598-018-36069-w	2019
Metabolism	Structural basis of the proteolytic and chaperone activity of Chlamydia trachomatis CT441.	Kohlmann F, Shima K, Hilgenfeld R, Solbach W, Rupp J, Hansen G.	J Bacteriol	10.1128/jb.02140-14	2015
Phylogeny	Mining the Human Gut Microbiota for Immunomodulatory Organisms.	Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, Yanortsang TB, Yang L, Jupp R, Mathis D, Benoist C, Kasper DL.	Cell	10.1016/j.cell.2017.01.022	2017
	Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans.	Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S.	Cell	10.1016/j.cell.2020.09.009	2020
Phylogeny	Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.	Li ZP, Liu HL, Li GY, Bao K, Wang KY, Xu C, Yang YF, Yang FH, Wright AD.	BMC Microbiol	10.1186/1471-2180-13-151	2013
Phylogeny	Influence of wet distillers grains diets on beef cattle fecal bacterial community structure.	Rice WC, Galyean ML, Cox SB, Dowd SE, Cole NA.	BMC Microbiol	10.1186/1471-2180-12-25	2012
Metabolism	Allelic variation in a simple sequence repeat element of neisserial pglB2 and its consequences for protein expression and protein glycosylation.	Viburiene R, Vik A, Koomey M, Borud B.	J Bacteriol	10.1128/jb.00276-13	2013
	Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice.	Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK.	Cell	10.1016/j.cell.2019.05.004	2019
	Fecal Microbiota Transplantation in Neurological Disorders.	Vendrik KEW, Ooijevaar RE, de Jong PRC, Laman JD, van Oosten BW, van Hilten JJ, Ducarmon QR, Keller JJ, Kuijper EJ, Contarino MF.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00098	2020
	Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD.	Gut Pathog	10.1186/1757-4749-5-8	2013
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
Phylogeny	Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.	Sakamoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64192-0	2006
Enzymology	Detection of Bacteroides fragilis in clinical specimens by polymerase chain reaction amplification of the neuraminidase gene.	Jotwani R, Kato N, Kato H, Watanabe K, Ueno K	Curr Microbiol	10.1007/BF00298376	1995
Enzymology	Taxonogenomics description of Parabacteroides timonensis sp. nov. isolated from a human stool sample.	Bilen M, Mbogning Fonkou MD, Khelaifia S, Tomei E, Cadoret F, Daoud Z, Armstrong N, Bittar F, Fournier PE, Raoult D, Dubourg G.	Microbiologyopen	10.1002/mbo3.702	2019
Genetics	Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.	Togo AH, Diop A, Dubourg G, Nguyen TT, Andrieu C, Caputo A, Couderc C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2016.07.010	2016
Phylogeny	Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters.	Jabari L, Gannoun H, Cayol JL, Hedi A, Sakamoto M, Falsen E, Ohkuma M, Hamdi M, Fauque G, Ollivier B, Fardeau ML.	Int J Syst Evol Microbiol	10.1099/ijs.0.032508-0	2012
Phylogeny	Parabacteroides pekinense sp. nov.: a new bacterium isolated from the stool of a healthy man living in China.	Li Z, Zhou X, Xu W, Chen R, Zhao B, Wu C	New Microbes New Infect	10.1016/j.nmni.2022.100973	2022
Phylogeny	Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen.	Bellali S, Lo CI, Naud S, Fonkou MDM, Armstrong N, Raoult D, Fournier PE, Fenollar F	New Microbes New Infect	10.1016/j.nmni.2019.100602	2019
Phylogeny	Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces.	Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.050146-0	2013
Phylogeny	Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill.	Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M, Zhu XF	Int J Syst Evol Microbiol	10.1099/ijs.0.038000-0	2011
Phylogeny	Parabacteroides johnsonii sp. nov., isolated from human faeces.	Sakamoto M, Kitahara M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64588-0	2007
Phylogeny	"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.	Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SM	J Clin Microbiol	10.1128/JCM.43.9.4522-4527.2005	2005

References

#8118	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19495
#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 )
#34044	; Curators of the CIP;
#54425	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38734
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#120896	Collection of Institut Pasteur ; Curators of the CIP; CIP 104202
#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 )

Rate our new design

Content

About us

Parabacteroides merdae (DSM 19495, ATCC 43184, CCUG 38734)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025151215

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media