Desulfovibrio piger (DSM 749, ATCC 29098, JCM 12224)

Name: Desulfovibrio piger (DSM 749, ATCC 29098, JCM 12224)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4070

Type strain

Culture col. no. DSM 749 ATCC 29098 JCM 12224 VPI 11112 VPI C3-23

NCBI tax ID(s) 411464 901

Special Collections DSMZ JCM

History DSMZ <- N. Pfennig, Gesellschaft für Strahlen- und Umweltforschung mbH München in Göttingen, Germany; VPI 11112 <- W. E. C. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA

Links

Desulfovibrio piger DSM 749 is an anaerobe bacterium that was isolated from human faeces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 39351

ATCC 29098,DSM 749,JCM 12224

@ref 20215

Last LPSN update 2026-05-29 08:25:51

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Desulfovibrio

Species Desulfovibrio piger

Full scientific name Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002

Synonyms (1)

Desulfomonas pigra

BacDive ID	Other strains from **Desulfovibrio piger** (1)	Type strain
158923	D. piger PG-251-APC-1, DSM 106036

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
422	DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
422	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
422	anaerobe
125439	obligate anaerobe	99.406

Spore formation

@ref	Spore formation	Confidence
125439		92.412

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	aspartate and asparagine metabolism	100	9 of 9
66794	chorismate metabolism	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B12 metabolism	82.35	28 of 34
66794	purine metabolism	80.85	76 of 94
66794	lipoate biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	polyamine pathway	69.57	16 of 23
66794	phenylalanine metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	alanine metabolism	68.97	20 of 29
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	acetoin degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	cysteine metabolism	66.67	12 of 18
66794	pyrimidine metabolism	66.67	30 of 45
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	heme metabolism	64.29	9 of 14
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	glycogen metabolism	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	oxidative phosphorylation	58.24	53 of 91
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	non-pathway related	52.63	20 of 38
66794	histidine metabolism	51.72	15 of 29
66794	sulfopterin metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	gluconeogenesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	lipid metabolism	48.39	15 of 31
66794	lysine metabolism	47.62	20 of 42
66794	tryptophan metabolism	47.37	18 of 38
66794	urea cycle	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	leucine metabolism	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	tyrosine metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	degradation of sugar acids	36	9 of 25
66794	phenol degradation	35	7 of 20
66794	methane metabolism	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	vitamin E metabolism	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species
422	human faeces	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AF192152 (>99% sequence identity) for Desulfovibrio piger subclade from Microbeatlas

Aquatic Samples	4606
Soil Samples	1726
Animal Samples	113854
Plant Samples	581
Total Samples	120767

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
422	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	ASM15637v1 assembly for Desulfovibrio piger ATCC 29098	scaffold	GCA_000156375	411464.8	642979316	411464	53.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	D.pigra 16S ribosomal rRNA	M34404	1378		901
422	Desulfomonas pigra 16S ribosomal RNA gene, complete sequence	AF192152	1542		411464

