Blautia producta (DSM 2950, ATCC 27340, CCUG 10976)

Name: Blautia producta (DSM 2950, ATCC 27340, CCUG 10976)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18068

Type strain

Strain Designation 2396

Culture col. no. DSM 2950 ATCC 27340 CCUG 10976 CCUG 9990 JCM 1471 6 more

NCBI tax ID(s) 1121114 33035

Special Collections DSMZ CCUG JCM KCTC

History DSMZ <- ATCC <- W.E.C. Moore, VPI 4299 <- A. Prévot, 2396 JCM <-- T. Mitsuoka S10-45. KCTC <- DSM <- ATCC <- WEC Moore, VPI 4299 <- A Prevot, 2396

Links

Blautia producta 2396 is an anaerobe, Gram-positive bacterium that was isolated from human septicemia.

Gram-positive anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 38945

KCTC 15607,ATCC 27340,CCUG 9990,CCUG 10976,DSM 2950,JCM 1471,KCTC 3242,KCTC 3695,NCTC 11829,VTT E-052786

@ref 20215

Last LPSN update 2026-05-29 08:29:10

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Blautia

Species Blautia producta

Full scientific name Blautia producta (Prévot 1941) Liu et al. 2008

Synonyms (5)

Peptostreptococcus productus
Ruminococcus productus
Clostridium coccoides
Blautia coccoides
"Streptococcus productus"

BacDive ID	Other strains from **Blautia producta** (3)	Type strain
18069	B. producta U-1, DSM 3507, ATCC 35244
18070	B. producta CS3Glu, DSM 14466
149907	B. producta CCUG 38656

Morphology

Cell morphology

67771

Gram stainpositive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1258	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
1258	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

Culture temp

@ref	Growth	Type	Temperature (°C)
1258	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1258	anaerobe
67771	anaerobe
125439	obligate anaerobe	98.787

Murein

@ref	Murein short key	Type
1258	A31	A1gamma m-Dpm-direct

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68375	22599 ChEBI	arabinose	-	fermentation	from API ID32STA
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68375	29016 ChEBI	arginine	-	hydrolysis	from API ID32STA
68375	17057 ChEBI	cellobiose	-	fermentation	from API ID32STA
68375	15824 ChEBI	D-fructose	+	fermentation	from API ID32STA
68375	17634 ChEBI	D-glucose	-	fermentation	from API ID32STA
68375	16899 ChEBI	D-mannitol	-	fermentation	from API ID32STA
68375	16024 ChEBI	D-mannose	+	fermentation	from API ID32STA
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68375	16988 ChEBI	D-ribose	-	fermentation	from API ID32STA
68375	4853 ChEBI	esculin	+	hydrolysis	from API ID32STA
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68375	17716 ChEBI	lactose	-	fermentation	from API ID32STA
68375	17306 ChEBI	maltose	+	fermentation	from API ID32STA
68375	59640 ChEBI	N-acetylglucosamine	-	fermentation	from API ID32STA
68375	17632 ChEBI	nitrate	-	reduction	from API ID32STA
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68375	18257 ChEBI	ornithine	+	degradation	from API ID32STA
68375	16634 ChEBI	raffinose	-	fermentation	from API ID32STA
68375	17992 ChEBI	sucrose	-	fermentation	from API ID32STA
68375	27082 ChEBI	trehalose	-	fermentation	from API ID32STA
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68375	32528 ChEBI	turanose	-	fermentation	from API ID32STA
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68375	16199 ChEBI	urea	-	hydrolysis	from API ID32STA

Antibiotic resistance

@ref	ChEBI	Group ID	Metabolite	Is sensitive	Sensitivity conc.
68375	28368	0	novobiocin		1.8 µg	from API ID32STA

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68375	15688 ChEBI	acetoin		from API ID32STA
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68375	15688 ChEBI	acetoin	-		from API ID32STA
68380	35581 ChEBI	indole		-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68375	alkaline phosphatase	-	3.1.3.1	from API ID32STA
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68375	arginine dihydrolase	-	3.5.3.6	from API ID32STA
68375	beta-galactosidase	-	3.2.1.23	from API ID32STA
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68375	beta-glucosidase	+	3.2.1.21	from API ID32STA
68375	beta-glucuronidase	-	3.2.1.31	from API ID32STA
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68375	L-arginine arylamidase	-		from API ID32STA
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68375	ornithine decarboxylase	+	4.1.1.17	from API ID32STA
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
68375	pyrrolidonyl arylamidase	-	3.4.19.3	from API ID32STA
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68375	urease	-	3.5.1.5	from API ID32STA
68380	urease	-	3.5.1.5	from API rID32A

API ID32STA

@ref	URE	ADH (Arg)	ODC	ESC	GLU	FRU	MNE	MAL	LAC	TRE	MAN	RAF	RIB	CEL	Reduction of nitrateNIT	Acetoin production (Voges Proskauer test)VP	beta GAL	L-arginine arylamidaseArgA	PAL	Pyrrolidonyl arylamidasePyrA	NOVO	SAC	NAG	TUR	ARA	beta GUR
1258	-	-	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
1258	-	-	+	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
1258	-	-	+	+	-	+	+	+	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
1258	-	-	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host	#Human	-
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Host species
1258	human septicemia	Homo sapiens
67770	Human feces	Homo sapiens
67771	From human septicemia	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence X94966 (>99% sequence identity) for Blautia from Microbeatlas

Aquatic Samples	130
Soil Samples	27
Animal Samples	4973
Plant Samples	5
Total Samples	5135

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1258	1	Risk group (German 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	ASM1066920v1 assembly for Blautia producta ATCC 27340 = DSM 2950 JCM 1471	complete	GCA_010669205	1121114.32	8113713614	1121114	95.1
66792	ASM1413171v1 assembly for Blautia producta DSM 2950	complete	GCA_014131715	33035.113	8003815505	33035	94.42
67771	ASM37388v1 assembly for Blautia producta ATCC 27340 = DSM 2950	scaffold	GCA_000373885	1121114.4	2515154176	1121114	62.08
67770	ASM43912v1 assembly for Blautia producta ATCC 27340 = DSM 2950	scaffold	GCA_000439125	1121114.7	2524023161	1121114	59.18

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Blautia producta gene for 16S ribosomal RNA, partial sequence	AB600998	1493	1121114
20218	Ruminococcus productus small subunit ribosomal RNA (16S rDNA) gene	L76595	1427	1121114
1258	Ruminococcus productus gene for 16S ribosomal RNA, partial sequence	D14144	1381	1121114
1258	P.productus 16S ribosomal RNA	X94966	1482	1121114

GC content

1258

GC-content (mol%)45.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1066920v1 assembly for Blautia producta ATCC 27340 = DSM 2950 JCM 1471
BV-BRC: 1121114.32

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	45.76	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.79	no
125439	motility	BacteriaNetⓘ	yes	81.65	no
125439	spore_formation	BacteriaNetⓘ	yes	84.48	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Blautia producta ATCC 27340 = DSM 2950 JCM 1471
NCBI: GCA_010669205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.44	yes
125438	anaerobic	anaerobicⓘ	yes	87.45	yes
125438	aerobic	aerobicⓘ	no	94.51	yes
125438	spore-forming	spore-formingⓘ	yes	60.85	no
125438	thermophilic	thermophileⓘ	no	94.06	yes
125438	flagellated	motile2+ⓘ	no	68.78	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome-based reclassification of Blautia coccoides (Kaneuchi et al. 1976) Liu et al. 2008 as a later heterotypic synonym of Blautia producta (Prévot 1941) Liu et al. 2008.	Fatahi-Bafghi M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006823	2025
	Changes in the intestinal microbiota of broiler chicken induced by dietary supplementation of the diatomite-bentonite mixture.	Wesierska E, Micek P, Adamski MG, Gondek K, Lis M, Trela M, Wojtysiak D, Kowal J, Wyrobisz-Papiewska A, Kunstman G, Mosiolek S, Smoron K.	BMC Vet Res	10.1186/s12917-024-04439-4	2025
Metabolism	Alternative pathway for dopamine production by acetogenic gut bacteria that O-Demethylate 3-Methoxytyramine, a metabolite of catechol O-Methyltransferase.	Rich BE, Jackson JC, de Ora LO, Long ZG, Uyeda KS, Bess EN.	J Appl Microbiol	10.1111/jam.15682	2022
Genetics	Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.	Hoang M, Marcais G, Kingsford C.	J Comput Biol	10.1089/cmb.2023.0212	2024
	Identification of proteoforms of short open reading frame-encoded peptides in Blautia producta under different cultivation conditions.	Genth J, Schafer K, Cassidy L, Graspeuntner S, Rupp J, Tholey A.	Microbiol Spectr	10.1128/spectrum.02528-23	2023
	Measuring and understanding information storage and transfer in a simulated human gut microbiome.	Zoller H, Garcia Perez C, Betel Geijo Fernandez J, Zu Castell W.	PLoS Comput Biol	10.1371/journal.pcbi.1012359	2024
	Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia	Sayavedra L, Yasir M, Goldson A, Brion A, Le Gall G, Moreno-Gonzalez M, Altera A, Paxhia M, Warren M, Savva G, Turner A, Beraza N, Narbad A.	Nat Commun		2025
Genetics	The media composition as a crucial element in high-throughput metabolic network reconstruction.	Borer B, Magnusdottir S.	Interface Focus	10.1098/rsfs.2022.0070	2023
Genetics	Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages.	Maturana JL, Cardenas JP.	Front Microbiol	10.3389/fmicb.2021.660920	2021
	Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria.	Rosenbaum FP, Muller V.	Extremophiles	10.1007/s00792-021-01241-0	2021
Pathogenicity	An oxidation resistant pediocin PA-1 derivative and penocin A display effective anti-Listeria activity in a model human gut environment.	Kuniyoshi TM, O'Connor PM, Lawton E, Thapa D, Mesa-Pereira B, Abulu S, Hill C, Ross RP, Oliveira RPS, Cotter PD.	Gut Microbes	10.1080/19490976.2021.2004071	2022
Pathogenicity	Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis.	Mohamed SS, Abdeltawab NF, Wadie W, Ahmed LA, Ammar RM, Rabini S, Abdel-Aziz H, Khayyal MT.	BMC Complement Med Ther	10.1186/s12906-021-03337-8	2021
Pathogenicity	Akkermansia muciniphila strain ATCC BAA-835 does not promote short-term intestinal inflammation in gnotobiotic interleukin-10-deficient mice.	Ring C, Klopfleisch R, Dahlke K, Basic M, Bleich A, Blaut M.	Gut Microbes	10.1080/19490976.2018.1511663	2019
	Design, Biological Evaluation, and Computer-Aided Analysis of Dihydrothiazepines as Selective Antichlamydial Agents.	de Campos LJ, Seleem MA, Feng J, Pires de Oliveira KM, de Andrade Dos Santos JV, Hayer S, Clayton JB, Kathi S, Fisher DJ, Ouellette SP, Conda-Sheridan M.	J Med Chem	10.1021/acs.jmedchem.2c01894	2023
Metabolism	Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.	Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.06.007	2017
	Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine.	Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Dore J, Bellier S, Blaut M.	Gut Microbes	10.4161/gmic.28203	2014
	Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol.	Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martin R, Gueimonde M, van Sinderen D, Margolles A, Ventura M.	PLoS One	10.1371/journal.pone.0068739	2013
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
Metabolism	The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
	Bifidobacteria support optimal infant vaccine responses.	Ryan FJ, Clarke M, Lynn MA, Benson SC, McAlister S, Giles LC, Choo JM, Rossouw C, Ng YY, Semchenko EA, Richard A, Leong LEX, Taylor SL, Blake SJ, Mugabushaka JI, Walker M, Wesselingh SL, Licciardi PV, Seib KL, Tumes DJ, Richmond P, Rogers GB, Marshall HS, Lynn DJ.	Nature	10.1038/s41586-025-08796-4	2025
	BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.	Bauer E, Zimmermann J, Baldini F, Thiele I, Kaleta C.	PLoS Comput Biol	10.1371/journal.pcbi.1005544	2017
Pathogenicity	Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.	Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ.	Nat Microbiol	10.1038/s41564-019-0655-7	2020
Metabolism	Clostridium ramosum regulates enterochromaffin cell development and serotonin release.	Mandic AD, Woting A, Jaenicke T, Sander A, Sabrowski W, Rolle-Kampcyk U, von Bergen M, Blaut M.	Sci Rep	10.1038/s41598-018-38018-z	2019
Metabolism	The Activation of Mucosal-Associated Invariant T (MAIT) Cells Is Affected by Microbial Diversity and Riboflavin Utilization in vitro.	Krause JL, Schape SS, Schattenberg F, Muller S, Ackermann G, Rolle-Kampczyk UE, Jehmlich N, Pierzchalski A, von Bergen M, Herberth G.	Front Microbiol	10.3389/fmicb.2020.00755	2020
Metabolism	Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models.	Woting A, Pfeiffer N, Loh G, Klaus S, Blaut M.	mBio	10.1128/mbio.01530-14	2014
	Alleviation of high fat diet-induced obesity by oligofructose in gnotobiotic mice is independent of presence of Bifidobacterium longum.	Woting A, Pfeiffer N, Hanske L, Loh G, Klaus S, Blaut M.	Mol Nutr Food Res	10.1002/mnfr.201500249	2015
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
Phylogeny	Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach.	Gagen EJ, Denman SE, Padmanabha J, Zadbuke S, Al Jassim R, Morrison M, McSweeney CS.	Appl Environ Microbiol	10.1128/aem.01679-10	2010
	Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella Typhimurium-infected gnotobiotic mice.	Ganesh BP, Klopfleisch R, Loh G, Blaut M.	PLoS One	10.1371/journal.pone.0074963	2013
Phylogeny	Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota.	Bartosch S, Fite A, Macfarlane GT, McMurdo ME.	Appl Environ Microbiol	10.1128/aem.70.6.3575-3581.2004	2004
	Discovery of a Gut Bacterial Pathway for Ergothioneine Catabolism.	Feng C, Yan Q, Li X, Zhao H, Huang H, Zhang X.	J Am Chem Soc	10.1021/jacs.4c09350	2025
	Biochemical characterization of bifunctional enzymatic activity of a recombinant protein (Bp0469) from Blautia producta ATCC 27340 and its role in the utilization of arabinogalactan oligosaccharides.	Bhaiyya R, Sharma SC, Singh RP.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.126736	2023
	Optimizing Precision Probiotics for Mitigating Graft-Versus-Host Disease.	Ebigbo N, Long A, Do P, Coughlin L, Poulides N, Jewell T, Gan S, Zhan X, Koh AY.	Microorganisms	10.3390/microorganisms13040706	2025
Metabolism	Utilization of dietary mixed-linkage beta-glucans by the Firmicute Blautia producta.	Singh RP, Niharika J, Thakur R, Wagstaff BA, Kumar G, Kurata R, Patel D, Levy CW, Miyazaki T, Field RA.	J Biol Chem	10.1016/j.jbc.2023.104806	2023
	Western diet contributes to the pathogenesis of non-alcoholic steatohepatitis in male mice via remodeling gut microbiota and increasing production of 2-oleoylglycerol.	Yang M, Qi X, Li N, Kaifi JT, Chen S, Wheeler AA, Kimchi ET, Ericsson AC, Rector RS, Staveley-O'Carroll KF, Li G.	Nat Commun	10.1038/s41467-023-35861-1	2023
Genetics	Prophages are associated with extensive CRISPR-Cas auto-immunity.	Nobrega FL, Walinga H, Dutilh BE, Brouns SJJ.	Nucleic Acids Res	10.1093/nar/gkaa1071	2020
	beta-glucans: a potential source for maintaining gut microbiota and the immune system.	Singh RP, Bhardwaj A.	Front Nutr	10.3389/fnut.2023.1143682	2023
Phylogeny	Blautia-a new functional genus with potential probiotic properties?	Liu X, Mao B, Gu J, Wu J, Cui S, Wang G, Zhao J, Zhang H, Chen W.	Gut Microbes	10.1080/19490976.2021.1875796	2021
Phylogeny	Berberine alters gut microbial function through modulation of bile acids.	Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM.	BMC Microbiol	10.1186/s12866-020-02020-1	2021
	Effect of Bile Salt Hydrolase Inhibitors on a Bile Salt Hydrolase from Lactobacillus acidophilus.	Lin J, Negga R, Zeng X, Smith K.	Pathogens	10.3390/pathogens3040947	2014
	A Gram-negative-selective antibiotic that spares the gut microbiome.	Munoz KA, Ulrich RJ, Vasan AK, Sinclair M, Wen PC, Holmes JR, Lee HY, Hung CC, Fields CJ, Tajkhorshid E, Lau GW, Hergenrother PJ.	Nature	10.1038/s41586-024-07502-0	2024
Pathogenicity	In Vitro and In Vivo Activities of DS-2969b, a Novel GyrB Inhibitor, against Clostridium difficile.	Mathur T, Barman TK, Kumar M, Singh D, Kumar R, Khera MK, Yamada M, Inoue SI, Upadhyay DJ, Masuda N.	Antimicrob Agents Chemother	10.1128/aac.02157-17	2018
	A selective antibiotic for Lyme disease.	Leimer N, Wu X, Imai Y, Morrissette M, Pitt N, Favre-Godal Q, Iinishi A, Jain S, Caboni M, Leus IV, Bonifay V, Niles S, Bargabos R, Ghiglieri M, Corsetti R, Krumpoch M, Fox G, Son S, Klepacki D, Polikanov YS, Freliech CA, McCarthy JE, Edmondson DG, Norris SJ, D'Onofrio A, Hu LT, Zgurskaya HI, Lewis K.	Cell	10.1016/j.cell.2021.09.011	2021
Enzymology	Energy-converting hydrogenases: the link between H₂ metabolism and energy conservation.	Schoelmerich MC, Muller V.	Cell Mol Life Sci	10.1007/s00018-019-03329-5	2020
Enzymology	Spatial organization of intestinal microbiota in the mouse ascending colon.	Nava GM, Friedrichsen HJ, Stappenbeck TS.	ISME J	10.1038/ismej.2010.161	2011
	Vitamin B12 analogues from gut microbes and diet differentially impact commensal propionate producers of the human gut.	Kundra P, Greppi A, Duppenthaler M, Pluss S, Pugin B, Lacroix C, Geirnaert A.	Front Nutr	10.3389/fnut.2024.1360199	2024
	Microbially-produced folate forms support the growth of Roseburia intestinalis but not its competitive fitness in fecal batch fermentations.	Kundra P, Geirnaert A, Pugin B, Pluss S, Kariluoto S, Lacroix C, Greppi A.	BMC Microbiol	10.1186/s12866-024-03528-6	2024