GC content

422

GC-content (mol%)67.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM15637v1 assembly for Desulfovibrio piger ATCC 29098
NCBI: GCA_000156375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.41	no
125439	gram_stain	BacteriaNetⓘ	negative	75.46	no
125439	motility	BacteriaNetⓘ	yes	66.43	no
125439	spore_formation	BacteriaNetⓘ	no	92.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfovibrio piger ATCC 29098 ATCC 29098
NCBI: GCA_000156375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	84.40	no
125438	anaerobic	anaerobicⓘ	yes	89.28	yes
125438	aerobic	aerobicⓘ	no	89.66	yes
125438	spore-forming	spore-formingⓘ	no	84.46	no
125438	thermophilic	thermophileⓘ	no	85.31	no
125438	flagellated	motile2+ⓘ	no	52.81	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Human gut strains of Desulfovibrio piger exhibit spontaneous induction of multiple prophages.	Mayer MJ, Sayavedra L, Gotts K, Wong N, Whiley H, Barham M, Narbad A.	Appl Environ Microbiol	10.1128/aem.01917-25	2025
	Effects of fermented rice bran extract with multi-microbial species on intestinal health and growth of nursery pigs.	Zheng L, Son J, Kim SW.	Anim Biosci	10.5713/ab.25.0402	2025
	Causal relationship between gut microbiota and hepatocellular carcinoma: a two-sample Mendelian randomization and case-control study.	Yang L, Wei W, Wang Y, Kuai W, Xu L.	Discov Oncol	10.1007/s12672-025-02806-7	2025
	Palmatine protects against atherosclerosis by gut microbiota and phenylalanine metabolism.	Wang A, Guan B, Yu L, Liu Q, Hou Y, Li Z, Sun D, Xu H.	Pharmacol Res	10.1016/j.phrs.2024.107413	2024
	Parent-child microbiota relationships involved in childhood obesity: A CORALS ancillary study.	de Cuevillas B, Riezu-Boj JI, Milagro FI, Galera Alquegui S, Babio N, Pastor-Villaescusa B, Gil-Campos M, Leis R, De Miguel-Etayo P, Moreno LA, Salas-Salvado J, Martinez JA, Navas-Carretero S.	Nutrition	10.1016/j.nut.2024.112603	2025
Phylogeny	Gut microbiota dysbiosis and short-chain fatty acid depletion in phlegm-dampness polycystic ovary syndrome: a cross-sectional 16S rRNA sequencing analysis.	Xia XY, Chen Y, Zhang XJ, Wang J, Xu HY, Zhao R.	BMC Endocr Disord	10.1186/s12902-025-02076-y	2025
	Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.	Berkhout MD, de Ram C, Boeren S, Plugge CM, Belzer C.	Microb Ecol	10.1007/s00248-025-02605-1	2025
	Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.	Mayer MH, Woldemariam S, Gisinger C, Dorner TE.	Int J Environ Res Public Health	10.3390/ijerph21091246	2024
Genetics	Gut microbiota and interstitial cystitis: exploring the gut-bladder axis through mendelian randomization, biological annotation and bulk RNA sequencing.	Fu C, Zhao Y, Zhou X, Lv J, Jin S, Zhou Y, Liu F, Feng N.	Front Immunol	10.3389/fimmu.2024.1395580	2024
	In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions.	Wang T, Leibrock N, Plugge CM, Smidt H, Zoetendal EG.	Gut Microbes	10.1080/19490976.2023.2261784	2023
	Exploring the causal relationship between gut microbiota and atopic dermatitis: A Mendelian randomization study.	Li W, Li A.	Medicine (Baltimore)	10.1097/md.0000000000040193	2024
Pathogenicity	Adverse childhood experiences and reoccurrence of illness impact the gut microbiome, which affects suicidal behaviours and the phenome of major depression: towards enterotypic phenotypes.	Maes M, Vasupanrajit A, Jirakran K, Klomkliew P, Chanchaem P, Tunvirachaisakul C, Plaimas K, Suratanee A, Payungporn S.	Acta Neuropsychiatr	10.1017/neu.2023.21	2023