Metabolism	Linear and branched beta-Glucans degrading enzymes from versatile Bacteroides uniformis JCM 13288^T and their roles in cooperation with gut bacteria.	Singh RP, Rajarammohan S, Thakur R, Hassan M.	Gut Microbes	10.1080/19490976.2020.1826761	2020
	Characterizing the mucin-degrading capacity of the human gut microbiota.	Glover JS, Ticer TD, Engevik MA.	Sci Rep	10.1038/s41598-022-11819-z	2022
	Description of a Newly Isolated Blautia faecis Strain and Its Benefit in Mouse Models of Post-Influenza Secondary Enteric and Pulmonary Infections.	Verstraeten S, Sencio V, Raise A, Huillet E, Layec S, Deruyter L, Heumel S, Auger S, Robert V, Langella P, Beney L, Trottein F, Thomas M.	Nutrients	10.3390/nu14071478	2022
Metabolism	Human Clostridium difficile infection: inhibition of NHE3 and microbiota profile.	Engevik MA, Engevik KA, Yacyshyn MB, Wang J, Hassett DJ, Darien B, Yacyshyn BR, Worrell RT.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00090.2014	2015
Phylogeny	Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study.	Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R.	BMC Microbiol	10.1186/s12866-016-0708-5	2016
Metabolism	Upregulation of colonic luminal polyamines produced by intestinal microbiota delays senescence in mice.	Kibe R, Kurihara S, Sakai Y, Suzuki H, Ooga T, Sawaki E, Muramatsu K, Nakamura A, Yamashita A, Kitada Y, Kakeyama M, Benno Y, Matsumoto M.	Sci Rep	10.1038/srep04548	2014
Metabolism	Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior.	Gacias M, Gaspari S, Santos PM, Tamburini S, Andrade M, Zhang F, Shen N, Tolstikov V, Kiebish MA, Dupree JL, Zachariou V, Clemente JC, Casaccia P.	Elife	10.7554/elife.13442	2016
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
	Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota.	Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A, Knol J.	PLoS One	10.1371/journal.pone.0158498	2016
	Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.	Kim MJ, Song MH, Ji YS, Park JW, Shin YK, Kim SC, Kim G, Cho B, Park H, Ku JL, Jeong SY.	Sci Rep	10.1038/s41598-024-83048-5	2025
Metabolism	Inter-kingdom lipid messengers sustain gut harmony.	Hou J, Song X.	Cell Host Microbe	10.1016/j.chom.2025.09.003	2025
	Exploring the role of acylated ghrelin and gut microbiome in delineating cognitive health in the elderly.	Rout S, Dash R, Satish V, Venugopal G, Rao BN, Bandhyopadhyay D, Bhoi SK, Ramadass B.	Aging (Albany NY)	10.18632/aging.206200	2025
	A Dual Therapeutic Approach to Diabetes Mellitus via Bioactive Phytochemicals Found in a Poly Herbal Extract by Restoration of Favorable Gut Flora and Related Short-Chain Fatty Acids.	Singh AK, Kumar P, Mishra SK, Rajput VD, Tiwari KN, Singh AK, Minkina T, Pandey AK, Upadhyay P.	Appl Biochem Biotechnol	10.1007/s12010-024-04879-6	2024
	Hepatic Steatosis Can Be Partly Generated by the Gut Microbiota-Mitochondria Axis via 2-Oleoyl Glycerol and Reversed by a Combination of Soy Protein, Chia Oil, Curcumin and Nopal.	Sanchez-Tapia M, Tobon-Cornejo S, Noriega LG, Vazquez-Manjarrez N, Coutino-Hernandez D, Granados-Portillo O, Roman-Calleja BM, Ruiz-Margain A, Macias-Rodriguez RU, Tovar AR, Torres N.	Nutrients	10.3390/nu16162594	2024
	Metagenomic Analysis of Intratumoral Microbiome Linking to Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer.	Huang X, Chen C, Xie W, Zhou C, Tian X, Zhang Z, Wang Q, Chang H, Xiao W, Zhang R, Gao Y.	Int J Radiat Oncol Biol Phys	10.1016/j.ijrobp.2023.06.2515	2023
	Association of the gut microbiota with type 2 diabetes: Links to disease and remission in the Japanese population.	Kinoshita K, Ozato N, Yamaguchi T, Mori K, Katsuragi Y, Sato N, Imoto S, Ihara K, Murashita K, Nakaji S, Mikami T.	J Diabetes Investig	10.1111/jdi.70061	2025
Metabolism	Association of gut microbiota and glucose metabolism in children with disparate degrees of adiposity.	Yuan X, Zhang Y, Lin X, Yang X, Chen R.	Pediatr Obes	10.1111/ijpo.13009	2023
	Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance.	Zhang X, Yu D, Wu D, Gao X, Shao F, Zhao M, Wang J, Ma J, Wang W, Qin X, Chen Y, Xia P, Wang S.	Cell Host Microbe	10.1016/j.chom.2023.01.013	2023
Phylogeny	Reoxygenation Mitigates Intermittent Hypoxia-Induced Systemic Inflammation and Gut Microbiota Dysbiosis in High-Fat Diet-Induced Obese Rats.	Dong M, Liang X, Zhu T, Xu T, Xie L, Feng Y.	Nat Sci Sleep	10.2147/nss.s454297	2024
	Degradation mechanism of difructose dianhydride III in Blautia species.	Ye T, Horigome A, Kaneko H, Odamaki T, Kitahara K, Fujita K.	Appl Microbiol Biotechnol	10.1007/s00253-024-13346-5	2024
	Lactobacillus rhamnosus Ameliorates Dyslipidemia and Liver Steatosis in a Rat Model Fed High-Fat Diet.	Liao YT, Huang J, Lin BR, Liang JT, Huang KW.	Gastroenterol Res Pract	10.1155/grp/5540686	2025
	Strain-level screening of human gut microbes identifies Blautia producta as a new anti-hyperlipidemic probiotic.	Xu W, Yu J, Yang Y, Li Z, Zhang Y, Zhang F, Wang Q, Xie Y, Zhao B, Wu C.	Gut Microbes	10.1080/19490976.2023.2228045	2023
	Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.	Birebent R, Drubay D, Alves Costa Silva C, Marmorino F, Vitali G, Piccinno G, Hurtado Y, Bonato A, Belluomini L, Messaoudene M, Routy B, Fidelle M, Zalcman G, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Reni A, Barlesi F, Albiges L, Planchard D, Martinez S, Besse B, Segata N, Cremolini C, Zitvogel L, Iebba V, Derosa L.	Oncoimmunology	10.1080/2162402x.2025.2484880	2025
	Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.	Lim MY, Hong S, Nam YD.	Front Immunol	10.3389/fimmu.2024.1512683	2024
Biotechnology	Dynamic metabolic modelling predicts efficient acetogen-gut bacterium cocultures for CO-to-butyrate conversion.	Li X, Henson MA.	J Appl Microbiol	10.1111/jam.15155	2021
Pathogenicity	Gut microbiota of patients with type 2 diabetes and gastrointestinal intolerance to metformin differs in composition and functionality from tolerant patients.	Diaz-Perdigones CM, Munoz-Garach A, Alvarez-Bermudez MD, Moreno-Indias I, Tinahones FJ.	Biomed Pharmacother	10.1016/j.biopha.2021.112448	2022
	A Review of Fecal Microbiota Transplantation in Children-Exploring Its Role in the Treatment of Inflammatory Bowel Diseases.	Ko Y, Alaedin S, Fernando D, Zhou J, Ho V.	Medicina (Kaunas)	10.3390/medicina60111899	2024
	The double-edged sword: impact of antibiotic use on immunotherapy efficacy in advanced hepatocellular carcinoma.	Li Y, Feng Z, Liang C, Lu S, Wang G, Meng G.	BMC Gastroenterol	10.1186/s12876-025-03819-w	2025
Phylogeny	Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens.	Stefanini R, Karekar S, Ale Enriquez F, Ahring B.	Microbiol Spectr	10.1128/spectrum.03183-23	2024
	Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken.	Jadhav VV, Fasina YO, Harrison SH.	Poult Sci	10.1016/j.psj.2025.105167	2025
	Gut microbiome and NAFLD: impact and therapeutic potential.	Li L, Cai F, Guo C, Liu Z, Qin J, Huang J.	Front Microbiol	10.3389/fmicb.2024.1500453	2024
Pathogenicity	Effects of Different Carbohydrate Content Diet on Gut Microbiota and Aortic Calcification in Diabetic Mice.	Shen X, Guo G, Feng G, Wang Z.	Diabetes Metab Syndr Obes	10.2147/dmso.s456571	2024
	Two Blautia Species Associated with Visceral Fat Accumulation: A One-Year Longitudinal Study.	Ozato N, Yamaguchi T, Mori K, Katashima M, Kumagai M, Murashita K, Katsuragi Y, Tamada Y, Kakuta M, Imoto S, Ihara K, Nakaji S.	Biology (Basel)	10.3390/biology11020318	2022
Metabolism	Identification of Gut Microbiome Signatures Associated with Indole Pathway in Tryptophan Metabolism in Patients Undergoing Hemodialysis	Huang J, Wu P, Chen Z, Liu P, Kuo C, Chuang Y, Lu M, Kuo M, Chiu Y, Lin Y.	Biomolecules		2024
	A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers.	Xing H, Zhang Y, Kramer M, Kissmann AK, Henkel M, Weil T, Knippschild U, Rosenau F.	Molecules	10.3390/molecules27175693	2022
	Specific gFET-Based Aptasensors for Monitoring of Microbiome Quality: Quantification of the Enteric Health-Relevant Bacterium Roseburia Intestinalis.	Zhang Y, Xing H, Li R, Andersson J, Bozdogan A, Strassl R, Draphoen B, Linden M, Henkel M, Knippschild U, Hasler R, Kleber C, Knoll W, Kissmann AK, Rosenau F.	Adv Healthc Mater	10.1002/adhm.202403827	2025
	Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine.	Ma W, Han Z, Liu X, Cui W, Zhen D, Zhou X, Song Y, Jiang S.	Microorganisms	10.3390/microorganisms13040731	2025
Pathogenicity	Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.	Gao Y, Borjihan Q, Zhang W, Li L, Wang D, Bai L, Zhu S, Chen Y.	Nutrients	10.3390/nu17050801	2025
Pathogenicity	Exploring the Role of Microglial Cells in the Gut-Brain Axis Communication: A Systematic Review.	Ortiz-Samur NS, Vijaya AK, Burokas A, Mela V.	J Neurochem	10.1111/jnc.70154	2025
	Changes in antioxidant capacity and gut microbiota in mice after intake of camel milk.	Wang J, Ren W, Liu S, Li Z, Zeng Y, Meng J, Yao X.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1621031	2025
Genetics	Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis.	Wang YJ, Li SC, Lin WC, Huang FC.	Pathogens	10.3390/pathogens10030266	2021
	The Relationship Between the Microbiome and Antimicrobial Resistance.	Nhu NTQ, Young VB.	Clin Infect Dis	10.1093/cid/ciad641	2023
	Impact of Ivermectin on the Gut Microbial Ecosystem	Liu L, Mahalak K, Bobokalonov J, Narrowe A, Firrman J, Lemons J, Bittinger K, Hu W, Jones S, Moustafa A.	Int J Mol Sci		2023
Phylogeny	Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data.	Zhang Y, Zhong W, Liu W, Wang X, Lin G, Lin J, Fang J, Mou X, Jiang S, Huang J, Zhao W, Zheng Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1363276	2024
	The nisin O cluster: species dissemination, candidate leader peptide proteases and the role of regulatory systems.	Scadden J, Ansorge R, Romano S, Telatin A, Baker DJ, Evans R, Gherghisan-Filip C, Zhang ZJ, Mayer MJ, Narbad A.	Microbiology (Reading)	10.1099/mic.0.001531	2025
Metabolism	Different Diet Energy Levels Alter Body Condition, Glucolipid Metabolism, Fecal Microbiota and Metabolites in Adult Beagle Dogs.	Sun H, Zhang Q, Xu C, Xu C, Mao A, Zhao H, Chen M, Sun W, Li G, Zhang T.	Metabolites	10.3390/metabo13040554	2023
	Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium.	Martin AJM, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D.	Microbiome Res Rep	10.20517/mrr.2023.10	2023
	Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.	Serrano-Gomez G, Yanez F, Soler Z, Pons-Tarin M, Mayorga L, Herrera-deGuise C, Borruel N, Rodriguez-Sinovas A, Consegal M, Manjon I, Vega-Abellaneda S, Manichanh C.	Biomark Res	10.1186/s40364-025-00802-1	2025
	Designing function-specific minimal microbiomes from large microbial communities.	Raghu AK, Palanikumar I, Raman K.	NPJ Syst Biol Appl	10.1038/s41540-024-00373-1	2024
	Integrated microbiome and metabolome analysis reveals a novel interplay between gut microbiota and metabolites in differentiated thyroid carcinoma.	Jiang X, Liu Q, Xu D, Pang H, Shi Y.	BMC Microbiol	10.1186/s12866-025-03877-w	2025
	Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms.	Long J, Wang J, Xiao C, You F, Jiang Y, Li X.	Cell Commun Signal	10.1186/s12964-024-01831-3	2024
	Mediation effect of gut microbiota on the relationship between physical activity and carotid plaque.	Ouyang W, Tang B, He Y, Wu H, Yang P, Yin L, Li X, Li Y, Huang X.	Front Microbiol	10.3389/fmicb.2024.1432008	2024
	Immunoglobulin-coating patterns reveal altered humoral responses to gut bacteria in pediatric cow milk allergies.	Augustine T, Murugesan S, Badri F, Gentilcore G, Grivel JC, Akobeng A, Elawad M, Adeli M, Al Khodor S, van Panhuys N.	J Transl Med	10.1186/s12967-024-05850-z	2024
	IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution.	Kissmann AK, Bolotnikov G, Li R, Muller F, Xing H, Kramer M, Gottschalk KE, Andersson J, Weil T, Rosenau F.	Appl Microbiol Biotechnol	10.1007/s00253-024-13085-7	2024
	Statistical modeling of gut microbiota for personalized health status monitoring.	Zhu J, Xie H, Yang Z, Chen J, Yin J, Tian P, Wang H, Zhao J, Zhang H, Lu W, Chen W.	Microbiome	10.1186/s40168-023-01614-x	2023
	A two-stage strategy for methanogenesis suppression and rapid acetogenic biofilm formation in microbial electrosynthesis.	Ferretti J, Zegers MAJ, Zeppilli M, Jourdin L.	Front Microbiol	10.3389/fmicb.2025.1655259	2025
	Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.	Zhang Z, Yang Z, Lin S, Jiang S, Zhou X, Li J, Lu W, Zhang J.	Gut Microbes	10.1080/19490976.2025.2520407	2025
	Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system.	Castaneda-Monsalve V, Haange SB, Frohlich LF, Fu Q, Rolle-Kampczyk U, von Bergen M, Jehmlich N.	ISME Commun	10.1093/ismeco/ycaf050	2025
	Fecal carriage of multidrug-resistant organisms increases the risk of hepatic encephalopathy in patients with cirrhosis: insights from gut microbiota and metabolite features.	Wu PS, Lee PC, Chang TE, Hsieh YC, Huang CW, Lin CH, Huang YL, Lin YT, Huo TI, Schnabl B, Lee KC, Hou MC.	Gut Pathog	10.1186/s13099-025-00706-3	2025
	The gut microbiome is associated with susceptibility to febrile malaria in Malian children.	Van Den Ham KM, Bower LK, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW.	Nat Commun	10.1038/s41467-024-52953-8	2024
	Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition.	Sardaro MLS, Grote V, Baik J, Atallah M, Amato KR, Ring M.	Nutrients	10.3390/nu17030458	2025
	Refocusing Human Microbiota Research in Infectious and Immune-mediated Diseases: Advancing to the Next Stage.	Giovanni MY, Schneider JS, Calder T, Fauci AS.	J Infect Dis	10.1093/infdis/jiaa706	2021
	Helicobacter pylori serology is associated with worse overall survival in patients with melanoma treated with immune checkpoint inhibitors.	Tonneau M, Nolin-Lapalme A, Kazandjian S, Auclin E, Panasci J, Benlaifaoui M, Ponce M, Al-Saleh A, Belkaid W, Naimi S, Mihalcioiu C, Watson I, Bouin M, Miller W, Hudson M, Wong MK, Pezo RC, Turcotte S, Belanger K, Jamal R, Oster P, Velin D, Richard C, Messaoudene M, Elkrief A, Routy B.	Oncoimmunology	10.1080/2162402x.2022.2096535	2022
	Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation.	Um CY, Peters BA, Choi HS, Oberstein P, Beggs DB, Usyk M, Wu F, Hayes RB, Gapstur SM, McCullough ML, Ahn J.	Cancer Res Commun	10.1158/2767-9764.crc-22-0154	2023
	Severe Cognitive Decline in Long-term Care Is Related to Gut Microbiome Production of Metabolites Involved in Neurotransmission, Immunomodulation, and Autophagy.	Shoubridge AP, Carpenter L, Flynn E, Papanicolas LE, Collins J, Gordon D, Lynn DJ, Whitehead C, Leong LEX, Cations M, De Souza DP, Narayana VK, Choo JM, Wesselingh SL, Crotty M, Inacio MC, Ivey K, Taylor SL, Rogers GB.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glaf053	2025
	Lacticaseibacillus paracasei Glu-07: A Promising Probiotic Candidate for the Management of Type 2 Diabetes Mellitus.	Xu W, Guan Y, Tian L, Fu Y, Zhang Y, Liu Y, Hu Y, Zhao B, Wu C.	Curr Microbiol	10.1007/s00284-025-04391-y	2025
	The dysbiosis of gut microbiota and dysregulation of metabolites in IgA nephropathy and membranous nephropathy.	Zhang L, Hu L, Tan L, Zhang Z, Chen M, Gan W, Chen L, Zou Y, Wang S, Pang Y, Fan Z, Liu J.	Front Med (Lausanne)	10.3389/fmed.2025.1618947	2025
	Leveraging strain competition to address antimicrobial resistance with microbiota therapies.	Barrios Steed D, Koundakjian D, Harris AD, Rosato AE, Konstantinidis KT, Woodworth MH.	Gut Microbes	10.1080/19490976.2025.2488046	2025
	Intestinal microbiota composition in broilers fed protein-free or casein-based diets.	Rubio LA.	Poult Sci	10.1016/j.psj.2024.104365	2024
Pathogenicity	Canagliflozin attenuates kidney injury, gut-derived toxins, and gut microbiota imbalance in high-salt diet-fed Dahl salt-sensitive rats.	He L, Zuo Q, Ma S, Zhang G, Wang Z, Zhang T, Zhai J, Guo Y.	Ren Fail	10.1080/0886022x.2023.2300314	2024
	Effects of Berries, Phytochemicals, and Probiotics on Atherosclerosis through Gut Microbiota Modification: A Meta-Analysis of Animal Studies.	Khalili L, Centner AM, Salazar G.	Int J Mol Sci	10.3390/ijms24043084	2023
Genetics	Seasonal stability of the rumen microbiome contributes to the adaptation patterns to extreme environmental conditions in grazing yak and cattle.	Guo W, Zhou M, Li F, Neves ALA, Ma T, Bi S, Wang W, Long R, Guan LL.	BMC Biol	10.1186/s12915-024-02035-4	2024
	FluCell-SELEX Aptamers as Specific Binding Molecules for Diagnostics of the Health Relevant Gut Bacterium Akkermansia muciniphila.	Raber HF, Kubiczek DH, Bodenberger N, Kissmann AK, D'souza D, Xing H, Mayer D, Xu P, Knippschild U, Spellerberg B, Weil T, Rosenau F.	Int J Mol Sci	10.3390/ijms221910425	2021
	The Role of the Microbiome in Gastroentero-Pancreatic Neuroendocrine Neoplasms (GEP-NENs).	Mohamed A, Asa SL, McCormick T, Al-Shakhshir H, Dasari A, Mauricio R, Salem I, Ocuin LM, Bajor D, Lee RT, Selfridge JE, Kardan A, Lee Z, Avril N, Kopp S, Winter JM, Hardacre JM, Ammori JB, Ghannoum MA.	Curr Issues Mol Biol	10.3390/cimb44050136	2022
Pathogenicity	Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut.	Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B.	Nat Commun	10.1038/s41467-025-56332-9	2025
	Structural Variances in Curcumin Degradants: Impact on Obesity in Mice.	Koh YC, Hsu HW, Ho PY, Hsu KY, Lin WS, Nagabhushanam K, Ho CT, Pan MH.	J Agric Food Chem	10.1021/acs.jafc.4c03768	2024
	Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production.	Volf J, Crhanova M, Karasova D, Faldynova M, Kubasova T, Seidlerova Z, Sebkova A, Zeman M, Juricova H, Matiasovicova J, Foltyn M, Tvrdon Z, Rychlik I.	Microorganisms	10.3390/microorganisms9071480	2021
	Modulative effect of Physalis alkekengi on both gut bacterial and fungal micro-ecosystem.	Yang Y, Zhao X, Xie Y, Wu C.	Chin Herb Med	10.1016/j.chmed.2023.02.003	2023
	Gut microbiota and bile acids: Metabolic interactions and impacts on diabetic kidney disease.	Liu P, Jin M, Hu P, Sun W, Tang Y, Wu J, Zhang D, Yang L, He H, Xu X.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100315	2024
	Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations.	Quagliariello A, Del Chierico F, Reddel S, Russo A, Onetti Muda A, D'Argenio P, Angelino G, Romeo EF, Dall'Oglio L, De Angelis P, Putignani L, All The Other Fmt Opbg Committee Collaborators.	Microorganisms	10.3390/microorganisms8101486	2020
Enzymology	A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach.	Barberio B, Facchin S, Patuzzi I, Ford AC, Massimi D, Valle G, Sattin E, Simionati B, Bertazzo E, Zingone F, Savarino EV.	Gut Microbes	10.1080/19490976.2022.2028366	2022
	The Relationship Between Gut Microbiome Features and Chemotherapy Response in Gastrointestinal Cancer.	Li N, Bai C, Zhao L, Sun Z, Ge Y, Li X.	Front Oncol	10.3389/fonc.2021.781697	2021
	Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals.	Zhang ZJ, Wu C, Moreira R, Dorantes D, Pappas T, Sundararajan A, Lin H, Pamer EG, van der Donk WA.	ACS Chem Biol	10.1021/acschembio.3c00577	2024
Pathogenicity	Fecal microbiota transplantation to prevent acute graft-versus-host disease: pre-planned interim analysis of donor effect.	Reddi S, Senyshyn L, Ebadi M, Podlesny D, Minot SS, Gooley T, Kabage AJ, Hill GR, Lee SJ, Khoruts A, Rashidi A.	Nat Commun	10.1038/s41467-025-56375-y	2025
	Elucidation of host diversity of the VanD-carrying genomic islands in enterococci and anaerobes.	Hashimoto Y, Hisatsune J, Suzuki M, Kurushima J, Nomura T, Hirakawa H, Kojima N, Ono Y, Hasegawa Y, Tanimoto K, Sugai M, Tomita H.	JAC Antimicrob Resist	10.1093/jacamr/dlab189	2022
	Intestinal microbiome characterization of adult Brazilian men with psoriasis compared to omnivore and vegetarian controls.	Polo TCF, Lai MRR, Miot LDB, Bento GFC, Silva MGD, Marques SA, Miot HA.	An Bras Dermatol	10.1016/j.abd.2022.08.008	2023
Pathogenicity	The Impact of Microbiome Dysbiosis on Hematopoietic Stem Cell Transplantation Outcomes: A Review Article.	Khalil Z, Maher S.	Cureus	10.7759/cureus.63995	2024
	Exploring the Relationship between MicroRNAs, Intratumoral Microbiota, and Breast Cancer Progression in Patients with and without Metastasis.	Laborda-Illanes A, Aranega-Martin L, Sanchez-Alcoholado L, Boutriq S, Plaza-Andrades I, Peralta-Linero J, Garrido Ruiz G, Pajares-Hachero B, Alvarez M, Alba E, Gonzalez-Gonzalez A, Queipo-Ortuno MI.	Int J Mol Sci	10.3390/ijms25137091	2024
	Gut microbiota characteristics of colorectal cancer patients in Hubei, China, and differences with cohorts from other Chinese regions.	Shi J, Shen H, Huang H, Zhan L, Chen W, Zhou Z, Lv Y, Xiong K, Jiang Z, Chen Q, Liu L.	Front Microbiol	10.3389/fmicb.2024.1395514	2024
	An in vitro model system for testing chemical effects on microbiome-immune interactions - examples with BPX and PFAS mixtures.	Fischer F, Pierzchalski A, Riesbeck S, Aldehoff AS, Castaneda-Monsalve VA, Haange SB, von Bergen M, Rolle-Kampczyk UE, Jehmlich N, Zenclussen AC, Herberth G.	Front Immunol	10.3389/fimmu.2024.1298971	2024