	Genetic insights into the gut microbiota and risk of psoriasis: a bidirectional mendelian randomization study.	Qian M, Shi J, Zhang Z, Bi D, Tan C.	Front Microbiol	10.3389/fmicb.2024.1434521	2024
	Dissecting the association between gut microbiota and hypertrophic scarring: a bidirectional Mendelian randomization study.	Xue K, Zhang G, Li Z, Zeng X, Li Z, Wang F, Zhang X, Lin C, Mao C.	Front Microbiol	10.3389/fmicb.2024.1345717	2024
Phenotype	Mediating Effects of Immunophenotypes on the Causal Relationship of Gut Microbiota and Their Metabolic Pathways With Osteonecrosis: A Mendelian Randomization Analysis.	Wang M, Meng Y, Shen Q, Meng H.	Mediators Inflamm	10.1155/mi/9323113	2025
	Assessment of the potential risks in SD rats gavaged with genetically modified yeast containing the cp4-epsps gene.	Bi B, Fu X, Jian X, Zhang Y, Jiang Y, Zhou W, Zhao H.	Front Vet Sci	10.3389/fvets.2024.1411520	2024
	Microbial Dysbiosis as an Emerging Pathology of Suicidal Behaviour? A Critical Review, Passing Through Depression to Chronic Pain.	Costanza A, Alexander J, Amerio A, Aguglia A, Magnani L, Parise A, Saverino D, Serafini G, Amore M, Nguyen KD.	Ann Neurosci	10.1177/09727531251349024	2025
	Gastrointestinal complaints after Roux-en-Y gastric bypass surgery. Impact of microbiota and its metabolites.	Custers E, van der Burgh YGR, Vreeken D, Schuren F, van den Broek TJ, Verschuren L, de Blaauw I, Bouwens M, Kleemann R, Kiliaan AJ, Hazebroek EJ.	Heliyon	10.1016/j.heliyon.2024.e39899	2024
	Fecal microbiota transplantation for hypertension: an exploratory, multicenter, randomized, blinded, placebo-controlled trial.	Fan L, Chen J, Zhang Q, Ren J, Chen Y, Yang J, Wang L, Guo Z, Bu P, Zhu B, Zhao Y, Wang Y, Liu X, Wang W, Chen Z, Gao Q, Zheng L, Cai J.	Microbiome	10.1186/s40168-025-02118-6	2025
	Straining to define a healthy microbiome.	Seekatz AM.	mSphere	10.1128/msphere.00797-24	2025
	Salmonella produces sulfide to compete with Escherichia coli in the gut lumen.	Larabi AB, Tiffany CR, Masson HLP, Nguyen H, Bejarano EJ, Liou MJ, Radlinski LC, Demars AM, Tsolis RM, Baumler AJ.	Proc Natl Acad Sci U S A	10.1073/pnas.2504095122	2025
Enzymology	Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.	Tang D, Hu W, Fu B, Zhao X, You G, Xie C, Wang HY, Guo X, Zhang Q, Liu Z, Ye L.	Gut Microbes	10.1080/19490976.2024.2387402	2024
Genetics	A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.	Yuan J, Sun Z, Sun R, Wang J, Wu C, Liu B, Zhao X, Li Q, Zhao J, Cai K.	Biology (Basel)	10.3390/biology14080980	2025
	A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.	Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD.	Nat Commun	10.1038/s41467-025-64822-z	2025
Genetics	Gut microbiome and major depressive disorder: insights from two-sample Mendelian randomization.	Zhao Q, Baranova A, Cao H, Zhang F.	BMC Psychiatry	10.1186/s12888-024-05942-6	2024
Metabolism	Unraveling the interplay between mesenchymal stem cells, gut microbiota, and systemic sclerosis: therapeutic implications.	Zhang L, Wang H, Zhao L, Zhang J, Sun W, Chu J, Zhao H, Yang C, Yan S, Chen X, Xu D.	Microbiol Spectr	10.1128/spectrum.01576-24	2025
	Hydrogen Sulfide Producers Drive a Diarrhea-Like Phenotype and a Methane Producer Drives a Constipation-Like Phenotype in Animal Models.	Villanueva-Millan MJ, Leite G, Morales W, Sanchez M, Parodi G, Weitsman S, Celly S, Cohrs D, Do H, Barlow GM, Mathur R, Rezaie A, Pimentel M.	Dig Dis Sci	10.1007/s10620-023-08197-5	2024
	Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes.	Berkhout MD, Ioannou A, de Ram C, Boeren S, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwae085	2024
	Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.	Zhu B, Liang L, Chen S, Li H, Huang Y, Wang W, Zhang H, Zhou J, Xiong D, Li X, Li J, Ning Y, Shi X, Wu F, Wu K.	Transl Psychiatry	10.1038/s41398-025-03449-6	2025
	Exploring the mediating role of the plasma lipidome in the pathway from the gut microbiota to dementia: a Mendelian randomization study.	Li B, Sun X, Luo X, Kan Y, Wang W, Wang T, Wu C, Hu Y, Bi X.	Arch Med Sci	10.5114/aoms/201447	2025
Metabolism	Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.	Dirks B, Davis TL, Carnero EA, Corbin KD, Smith SR, Rittmann BE, Krajmalnik-Brown R.	ISME J	10.1093/ismejo/wraf103	2025
Genetics	Causal relationship between the gut microbiota, immune cells, and coronary heart disease: a mediated Mendelian randomization analysis.	Yang F, Song H, Tang W, Liu L, Zhu Z, Ouyang B, Zhang L, He G, Qin W.	Front Microbiol	10.3389/fmicb.2024.1449935	2024
	Emerging probiotics: future therapeutics for human gut health.	Duncan SH, Sabater C.	FEMS Microbiol Ecol	10.1093/femsec/fiaf077	2025
Genetics	Population-based metagenomics analysis reveals altered gut microbiome in sarcopenia: data from the Xiangya Sarcopenia Study.	Wang Y, Zhang Y, Lane NE, Wu J, Yang T, Li J, He H, Wei J, Zeng C, Lei G.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13037	2022
	The gastric microbiome altered by A4GNT deficiency in mice.	Gong D, Gao Y, Shi R, Xu X, Yu M, Zhang S, Wang L, Dong Q.	Front Microbiol	10.3389/fmicb.2025.1541800	2025
	High-risk genotypes for type 1 diabetes are associated with the imbalance of gut microbiome and serum metabolites.	Yue T, Tan H, Wang C, Liu Z, Yang D, Ding Y, Xu W, Yan J, Zheng X, Weng J, Luo S.	Front Immunol	10.3389/fimmu.2022.1033393	2022
	NADH and NADPH peroxidases as antioxidant defense mechanisms in intestinal sulfate-reducing bacteria.	Kushkevych I, Dordevic D, Alberfkani MI, Gajdacs M, Ostorhazi E, Vitezova M, Rittmann SKR.	Sci Rep	10.1038/s41598-023-41185-3	2023
Genetics	Exploring the gut microbiome and immunological landscape in kidney cancer: a Mendelian randomization analysis.	Lv S, Guo Q, He Y, Yu Z, Zhan X, Li H, Pan Y.	Front Immunol	10.3389/fimmu.2024.1459967	2024
	Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples.	Cisek AA, Bak I, Cukrowska B.	Microorganisms	10.3390/microorganisms11030660	2023
	Gut microbial features may influence antiviral IgG levels after vaccination against viral respiratory infectious diseases: the evidence from two-sample bidirectional mendelian randomization.	Tu J, Wang Y, Ye X, Wang Y, Zou Y, Jia L, Yang S, Yu R, Liu W, Huang P.	BMC Infect Dis	10.1186/s12879-024-09189-0	2024
	Gut microbiota causally affects ulcerative colitis by potential mediation of plasma metabolites: A Mendelian randomization study.	Zhao S, Zheng X, Yang C, Shen W, Shen Z.	Medicine (Baltimore)	10.1097/md.0000000000042791	2025
Pathogenicity	Exploration of the Gut Microbiome in Thai Patients with Major Depressive Disorder Shows a Specific Bacterial Profile with Depletion of the Ruminococcus Genus as a Putative Biomarker.	Maes M, Vasupanrajit A, Jirakran K, Klomkliew P, Chanchaem P, Tunvirachaisakul C, Payungporn S.	Cells	10.3390/cells12091240	2023
	Circulating Inflammatory Proteins Mediate the Causal Effect of Gut Microbiota on Inflammatory Bowel Disease: Bayesian and Mediated Mendelian Randomization.	Li Z, Jia L, Huai S.	FASEB Bioadv	10.1096/fba.2025-00114	2025
	Lactobacillus plantarum Decreased Ammonia Emissions through Modulating Cecal Microbiotain Broilers Challenged with Ammonia.	Liu X, Cao G, Qiu K, Dong Y, Hu C.	Animals (Basel)	10.3390/ani13172739	2023