	The microbial and host factors that govern Candida gastrointestinal colonization and dissemination.	Mishra AA, Koh AY.	Curr Opin Microbiol	10.1016/j.mib.2021.05.012	2021
Metabolism	Microbial transformation of dietary xenobiotics shapes gut microbiome composition.	Culp EJ, Nelson NT, Verdegaal AA, Goodman AL.	Cell	10.1016/j.cell.2024.08.038	2024
	The Gut Microbiome and Cancer Immunotherapy: Can We Use the Gut Microbiome as a Predictive Biomarker for Clinical Response in Cancer Immunotherapy?	Oh B, Boyle F, Pavlakis N, Clarke S, Eade T, Hruby G, Lamoury G, Carroll S, Morgia M, Kneebone A, Stevens M, Liu W, Corless B, Molloy M, Kong B, Libermann T, Rosenthal D, Back M.	Cancers (Basel)	10.3390/cancers13194824	2021
	Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years.	Laue HE, Korrick SA, Baker ER, Karagas MR, Madan JC.	Sci Rep	10.1038/s41598-020-72386-9	2020
	Beneficial Effects of Probiotic Lactobacillus paraplantarum BGCG11 on Pancreatic and Duodenum Function in Diabetic Rats.	Mihailovic M, Sokovic Bajic S, Arambasic Jovanovic J, Brdaric E, Dinic S, Grdovic N, Uskokovic A, Rajic J, Dordevic M, Tolinacki M, Golic N, Zivkovic M, Vidakovic M.	Int J Mol Sci	10.3390/ijms25147697	2024
Genetics	Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.	Mori H, Kato T, Ozawa H, Sakamoto M, Murakami T, Taylor TD, Toyoda A, Ohkuma M, Kurokawa K, Ohno H.	DNA Res	10.1093/dnares/dsad010	2023
	A Combined Supplement of Probiotic Strains AP-32, bv-77, and CP-9 Increased Akkermansia mucinphila and Reduced Non-Esterified Fatty Acids and Energy Metabolism in HFD-Induced Obese Rats.	Liao CA, Huang CH, Ho HH, Chen JF, Kuo YW, Lin JH, Tsai SY, Tsai HY, Yeh YT.	Nutrients	10.3390/nu14030527	2022
Genetics	Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.	Chen SJ, Zhang DY, Wu X, Zhang FM, Cui BT, Huang YH, Zhang ZL, Wang R, Bai FH.	World J Gastroenterol	10.3748/wjg.v30.i11.1572	2024
	Contact with adult hen affects development of caecal microbiota in newly hatched chicks.	Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, Matiasovicova J, Faldynova M, Pokorna A, Cizek A, Rychlik I.	PLoS One	10.1371/journal.pone.0212446	2019
	Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.	Chu Y, Meng Q, Yu J, Zhang J, Chen J, Kang Y.	Microbiol Spectr	10.1128/spectrum.04551-22	2023
	High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study	Castaneda-Monsalve V, Frohlich L, Haange S, Homsi M, Rolle-Kampczyk U, Fu Q, von Bergen M, Jehmlich N.	Front Microbiol		2024
	Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis.	Xing H, Kissmann AK, Raber HF, Kramer M, Amann V, Kohn K, Weil T, Rosenau F.	Microorganisms	10.3390/microorganisms9112284	2021
	Association of Moderate Beer Consumption with the Gut Microbiota and SCFA of Healthy Adults.	Gonzalez-Zancada N, Redondo-Useros N, Diaz LE, Gomez-Martinez S, Marcos A, Nova E.	Molecules	10.3390/molecules25204772	2020
	Gut microbiota signatures of vulnerability to food addiction in mice and humans.	Samulenaite S, Garcia-Blanco A, Mayneris-Perxachs J, Domingo-Rodriguez L, Cabana-Dominguez J, Fernandez-Castillo N, Gago-Garcia E, Pineda-Cirera L, Burokas A, Espinosa-Carrasco J, Arboleya S, Latorre J, Stanton C, Hosomi K, Kunisawa J, Cormand B, Fernandez-Real JM, Maldonado R, Martin-Garcia E.	Gut	10.1136/gutjnl-2023-331445	2024
	Gut microbiota links to serum ferritin and cognition.	Rosell-Diaz M, Santos-Gonzalez E, Motger-Alberti A, Ramio-Torrenta L, Garre-Olmo J, Perez-Brocal V, Moya A, Jove M, Pamplona R, Puig J, Ramos R, Fernandez-Real JM, Mayneris-Perxachs J.	Gut Microbes	10.1080/19490976.2023.2290318	2023
Transcriptome	Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.	Peters BA, Wilson M, Moran U, Pavlick A, Izsak A, Wechter T, Weber JS, Osman I, Ahn J.	Genome Med	10.1186/s13073-019-0672-4	2019
	Accounting Gut Microbiota as the Mediator of Beneficial Effects of Dietary (Poly)phenols on Skeletal Muscle in Aging.	Ticinesi A, Nouvenne A, Cerundolo N, Parise A, Meschi T.	Nutrients	10.3390/nu15102367	2023
	Intratumoral microbiome: implications for immune modulation and innovative therapeutic strategies in cancer.	Wang N, Wu S, Huang L, Hu Y, He X, He J, Hu B, Xu Y, Rong Y, Yuan C, Zeng X, Wang F.	J Biomed Sci	10.1186/s12929-025-01117-x	2025
	ATG16L1 in myeloid cells limits colorectal tumor growth in Apc^Min/+ mice infected with colibactin-producing Escherichia coli via decreasing inflammasome activation.	Salesse L, Duval A, Sauvanet P, Da Silva A, Barnich N, Godfraind C, Dalmasso G, Nguyen HTT.	Autophagy	10.1080/15548627.2024.2359770	2024
	2'-Fucosyllactose Increases the Abundance of Blautia in the Presence of Extracellular Fucosidase-Possessing Bacteria.	Horigome A, Hashikura N, Yoshida K, Xiao JZ, Odamaki T.	Front Microbiol	10.3389/fmicb.2022.913624	2022
	Call to Action: How to Tackle Emerging Nosocomial Fungal Infections.	Lionakis MS, Hohl TM.	Cell Host Microbe	10.1016/j.chom.2020.04.011	2020
Pathogenicity	Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.	Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.	Sci Rep	10.1038/s41598-024-53784-9	2024
Pathogenicity	Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study.	Toscano M, De Grandi R, Stronati L, De Vecchi E, Drago L.	World J Gastroenterol	10.3748/wjg.v23.i15.2696	2017
	The prebiotic and anti-fatigue effects of hyaluronan.	Huang G, Su L, Zhang N, Han R, Leong WK, Li X, Ren X, Hsiao WLW.	Front Nutr	10.3389/fnut.2022.977556	2022
Enzymology	A double-blind, 377-subject randomized study identifies Ruminococcus, Coprococcus, Christensenella, and Collinsella as long-term potential key players in the modulation of the gut microbiome of lactose intolerant individuals by galacto-oligosaccharides.	Azcarate-Peril MA, Roach J, Marsh A, Chey WD, Sandborn WJ, Ritter AJ, Savaiano DA, Klaenhammer TR.	Gut Microbes	10.1080/19490976.2021.1957536	2021
Metabolism	Lignan transformation by gut bacteria lowers tumor burden in a gnotobiotic rat model of breast cancer.	Mabrok HB, Klopfleisch R, Ghanem KZ, Clavel T, Blaut M, Loh G.	Carcinogenesis	10.1093/carcin/bgr256	2012
Metabolism	The Possible Role of Bifidobacterium longum BB536 and Lactobacillus rhamnosus HN001 on Locomotor Activity and Oxidative Stress in a Rotenone-Induced Zebrafish Model of Parkinson's Disease.	Ilie OD, Paduraru E, Robea MA, Balmus IM, Jijie R, Nicoara M, Ciobica A, Nita IB, Dobrin R, Doroftei B.	Oxid Med Cell Longev	10.1155/2021/9629102	2021
	Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.	Brochu E, Huletsky A, Boudreau DK, Raymond F, Berube E, Ouameur AA, Frenette J, Boissinot M, Corbeil J, Bergeron MG.	JAC Antimicrob Resist	10.1093/jacamr/dlad026	2023
Metabolism	Human intestinal microbiota: characterization of a simplified and stable gnotobiotic rat model.	Becker N, Kunath J, Loh G, Blaut M.	Gut Microbes	10.4161/gmic.2.1.14651	2011
Metabolism	Effect of Microbial Status on Hepatic Odd-Chain Fatty Acids Is Diet-Dependent.	Weitkunat K, Bishop CA, Wittmuss M, Machate T, Schifelbein T, Schulze MB, Klaus S.	Nutrients	10.3390/nu13051546	2021
Metabolism	Type-2 Diabetes Mellitus and the Gut Microbiota: Systematic Review.	Slouha E, Rezazadah A, Farahbod K, Gerts A, Clunes LA, Kollias TF.	Cureus	10.7759/cureus.49740	2023
Pathogenicity	Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer.	Hamamah S, Lobiuc A, Covasa M.	Int J Mol Sci	10.3390/ijms25169026	2024
	MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data.	Canderan J, Stamboulian M, Ye Y.	J Proteome Res	10.1021/acs.jproteome.2c00614	2023
	Low-calcium diet in mice leads to reduced gut colonization by Enterococcus faecium.	Top J, Hendrickx APA, van Ampting MTJ, van Limpt K, Knol J, van de Kamer D, Braat JC, Viveen M, Rogers MR, Kemperman H, Willems RJL, Paganelli FL.	Microbiologyopen	10.1002/mbo3.936	2019
Metabolism	Bacterial transformation of dietary lignans in gnotobiotic rats.	Woting A, Clavel T, Loh G, Blaut M.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2010.00863.x	2010
	Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.	Liu J, Sun J, Yu J, Chen H, Zhang D, Zhang T, Ma Y, Zou C, Zhang Z, Ma L, Yu X.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00399-z	2023
Genetics	Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake.	Xie Y, Sun H, Xue M, Liu J.	Anim Microbiome	10.1186/s42523-022-00170-3	2022
	Escherichia coli on colorectal cancer: A two-edged sword.	Jian C, Yinhang W, Jing Z, Zhanbo Q, Zefeng W, Shuwen H.	Microb Biotechnol	10.1111/1751-7915.70029	2024
	Effects of Mexican Ganoderma lucidum extracts on liver, kidney, and the gut microbiota of Wistar rats: A repeated dose oral toxicity study.	Meneses ME, Martinez-Carrera D, Gonzalez-Ibanez L, Torres N, Sanchez-Tapia M, Marquez-Mota CC, Rendon G, Mitzi V, Morales A, Tello-Salgado I, Tovar AR.	PLoS One	10.1371/journal.pone.0283605	2023
Pathogenicity	A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.	Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H.	Cell Host Microbe	10.1016/j.chom.2023.12.014	2024
Enzymology	Minority report: the intestinal mycobiota in systemic infections.	Rolling T, Hohl TM, Zhai B.	Curr Opin Microbiol	10.1016/j.mib.2020.05.004	2020
	MICROBIOTA INSIGHTS IN CLOSTRIDIUM DIFFICILE INFECTION AND INFLAMMATORY BOWEL DISEASE.	Rodriguez C, Romero E, Garrido-Sanchez L, Alcain-Martinez G, Andrade RJ, Taminiau B, Daube G, Garcia-Fuentes E.	Gut Microbes	10.1080/19490976.2020.1725220	2020
Phylogeny	Vasopressin deletion is associated with sex-specific shifts in the gut microbiome.	Fields CT, Chassaing B, Paul MJ, Gewirtz AT, de Vries GJ.	Gut Microbes	10.1080/19490976.2017.1356557	2018
Transcriptome	Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation.	Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG.	Cell Host Microbe	10.1016/j.chom.2021.01.003	2021
Phylogeny	Gut Microbiota Signatures in Gestational Anemia.	Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S, Yang H.	Front Cell Infect Microbiol	10.3389/fcimb.2021.549678	2021
	SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level.	Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX.	Proc Natl Acad Sci U S A	10.1073/pnas.2203519119	2022
Genetics	Metabolic Potential of the Gut Microbiome Is Significantly Impacted by Conditioning Regimen in Allogeneic Hematopoietic Stem Cell Transplantation Recipients.	Jorgensen M, Norgaard JC, Ilett EE, Marandi RZ, Noguera-Julian M, Paredes R, Murray DD, Lundgren J, MacPherson CR, Sengelov H.	Int J Mol Sci	10.3390/ijms231911115	2022
	Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium.	Caballero S, Kim S, Carter RA, Leiner IM, Susac B, Miller L, Kim GJ, Ling L, Pamer EG.	Cell Host Microbe	10.1016/j.chom.2017.04.002	2017
Metabolism	Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy.	Li G, Yin P, Chu S, Gao W, Cui S, Guo S, Xu Y, Yuan E, Zhu T, You J, Zhang J, Yang M.	J Diabetes Res	10.1155/2021/8892849	2021
	Gut microbiota modulation in patients with non-alcoholic fatty liver disease: Effects of current treatments and future strategies.	Maestri M, Santopaolo F, Pompili M, Gasbarrini A, Ponziani FR.	Front Nutr	10.3389/fnut.2023.1110536	2023
	Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics.	Miura N, Okuda S.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.01.015	2023
	Effects of Alternative Administration Programs of a Synbiotic Supplement on Broiler Performance, Foot Pad Dermatitis, Caecal Microbiota, and Blood Metabolites.	Brugaletta G, De Cesare A, Zampiga M, Laghi L, Oliveri C, Zhu C, Manfreda G, Syed B, Valenzuela L, Sirri F.	Animals (Basel)	10.3390/ani10030522	2020
	Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.	Avuthu N, Guda C.	Microbiol Spectr	10.1128/spectrum.00013-22	2022
	Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn's Disease: Results from the IMPACT Study.	Park SK, Kim HN, Choi CH, Im JP, Cha JM, Eun CS, Kim TO, Kang SB, Bang KB, Kim HG, Jung Y, Yoon H, Han DS, Lee CW, Ahn K, Kim HL, Park DI.	J Clin Med	10.3390/jcm9061748	2020
	Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context.	Almeida-Santos AC, Novais C, Peixe L, Freitas AR.	Antibiotics (Basel)	10.3390/antibiotics10101215	2021
	Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire.	Andreu-Sanchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Lifelines Cohort Study, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A.	Immunity	10.1016/j.immuni.2023.04.003	2023
Pathogenicity	Microbiota translocation following intestinal barrier disruption promotes Mincle-mediated training of myeloid progenitors in the bone marrow.	Robles-Vera I, Jarit-Cabanillas A, Brandi P, Martinez-Lopez M, Martinez-Cano S, Rodrigo-Tapias M, Femenia-Muina M, Redondo-Urzainqui A, Nunez V, Gonzalez-Correa C, Moleon J, Duarte J, Conejero L, Mata-Martinez P, Diez-Rivero CM, Bergon-Gutierrez M, Fernandez-Lopez I, Gomez MJ, Quintas A, Dopazo A, Sanchez-Cabo F, Pariente E, Del Fresno C, Subiza JL, Iborra S, Sancho D.	Immunity	10.1016/j.immuni.2024.12.012	2025
	Oral Health of Patients Treated with Acrylic Partial Dentures Using a Toothpaste Containing Bee Product.	Wiatrak K, Morawiec T, Roj R, Mertas A, Machorowska-Pieniazek A, Kownacki P, Tanasiewicz M, Skucha-Nowak M, Baron S, Piekarz T, Wrzol M, Bogacz M, Kasperski J, Niedzielska I.	Evid Based Complement Alternat Med	10.1155/2017/4034179	2017
	Oral Administration of Compound Probiotics Improved Canine Feed Intake, Weight Gain, Immunity and Intestinal Microbiota.	Xu H, Huang W, Hou Q, Kwok LY, Laga W, Wang Y, Ma H, Sun Z, Zhang H.	Front Immunol	10.3389/fimmu.2019.00666	2019
	Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.	Stamboulian M, Li S, Ye Y.	Microbiome	10.1186/s40168-021-01035-8	2021
	H. pylori Eradication Treatment Alters Gut Microbiota and GLP-1 Secretion in Humans.	Cornejo-Pareja I, Martin-Nunez GM, Roca-Rodriguez MM, Cardona F, Coin-Araguez L, Sanchez-Alcoholado L, Gutierrez-Repiso C, Munoz-Garach A, Fernandez-Garcia JC, Moreno-Indias I, Tinahones FJ.	J Clin Med	10.3390/jcm8040451	2019
	Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications.	van Leeuwen PT, Brul S, Zhang J, Wortel MT.	FEMS Microbiol Rev	10.1093/femsre/fuad012	2023
	Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR.	Sagheddu V, Patrone V, Miragoli F, Morelli L.	Front Nutr	10.3389/fnut.2017.00029	2017
	Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations.	Kleigrewe K, Haack M, Baudin M, Menabreaz T, Crovadore J, Masri M, Beyrer M, Andlauer W, Lefort F, Dawid C, Bruck TB, Bruck WM.	Int J Mol Sci	10.3390/ijms231810473	2022
	Novel genomic islands and a new vanD-subtype in the first sporadic VanD-type vancomycin resistant enterococci in Norway.	Al Rubaye MTS, Janice J, Bjornholt JV, Jakovljev A, Hultstrom ME, Sundsfjord A, Hegstad K.	PLoS One	10.1371/journal.pone.0255187	2021
Metabolism	Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude.	Han Y, Liu X, Jia Q, Xu J, Shi J, Li X, Xie G, Zhao X, He K.	Microbiome	10.1186/s40168-024-01781-5	2024
	A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.	Krigul KL, Feeney RH, Wongkuna S, Aasmets O, Holmberg SM, Andreson R, Puertolas-Balint F, Pantiukh K, Sootak L, Org T, Tenson T, Org E, Schroeder BO.	Gut Microbes	10.1080/19490976.2024.2377570	2024
Pathogenicity	Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry.	McCann SE, Hullar MAJ, Tritchler DL, Cortes-Gomez E, Yao S, Davis W, O'Connor T, Erwin D, Thompson LU, Yan L, Lampe JW.	Nutrients	10.3390/nu13030919	2021
Metabolism	Sensitivity to oxazolone induced dermatitis is transferable with gut microbiota in mice.	Zachariassen LF, Krych L, Engkilde K, Nielsen DS, Kot W, Hansen CH, Hansen AK.	Sci Rep	10.1038/srep44385	2017
	Fungal beta-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species.	Fernandez-Julia P, Black GW, Cheung W, Van Sinderen D, Munoz-Munoz J.	Commun Biol	10.1038/s42003-023-04970-4	2023
Pathogenicity	Developmental exposure of California mice to endocrine disrupting chemicals and potential effects on the microbiome-gut-brain axis at adulthood.	Kaur S, Sarma SJ, Marshall BL, Liu Y, Kinkade JA, Bellamy MM, Mao J, Helferich WG, Schenk AK, Bivens NJ, Lei Z, Sumner LW, Bowden JA, Koelmel JP, Joshi T, Rosenfeld CS.	Sci Rep	10.1038/s41598-020-67709-9	2020
	Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation.	Lima SF, Gogokhia L, Viladomiu M, Chou L, Putzel G, Jin WB, Pires S, Guo CJ, Gerardin Y, Crawford CV, Jacob V, Scherl E, Brown SE, Hambor J, Longman RS.	Gastroenterology	10.1053/j.gastro.2021.09.061	2022
Metabolism	A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema.	Ta LDH, Chan JCY, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YM, Tay CJX, Huang CH, Kioh DYQ, Woon JY, Tham EH, Loo EXL, Shek LPC, Karnani N, Goh A, Van Bever HPS, Teoh OH, Chan YH, Lay C, Knol J, Yap F, Tan KH, Chong YS, Godfrey KM, Kjelleberg S, Schuster SC, Chan ECY, Lee BW.	Gut Microbes	10.1080/19490976.2020.1801964	2020
	Evaluation of Antioxidant Activity and Biotransformation of Opuntia Ficus Fruit: The Effect of In Vitro and Ex Vivo Gut Microbiota Metabolism.	Sallam IE, Rolle-Kampczyk U, Schape SS, Zaghloul SS, El-Dine RS, Shao P, Bergen MV, Farag MA.	Molecules	10.3390/molecules27217568	2022
	Gut Dysbiosis and Its Associations with Gut Microbiota-Derived Metabolites in Dogs with Myxomatous Mitral Valve Disease.	Li Q, Larouche-Lebel E, Loughran KA, Huh TP, Suchodolski JS, Oyama MA.	mSystems	10.1128/msystems.00111-21	2021
	Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats.	Xiao K, Liang X, Lu H, Li X, Zhang Z, Lu X, Wang H, Meng Y, Roy A, Luo W, Shen X, Irwin DM, Shen Y.	ISME J	10.1038/s41396-022-01247-2	2022
Metabolism	The Central Role of Interbacterial Antagonism in Bacterial Life.	Peterson SB, Bertolli SK, Mougous JD.	Curr Biol	10.1016/j.cub.2020.06.103	2020
Enzymology	Eggerthella lenta DSM 2243 Alleviates Bile Acid Stress Response in Clostridium ramosum and Anaerostipes caccae by Transformation of Bile Acids.	Pedersen KJ, Haange SB, Zizalova K, Viehof A, Clavel T, Lenicek M, Engelmann B, Wick LY, Schaap FG, Jehmlich N, Rolle-Kampczyk U, von Bergen M.	Microorganisms	10.3390/microorganisms10102025	2022
Pathogenicity	Microflora Disturbance during Progression of Glucose Intolerance and Effect of Sitagliptin: An Animal Study.	Yan X, Feng B, Li P, Tang Z, Wang L.	J Diabetes Res	10.1155/2016/2093171	2016
	Distribution, biosynthesis and therapeutic potential of lignans.	Plaha NS, Awasthi S, Sharma A, Kaushik N.	3 Biotech	10.1007/s13205-022-03318-9	2022
	Development of the equine gut microbiota.	Lindenberg F, Krych L, Kot W, Fielden J, Frokiaer H, van Galen G, Nielsen DS, Hansen AK.	Sci Rep	10.1038/s41598-019-50563-9	2019
	Changes in the Intestinal Microbiota Are Seen Following Treatment with Infliximab in Children with Crohn's Disease.	Kowalska-Duplaga K, Kapusta P, Gosiewski T, Sroka-Oleksiak A, Ludwig-Slomczynska AH, Wolkow PP, Fyderek K.	J Clin Med	10.3390/jcm9030687	2020
	Identification of Clinical Isolates of Candida albicans with Increased Fitness in Colonization of the Murine Gut.	Alonso-Monge R, Prieto D, Coman I, Rochas S, Arana DM, Hidalgo-Vico S, Roman E, Pla J.	J Fungi (Basel)	10.3390/jof7090695	2021
	Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesity.	Pesoa SA, Portela N, Fernandez E, Elbarcha O, Gotteland M, Magne F.	Sci Rep	10.1038/s41598-021-87365-x	2021
	Prediction of advanced fibrosis in non-alcoholic fatty liver disease using gut microbiota-based approaches compared with simple non-invasive tools.	Lang S, Farowski F, Martin A, Wisplinghoff H, Vehreschild MJGT, Krawczyk M, Nowag A, Kretzschmar A, Scholz C, Kasper P, Roderburg C, Lammert F, Goeser T, Steffen HM, Demir M.	Sci Rep	10.1038/s41598-020-66241-0	2020
Pathogenicity	Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions.	Upadhyaya B, McCormack L, Fardin-Kia AR, Juenemann R, Nichenametla S, Clapper J, Specker B, Dey M.	Sci Rep	10.1038/srep28797	2016
	Ergothioneine, a metabolite of the gut bacterium Lactobacillus reuteri, protects against stress-induced sleep disturbances.	Matsuda Y, Ozawa N, Shinozaki T, Wakabayashi KI, Suzuki K, Kawano Y, Ohtsu I, Tatebayashi Y.	Transl Psychiatry	10.1038/s41398-020-0855-1	2020
	Lactulose Suppresses Osteoclastogenesis and Ameliorates Estrogen Deficiency-Induced Bone Loss in Mice.	Chen X, Zhang Z, Hu Y, Cui J, Zhi X, Li X, Jiang H, Wang Y, Gu Z, Qiu Z, Dong X, Li Y, Su J.	Aging Dis	10.14336/ad.2019.0613	2020
Pathogenicity	Synergistic depletion of gut microbial consortia, but not individual antibiotics, reduces amyloidosis in APPPS1-21 Alzheimer's transgenic mice.	Dodiya HB, Frith M, Sidebottom A, Cao Y, Koval J, Chang E, Sisodia SS.	Sci Rep	10.1038/s41598-020-64797-5	2020
Pathogenicity	Protective effects of PX478 on gut barrier in a mouse model of ethanol and burn injury.	Morris NL, Cannon AR, Li X, Choudhry MA.	J Leukoc Biol	10.1002/jlb.3a0820-323rr	2021
	Gut Microbiota in a Rat Oral Sensitization Model: Effect of a Cocoa-Enriched Diet.	Camps-Bossacoma M, Perez-Cano FJ, Franch A, Castell M.	Oxid Med Cell Longev	10.1155/2017/7417505	2017
	Nutraceuticals and Herbal Food Supplements for Weight Loss: Is There a Prebiotic Role in the Mechanism of Action?	Bertuccioli A, Cardinali M, Biagi M, Moricoli S, Morganti I, Zonzini GB, Rigillo G.	Microorganisms	10.3390/microorganisms9122427	2021