Genetics	Shotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy.	Nirmalkar K, Qureshi F, Kang DW, Hahn J, Adams JB, Krajmalnik-Brown R.	Int J Mol Sci	10.3390/ijms232113481	2022
	Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.	Luo G, Cheng Y, Xu Y, Liu J, Yang W, Liu J, Guo B, Zhu H.	Animals (Basel)	10.3390/ani15121815	2025
	The causal relationship between immune cell-mediated gut microbiota and ulcerative colitis: a bidirectional two-sample, mediation Mendelian randomization analysis.	Xiao J, Guo X, Lin Y, Wang Z.	Front Nutr	10.3389/fnut.2024.1433545	2024
	Plasma TMAO Concentrations and Gut Microbiota Composition in Subjects with and Without Metabolic Syndrome: Results from Pilot Study.	Hefni ME, Witthoft CM, Hellstrom P, Johansson I, Esberg A.	Metabolites	10.3390/metabo15060364	2025
	Mendelian randomization suggests a causal relationship between gut microbiota and nonalcoholic fatty liver disease in humans.	Dai X, Jiang K, Ma X, Hu H, Mo X, Huang K, Jiang Q, Chen Y, Liu C.	Medicine (Baltimore)	10.1097/md.0000000000037478	2024
	Hydrogen Sulfide and Methane on Breath Test Correlate with Human Small Intestinal Hydrogen Sulfide Producers and Methanogens.	Villanueva-Millan MJ, Leite G, Mathur R, Rezaie A, Fajardo CM, de Freitas Germano J, Morales W, Sanchez M, Rivera I, Parodi G, Weitsman S, Rashid M, Hosseini A, Brimberry D, Barlow GM, Pimentel M.	Dig Dis Sci	10.1007/s10620-025-09156-y	2025
Genetics	Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.	Li C, Luan Z, Zhao Y, Chen J, Yang Y, Wang C, Jing Y, Qi S, Li Z, Guo H, Xu W, Zhao B, Wu C, Wang S, Yang Y, Sun G.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00282-3	2022
	Assessing the gut microbiota composition in older adults: connections to physical activity and healthy ageing.	Ramos C, Magistro D, Walton GE, Whitham A, Camp N, Poveda C, Gibson GR, Hough J, Kinnear W, Hunter K.	Geroscience	10.1007/s11357-025-01605-w	2025
Pathogenicity	Unravelling three-way interactions between Clostridioides difficile, microbiota and the host.	Bywater-Brenna KK, Unnikrishnan M.	J Med Microbiol	10.1099/jmm.0.002067	2025
	Individual and Combined Effects of 2'-Fucosyllactose and Bifidobacterium longum subsp. infantis on the Gut Microbiota Composition of Piglets.	Wang M, Monaco MH, Daniels VC, Hirvonen J, Jensen HM, Ouwehand AC, Mukherjea R, Christensen N, Lehtinen MJ, Hibberd AA, Dilger RN, Donovan SM.	J Nutr	10.1016/j.tjnut.2024.12.022	2025
	919 Syrup Alleviates Postpartum Depression by Modulating the Structure and Metabolism of Gut Microbes and Affecting the Function of the Hippocampal GABA/Glutamate System.	Tian XY, Xing JW, Zheng QQ, Gao PF.	Front Cell Infect Microbiol	10.3389/fcimb.2021.694443	2021
	Distinct in vitro utilization and degradation of porcine gastric mucin glycans by human intestinal bacteria.	de Ram C, Berkhout MD, O Pandeirada C, Vincken JP, Hooiveld GJEJ, Belzer C, Schols HA.	FEMS Microbiol Ecol	10.1093/femsec/fiaf066	2025
Phylogeny	Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs.	Lan Q, Lian Y, Peng P, Yang L, Zhao H, Huang P, Ma H, Wei H, Yin Y, Liu M.	Front Microbiol	10.3389/fmicb.2023.1117965	2023
	Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines.	Finazzi M, Bovio F, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Microorganisms	10.3390/microorganisms13010192	2025
	From Microbes to Metabolites: Advances in Gut Microbiome Research in Type 1 Diabetes.	Blok L, Hanssen N, Nieuwdorp M, Rampanelli E.	Metabolites	10.3390/metabo15020138	2025
	Exploring a Possible Link between the Fecal Microbiota and the Production Performance of Pigs.	Cao Y, Wang F, Wang H, Wu S, Bao W.	Vet Sci	10.3390/vetsci9100527	2022
	Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury.	Li J, Barnes S, Lefkowitz E, Yarar-Fisher C.	Physiol Genomics	10.1152/physiolgenomics.00107.2023	2024
	Virological response to nucleos(t)ide analogues treatment in chronic hepatitis B patients is associated with Bacteroides-dominant gut microbiome.	Zhang S, Chau HT, Tun HM, Huang FY, Wong DK, Mak LY, Yuen MF, Seto WK.	EBioMedicine	10.1016/j.ebiom.2024.105101	2024
	Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma.	Zhang J, Yang J, Luo J, Wu W, Luo H, Wei W, Lyu H, Wang Y, Yi H, Zhang Y, Fan Z, Lyu H, Kanakaveti VP, Qin B, Yuan P, Yang R, Zhang H, Zuo T, Felsher DW, Lee MH, Li K.	Nat Commun	10.1038/s41467-025-58407-z	2025
	Association of Circulating Phenylacetylglutamine With Multi-Vessel Coronary Disease Severity and Outcomes in ST-Segment-Elevation Myocardial Infarction.	Zhao P, Dong N, Wang Y, Zhao S, Tian Y, Qin Z, Ban X, Han F, Meng L, Yang F, Wang Y, Wu Y, Yu Z, Xu Q, Li X, Li S, Liu H, Fang S, Xie W, Yu B, Liu X, Tian J.	J Am Heart Assoc	10.1161/jaha.124.038175	2025
	"Trust your gut": exploring the connection between gut microbiome dysbiosis and the advancement of Metabolic Associated Steatosis Liver Disease (MASLD)/Metabolic Associated Steatohepatitis (MASH): a systematic review of animal and human studies.	Bahitham W, Banoun Y, Aljahdali M, Almuaiqly G, Bahshwan SM, Aljahdali L, Sanai FM, Rosado AS, Sergi CM.	Front Nutr	10.3389/fnut.2025.1637071	2025
Pathogenicity	Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.	Liu F, McNally J, Fleming DS, Ingham AB, Hunt PW, Li RW.	Vet Res	10.1186/s13567-025-01565-1	2025
	Chondroitin Sulfate Ameliorates Hypertension in Male Offspring Rat Born to Mothers Fed an Adenine Diet.	Tain YL, Hou CY, Chang-Chien GP, Lin SF, Hsu CN.	Antioxidants (Basel)	10.3390/antiox13080944	2024
	Potential application of pig (Sus scrofa domestica) skin peptide-iron chelates in the treatment of iron deficiency anemia and regulation of intestinal flora metabolism.	Huang S, Deng H, Liang K, Zhao X, Zhang J.	Front Nutr	10.3389/fnut.2025.1553668	2025
	The infants' gut microbiome: setting the stage for the early onset of obesity.	Valles Y, Arshad M, Abdalbaqi M, Inman CK, Ahmad A, Drou N, Gunsalus KC, Ali R, Tahlak M, Abdulle A.	Front Microbiol	10.3389/fmicb.2024.1371292	2024
Pathogenicity	Metabolic modeling of host-microbe interactions.	Srinak N, Kruger F, Kaleta C, Taubenheim J.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.10.006	2025
Pathogenicity	Hydrogen Sulfide and Sulfate Prebiotic Stimulates the Secretion of GLP-1 and Improves Glycemia in Male Mice.	Pichette J, Fynn-Sackey N, Gagnon J.	Endocrinology	10.1210/en.2017-00391	2017
	Synergistic Effects of Probiotics and Lifestyle Interventions on Intestinal Microbiota Composition and Clinical Outcomes in Obese Adults.	Florencio GP, Xavier AR, Natal ACC, Sadoyama LP, Pena GDG, Menezes RP, Sadoyama Leal G, Patrizzi LJ, Roder DVDB.	Metabolites	10.3390/metabo15020070	2025
	Associations between gut microbiota and sarcopenia or its defining parameters in older adults: A systematic review.	Lapauw L, Rutten A, Dupont J, Amini N, Vercauteren L, Derrien M, Raes J, Raes J, Gielen E.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13569	2024
	Methanogen Levels Are Significantly Associated with Fecal Microbiota Composition and Alpha Diversity in Healthy Adults and Irritable Bowel Syndrome Patients.	Wang T, van Dijk L, Rijnaarts I, Hermes GDA, de Roos NM, Witteman BJM, de Wit NJW, Govers C, Smidt H, Zoetendal EG.	Microbiol Spectr	10.1128/spectrum.01653-22	2022