	Novel Inter-omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA-B27-Induced Experimental Spondyloarthritis.	Gill T, Brooks SR, Rosenbaum JT, Asquith M, Colbert RA.	Arthritis Rheumatol	10.1002/art.41018	2019
	Distinct responsiveness to rifaximin in patients with hepatic encephalopathy depends on functional gut microbial species.	Yukawa-Muto Y, Kamiya T, Fujii H, Mori H, Toyoda A, Sato I, Konishi Y, Hirayama A, Hara E, Fukuda S, Kawada N, Ohtani N.	Hepatol Commun	10.1002/hep4.1954	2022
Metabolism	Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples.	Palakawong Na Ayudthaya S, van der Oost H, van der Oost J, van Vliet DM, Plugge CM.	Curr Microbiol	10.1007/s00284-019-01630-x	2019
Phylogeny	Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens.	Proszkowiec-Weglarz M, Miska KB, Ellestad LE, Schreier LL, Kahl S, Darwish N, Campos P, Shao J.	BMC Microbiol	10.1186/s12866-022-02619-6	2022
	Metabolomics reveals impact of seven functional foods on metabolic pathways in a gut microbiota model.	Farag MA, Abdelwareth A, Sallam IE, El Shorbagi M, Jehmlich N, Fritz-Wallace K, Serena Schape S, Rolle-Kampczyk U, Ehrlich A, Wessjohann LA, von Bergen M.	J Adv Res	10.1016/j.jare.2020.01.001	2020
	Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus.	Sagheddu V, Patrone V, Miragoli F, Puglisi E, Morelli L.	Front Pediatr	10.3389/fped.2016.00057	2016
	Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx.	Schape SS, Krause JL, Masanetz RK, Riesbeck S, Starke R, Rolle-Kampczyk U, Eberlein C, Heipieper HJ, Herberth G, von Bergen M, Jehmlich N.	Microorganisms	10.3390/microorganisms8091436	2020
	Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet.	Liu S, Tun HM, Leung FC, Bennett DC, Zhang H, Cheng KM.	Sci Rep	10.1038/s41598-018-20508-9	2018
Phylogeny	Imaging the in vivo growth patterns of bacteria in human gut Microbiota.	Lin L, Song J, Li J, Zuo X, Wei H, Yang C, Wang W.	Gut Microbes	10.1080/19490976.2021.1960134	2021
	Probiotics in the Intensive Care Unit.	Schuurman AR, Kullberg RFJ, Wiersinga WJ.	Antibiotics (Basel)	10.3390/antibiotics11020217	2022
	Microbiome in Cancer Development and Treatment.	Ciernikova S, Sevcikova A, Mladosievicova B, Mego M.	Microorganisms	10.3390/microorganisms12010024	2023
	Berberine-microbiota interplay: orchestrating gut health through modulation of the gut microbiota and metabolic transformation into bioactive metabolites.	Dehau T, Cherlet M, Croubels S, Van De Vliet M, Goossens E, Van Immerseel F.	Front Pharmacol	10.3389/fphar.2023.1281090	2023
	Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice.	Vasquez Ayala A, Hsu CY, Oles RE, Matsuo K, Loomis LR, Buzun E, Carrillo Terrazas M, Gerner RR, Lu HH, Kim S, Zhang Z, Park JH, Rivaud P, Thomson M, Lu LF, Min B, Chu H.	J Exp Med	10.1084/jem.20230063	2024
	A Novel Role of SLC26A3 in the Maintenance of Intestinal Epithelial Barrier Integrity.	Kumar A, Priyamvada S, Ge Y, Jayawardena D, Singhal M, Anbazhagan AN, Chatterjee I, Dayal A, Patel M, Zadeh K, Saksena S, Alrefai WA, Gill RK, Zadeh M, Zhao N, Mohamadzadeh M, Dudeja PK.	Gastroenterology	10.1053/j.gastro.2020.11.008	2021
	Following the community development of SIHUMIx - a new intestinal in vitro model for bioreactor use.	Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N, Von Bergen M, Herberth G.	Gut Microbes	10.1080/19490976.2019.1702431	2020
Phylogeny	Fecal microbiota composition changes after a BW loss diet in Beagle dogs.	Salas-Mani A, Jeusette I, Castillo I, Manuelian CL, Lionnet C, Iraculis N, Sanchez N, Fernandez S, Vilaseca L, Torre C.	J Anim Sci	10.1093/jas/sky193	2018
	Interactions between species introduce spurious associations in microbiome studies.	Menon R, Ramanan V, Korolev KS.	PLoS Comput Biol	10.1371/journal.pcbi.1005939	2018
Genetics	Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics.	Podlesny D, Durdevic M, Paramsothy S, Kaakoush NO, Hogenauer C, Gorkiewicz G, Walter J, Fricke WF.	Cell Rep Med	10.1016/j.xcrm.2022.100711	2022
	Effects of the Water Extract of Fermented Rice Bran on Liver Damage and Intestinal Injury in Aged Rats with High-Fat Diet Feeding.	Chen TY, Chen YL, Chiu WC, Yeh CL, Tung YT, Shirakawa H, Liao WT, Yang SC.	Plants (Basel)	10.3390/plants11050607	2022
	Factors Explaining Interpersonal Variation in Plasma Enterolactone Concentrations in Humans.	Halldin E, Eriksen AK, Brunius C, da Silva AB, Bronze M, Hanhineva K, Aura AM, Landberg R.	Mol Nutr Food Res	10.1002/mnfr.201801159	2019
Phylogeny	Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal.	Abbas-Egbariya H, Haberman Y, Braun T, Hadar R, Denson L, Gal-Mor O, Amir A.	Genome Biol	10.1186/s13059-022-02637-7	2022
	Role of the gut microbiome in three major psychiatric disorders.	Borkent J, Ioannou M, Laman JD, Haarman BCM, Sommer IEC, Sommer IEC.	Psychol Med	10.1017/s0033291722000897	2022
	Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.	Clooney AG, Eckenberger J, Laserna-Mendieta E, Sexton KA, Bernstein MT, Vagianos K, Sargent M, Ryan FJ, Moran C, Sheehan D, Sleator RD, Targownik LE, Bernstein CN, Shanahan F, Claesson MJ.	Gut	10.1136/gutjnl-2020-321106	2021
	Effects of Banana Resistant Starch on the Biochemical Indexes and Intestinal Flora of Obese Rats Induced by a High-Fat Diet and Their Correlation Analysis.	Fu J, Wang Y, Tan S, Wang J.	Front Bioeng Biotechnol	10.3389/fbioe.2021.575724	2021
Metabolism	Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease.	Sankarasubramanian J, Ahmad R, Avuthu N, Singh AB, Guda C.	Front Med (Lausanne)	10.3389/fmed.2020.606298	2020
Genetics	The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet.	Liu S, Bennett DC, Tun HM, Kim JE, Cheng KM, Zhang H, Leung FC.	Front Microbiol	10.3389/fmicb.2015.01092	2015
Metabolism	Frozen Autoclaved Sorghum Enhanced Colonic Fermentation and Lower Visceral Fat Accumulation in Rats.	Pelpolage SW, Yoshida A, Nagata R, Shimada K, Fukuma N, Bochimoto H, Hamamoto T, Hoshizawa M, Nakano K, Han KH, Fukushima M.	Nutrients	10.3390/nu12082412	2020
	The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors.	Schape SS, Krause JL, Engelmann B, Fritz-Wallace K, Schattenberg F, Liu Z, Muller S, Jehmlich N, Rolle-Kampczyk U, Herberth G, von Bergen M.	Microorganisms	10.3390/microorganisms7120641	2019
	Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis.	Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lahdesmaki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ.	Genome Med	10.1186/s13073-021-00853-7	2021
Pathogenicity	Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans.	Guinan J, Wang S, Hazbun TR, Yadav H, Thangamani S.	Sci Rep	10.1038/s41598-019-45467-7	2019
Phylogeny	First Korean case of Robinsoniella peoriensis bacteremia in a patient with aspiration pneumonia.	Jeon Y, Kim TS, Kim HB, Park KU, Song J, Kim EC.	Ann Lab Med	10.3343/alm.2012.32.5.370	2012
Metabolism	Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters.	Lecomte V, Kaakoush NO, Maloney CA, Raipuria M, Huinao KD, Mitchell HM, Morris MJ.	PLoS One	10.1371/journal.pone.0126931	2015
Genetics	Contribution of Host Genetics to the Variation of Microbial Composition of Cecum Lumen and Feces in Pigs.	Chen C, Huang X, Fang S, Yang H, He M, Zhao Y, Huang L.	Front Microbiol	10.3389/fmicb.2018.02626	2018
Metabolism	Propionate-producing bacteria in the intestine may associate with skewed responses of IL10-producing regulatory T cells in patients with relapsing polychondritis.	Shimizu J, Kubota T, Takada E, Takai K, Fujiwara N, Arimitsu N, Murayama MA, Ueda Y, Wakisaka S, Suzuki T, Suzuki N.	PLoS One	10.1371/journal.pone.0203657	2018
	Faecalibacterium prausnitzii and a Prebiotic Protect Intestinal Health in a Mouse Model of Antibiotic and Clostridium difficile Exposure.	Roychowdhury S, Cadnum J, Glueck B, Obrenovich M, Donskey C, Cresci GAM.	JPEN J Parenter Enteral Nutr	10.1002/jpen.1053	2018
	Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.	Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR.	Front Microbiol	10.3389/fmicb.2018.03220	2018
	Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation.	Fan P, Bian B, Teng L, Nelson CD, Driver J, Elzo MA, Jeong KC.	ISME J	10.1038/s41396-019-0529-2	2020
Phylogeny	Taxonomy-aware feature engineering for microbiome classification.	Oudah M, Henschel A.	BMC Bioinformatics	10.1186/s12859-018-2205-3	2018
	Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens.	Zhou M, Hunerberg M, Chen Y, Reuter T, McAllister TA, Evans F, Critchley AT, Guan LL.	mSphere	10.1128/msphere.00017-18	2018
Phylogeny	Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria.	Helfrich EJN, Ueoka R, Ueoka R, Chevrette MG, Hemmerling F, Lu X, Leopold-Messer S, Minas HA, Burch AY, Lindow SE, Piel J, Medema MH.	Nat Commun	10.1038/s41467-021-21163-x	2021
Genetics	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium.	Mu A, Carter GP, Li L, Isles NS, Vrbanac AF, Morton JT, Jarmusch AK, De Souza DP, Narayana VK, Kanojia K, Nijagal B, McConville MJ, Knight R, Howden BP, Stinear TP.	mSystems	10.1128/msystems.00452-20	2020
Genetics	Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.	Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M.	Microbiome	10.1186/s40168-020-00981-z	2021
Pathogenicity	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness.	Marfil-Sanchez A, Zhang L, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M, Panagiotou G.	Gut Microbes	10.1080/19490976.2021.1993598	2021
	Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches.	Chiu CM, Huang WC, Weng SL, Tseng HC, Liang C, Wang WC, Yang T, Yang TL, Weng CT, Chang TH, Huang HD.	Biomed Res Int	10.1155/2014/906168	2014
Metabolism	Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro.	Perdijk O, van Baarlen P, Fernandez-Gutierrez MM, van den Brink E, Schuren FHJ, Brugman S, Savelkoul HFJ, Kleerebezem M, van Neerven RJJ.	Front Immunol	10.3389/fimmu.2019.00094	2019
	Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge.	Crouzet L, Derrien M, Cherbuy C, Plancade S, Foulon M, Chalin B, van Hylckama Vlieg JET, Grompone G, Rigottier-Gois L, Serror P.	Sci Rep	10.1038/s41598-018-23437-9	2018
Metabolism	In Vivo Effects of Einkorn Wheat (Triticum monococcum) Bread on the Intestinal Microbiota, Metabolome, and on the Glycemic and Insulinemic Response in the Pig Model.	Barone F, Laghi L, Gianotti A, Ventrella D, Saa DLT, Bordoni A, Forni M, Brigidi P, Bacci ML, Turroni S.	Nutrients	10.3390/nu11010016	2018
Pathogenicity	Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.	Montassier E, Valdes-Mas R, Batard E, Zmora N, Dori-Bachash M, Suez J, Elinav E.	Nat Microbiol	10.1038/s41564-021-00920-0	2021
	Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1.	McCulloch JA, Davar D, Rodrigues RR, Badger JH, Fang JR, Cole AM, Balaji AK, Vetizou M, Prescott SM, Fernandes MR, Costa RGF, Yuan W, Salcedo R, Bahadiroglu E, Roy S, DeBlasio RN, Morrison RM, Chauvin JM, Ding Q, Zidi B, Lowin A, Chakka S, Gao W, Pagliano O, Ernst SJ, Rose A, Newman NK, Morgun A, Zarour HM, Trinchieri G, Dzutsev AK.	Nat Med	10.1038/s41591-022-01698-2	2022
Metabolism	Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.	Pareek S, Kurakawa T, Das B, Motooka D, Nakaya S, Rongsen-Chandola T, Goyal N, Kayama H, Dodd D, Okumura R, Maeda Y, Fujimoto K, Nii T, Ogawa T, Iida T, Bhandari N, Kida T, Nakamura S, Nair GB, Takeda K.	NPJ Biofilms Microbiomes	10.1038/s41522-019-0110-9	2019
Enzymology	Identification and characterization of a 20beta-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058.	Devendran S, Mendez-Garcia C, Ridlon JM.	J Lipid Res	10.1194/jlr.m074914	2017
	Polyphenols as Drivers of a Homeostatic Gut Microecology and Immuno-Metabolic Traits of Akkermansia muciniphila: From Mouse to Man.	Rodriguez-Daza MC, de Vos WM.	Int J Mol Sci	10.3390/ijms24010045	2022
	Intestinal Flora Disruption and Novel Biomarkers Associated With Nasopharyngeal Carcinoma.	Jiang H, Li J, Zhang B, Huang R, Zhang J, Chen Z, Shang X, Li X, Nie X.	Front Oncol	10.3389/fonc.2019.01346	2019
	In Vitro and In Vivo Models for Evaluating the Oral Toxicity of Nanomedicines.	Lama S, Merlin-Zhang O, Yang C.	Nanomaterials (Basel)	10.3390/nano10112177	2020
Metabolism	Nopal (Opuntia ficus indica) protects from metabolic endotoxemia by modifying gut microbiota in obese rats fed high fat/sucrose diet.	Sanchez-Tapia M, Aguilar-Lopez M, Perez-Cruz C, Pichardo-Ontiveros E, Wang M, Donovan SM, Tovar AR, Torres N.	Sci Rep	10.1038/s41598-017-05096-4	2017
Pathogenicity	Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation.	Annavajhala MK, Gomez-Simmonds A, Macesic N, Sullivan SB, Kress A, Khan SD, Giddins MJ, Stump S, Kim GI, Narain R, Verna EC, Uhlemann AC.	Nat Commun	10.1038/s41467-019-12633-4	2019
Metabolism	CO Metabolism in the Thermophilic Acetogen Thermoanaerobacter kivui.	Weghoff MC, Muller V.	Appl Environ Microbiol	10.1128/aem.00122-16	2016
	Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae.	Djukovic A, Garzon MJ, Canlet C, Cabral V, Lalaoui R, Garcia-Garcera M, Rechenberger J, Tremblay-Franco M, Penaranda I, Puchades-Carrasco L, Pineda-Lucena A, Gonzalez-Barbera EM, Salavert M, Lopez-Hontangas JL, Sanz MA, Sanz J, Kuster B, Rolain JM, Debrauwer L, Xavier KB, Xavier JB, Ubeda C.	Nat Commun	10.1038/s41467-022-33313-w	2022
Pathogenicity	Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.	Zhang XS, Yin YS, Wang J, Battaglia T, Krautkramer K, Li WV, Li J, Brown M, Zhang M, Badri MH, Armstrong AJS, Strauch CM, Wang Z, Nemet I, Altomare N, Devlin JC, He L, Morton JT, Chalk JA, Needles K, Liao V, Mount J, Li H, Ruggles KV, Bonneau RA, Dominguez-Bello MG, Backhed F, Hazen SL, Blaser MJ.	Cell Host Microbe	10.1016/j.chom.2021.06.014	2021
Metabolism	Novel Probiotic Mechanisms of the Oral Bacterium Streptococcus sp. A12 as Explored with Functional Genomics.	Lee K, Walker AR, Chakraborty B, Kaspar JR, Nascimento MM, Burne RA.	Appl Environ Microbiol	10.1128/aem.01335-19	2019
Metabolism	CO Metabolism in the Acetogen Acetobacterium woodii.	Bertsch J, Muller V.	Appl Environ Microbiol	10.1128/aem.01772-15	2015
Genetics	The impact of sequence database choice on metaproteomic results in gut microbiota studies.	Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S.	Microbiome	10.1186/s40168-016-0196-8	2016
Metabolism	A biosynthetic pathway for a prominent class of microbiota-derived bile acids.	Devlin AS, Fischbach MA.	Nat Chem Biol	10.1038/nchembio.1864	2015
Metabolism	An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis.	Poehlein A, Schmidt S, Kaster AK, Goenrich M, Vollmers J, Thurmer A, Bertsch J, Schuchmann K, Voigt B, Hecker M, Daniel R, Thauer RK, Gottschalk G, Muller V.	PLoS One	10.1371/journal.pone.0033439	2012
	Enterococci and Their Interactions with the Intestinal Microbiome.	Dubin K, Pamer EG.	Microbiol Spectr	10.1128/microbiolspec.bad-0014-2016	2014
Pathogenicity	A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.	Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Muller CL, Cadwell K, Bonneau R, Perez-Perez GI, Blaser MJ.	Nat Commun	10.1038/s41467-017-00531-6	2017
	A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.	Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, Asadourian M, Moon BH, Ayson A, Borneman J, McGovern DP, Fornace AJ, Braun J, Dubinsky M.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2016.06.004	2016
	Candida albicans Inhibits Pseudomonas aeruginosa Virulence through Suppression of Pyochelin and Pyoverdine Biosynthesis.	Lopez-Medina E, Fan D, Coughlin LA, Ho EX, Lamont IL, Reimmann C, Hooper LV, Koh AY.	PLoS Pathog	10.1371/journal.ppat.1005129	2015
Metabolism	Evidence for a hexaheteromeric methylenetetrahydrofolate reductase in Moorella thermoacetica.	Mock J, Wang S, Huang H, Kahnt J, Thauer RK.	J Bacteriol	10.1128/jb.01839-14	2014
Phylogeny	Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.	Nowinski B, Smith CB, Thomas CM, Esson K, Marin R, Preston CM, Birch JM, Scholin CA, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Glavina Del Rio T, Whitman WB, Kiene RP, Eloe-Fadrosh EA, Moran MA.	Sci Data	10.1038/s41597-019-0132-4	2019
	Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD⁺ (Rnf) as Electron Acceptors: A Historical Review.	Buckel W, Thauer RK.	Front Microbiol	10.3389/fmicb.2018.00401	2018
Phylogeny	A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.	Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernandez SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischoder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Sproer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-020-19929-w	2020
Pathogenicity	Adjusting for age improves identification of gut microbiome alterations in multiple diseases.	Ghosh TS, Das M, Jeffery IB, O'Toole PW.	Elife	10.7554/elife.50240	2020
	The first 1000 cultured species of the human gastrointestinal microbiota.	Rajilic-Stojanovic M, de Vos WM.	FEMS Microbiol Rev	10.1111/1574-6976.12075	2014
Pathogenicity	A discovery platform for identification of host-induced bacterial biosensors from diverse sources.	Robinson CM, Carreno D, Weber T, Chen Y, Riglar DT.	Mol Syst Biol	10.1038/s44320-025-00123-3	2025
Metabolism	Biochemical Basis of Xylooligosaccharide Utilisation by Gut Bacteria.	Singh RP, Bhaiyya R, Thakur R, Niharika J, Singh C, Latousakis D, Saalbach G, Nepogodiev SA, Singh P, Sharma SC, Sengupta S, Juge N, Field RA	Int J Mol Sci	10.3390/ijms23062992	2022
Metabolism	The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.	Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR	Gut Microbes	10.1080/19490976.2019.1618173	2019
Pathogenicity	Effects of difructose anhydride III (DFA III) administration on rat intestinal microbiota.	Minamida K, Shiga K, Sujaya IN, Sone T, Yokota A, Hara H, Asano K, Tomita F	J Biosci Bioeng	10.1263/jbb.99.230	2005
Phylogeny	16S ribosomal DNA sequences of anaerobic cocci and proposal of Ruminococcus hansenii comb. nov. and Ruminococcus productus comb. nov.	Ezaki T, Li N, Hashimoto Y, Miura H, Yamamoto H	Int J Syst Bacteriol	10.1099/00207713-44-1-130	1994
Pathogenicity	Serological studies of peptostreptococci using an indirect fluorescent antibody test.	Collins ML, Falkler WA Jr, Hall ER, Graham MB	J Dent Res	10.1177/00220345890680110801	1989
	A Comprehensive Assessment of the Safety of Blautia producta DSM 2950.	Liu X, Guo W, Cui S, Tang X, Zhao J, Zhang H, Mao B, Chen W	Microorganisms	10.3390/microorganisms9050908	2021
Genetics	Complete Genome Sequence of Blautia producta JCM 1471(T).	Tourlousse DM, Sakamoto M, Miura T, Narita K, Ohashi A, Uchino Y, Yamazoe A, Kameyama K, Terauchi J, Ohkuma M, Kawasaki H, Sekiguchi Y	Microbiol Resour Announc	10.1128/MRA.00141-20	2020
Metabolism	Comparative evaluation of the metabolic potentials of different strains of Peptostreptococcus productus: utilization and transformation of aromatic compounds.	Parekh M, Keith ES, Daniel SL, Drake HL	FEMS Microbiol Lett	10.1016/0378-1097(92)90585-c	1992
Phylogeny	Blautia parvula sp. nov., isolated from Japanese faecal samples.	Miura T, Shimamura M, Yamazoe A, Kawasaki H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005871	2023
Phylogeny	Blautia hominis sp. nov., isolated from human faeces.	Shin NR, Kang W, Tak EJ, Hyun DW, Kim PS, Kim HS, Lee JY, Sung H, Whon TW, Bae JW.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002623	2018
Phylogeny	Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut.	Klaring K, Just S, Lagkouvardos I, Hanske L, Haller D, Blaut M, Wenning M, Clavel T.	Int J Syst Evol Microbiol	10.1099/ijs.0.000030	2015
Phylogeny	Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces.	Liu C, Finegold SM, Song Y, Lawson PA.	Int J Syst Evol Microbiol	10.1099/ijs.0.65208-0	2008
Phylogeny	Blautia faecicola sp. nov., isolated from faeces from a healthy human.	Kim JS, Park JE, Lee KC, Choi SH, Oh BS, Yu SY, Eom MK, Kang SW, Han KI, Suh MK, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JH, Lee JS, Park SH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004015	2020
Phylogeny	Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces.	Paek J, Shin Y, Kook JK, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002981	2018
Phylogeny	Blautia stercoris sp. nov., isolated from human faeces.	Park SK, Kim MS, Roh SW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.031625-0	2011

References

#1258	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2950
#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 )
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68375	Automatically annotated from API ID32STA .
#68380	Automatically annotated from API rID32A .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Blautia producta (DSM 2950, ATCC 27340, CCUG 10976)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

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Physiology and metabolism

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Murein

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Genome browser: GCA_010669205

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