Genetics	Effects of data transformation and model selection on feature importance in microbiome classification data.	Karwowska Z, Aasmets O, Estonian Biobank research team, Kosciolek T, Org E.	Microbiome	10.1186/s40168-024-01996-6	2025
	Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up	Wilson B, Zuppi M, Derraik J, Albert B, Tweedie-Cullen R, Leong K, Beck K, Vatanen T, O'Sullivan J, Cutfield W.	Nat Commun		2025
Pathogenicity	Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes.	Belkessa S, Pasolli E, Medrouh B, Berg RPKD, Andersen LO', Nielsen HV, Stensvold CR.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.06.006	2025
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
Enzymology	Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens.	Cisek AA, Dolka B, Bak I, Cukrowska B.	Int J Mol Sci	10.3390/ijms24076674	2023
	Identification of Lawsonia intracellularis putative hemolysin protein A and characterization of its immunoreactivity.	Kim J, Won G, Park S, Lee JH.	Vet Microbiol	10.1016/j.vetmic.2017.05.007	2017
	Possible synergy effect of hydrogen sulfide and acetate produced by sulfate-reducing bacteria on inflammatory bowel disease development.	Kushkevych I, Dordevic D, Vitezova M.	J Adv Res	10.1016/j.jare.2020.03.007	2021
	A comprehensive narrative review on precision medicine approach to hypertension: exploring the role of genetics, epigenetics, microbiome, and artificial intelligence.	Sami A, Ashraf R, Nisar S, Mustehsan ZH, Javed MA, Ozsahin DU, Waheed Y.	J Health Popul Nutr	10.1186/s41043-025-01058-z	2025
Enzymology	Kinetic Properties of Pyruvate Ferredoxin Oxidoreductase of Intestinal Sulfate-Reducing Bacteria Desulfovibrio piger Vib-7 and Desulfomicrobium sp. Rod-9.	Kushkevych IV.	Pol J Microbiol	10.33073/pjm-2015-016	2015
Phylogeny	Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans.	Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C, Rotimi CN.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00063	2020
Metabolism	Gut Microbiota as a Source of Uremic Toxins.	Popkov VA, Zharikova AA, Demchenko EA, Andrianova NV, Zorov DB, Plotnikov EY.	Int J Mol Sci	10.3390/ijms23010483	2022
	Gut microbiota in systemic lupus erythematosus patients and lupus mouse model: a cross species comparative analysis for biomarker discovery.	Toumi E, Goutorbe B, Plauzolles A, Bonnet M, Mezouar S, Militello M, Mege JL, Chiche L, Halfon P.	Front Immunol	10.3389/fimmu.2022.943241	2022
Pathogenicity	Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project.	Chen YR, Jing QL, Chen FL, Zheng H, Chen LD, Yang ZC.	PeerJ	10.7717/peerj.12033	2021
Pathogenicity	The Effects of Glucosamine and Chondroitin Sulfate on Gut Microbial Composition: A Systematic Review of Evidence from Animal and Human Studies.	Shmagel A, Demmer R, Knights D, Butler M, Langsetmo L, Lane NE, Ensrud K.	Nutrients	10.3390/nu11020294	2019
	The microbiome compositional and functional differences between rectal mucosa and feces.	Yin X-F, Ye T, Chen H-L, Liu J, Mu X-F, Li H, Wang J, Hu Y-J, Cao H, Kang W-Q.	Microbiol Spectr	10.1128/spectrum.03549-23	2024
Genetics	Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.	Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I.	Gut Microbes	10.1080/19490976.2023.2226921	2023
Metabolism	Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria.	Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, Hua G, N Nanjaraj Urs A, Liu D, Wang F, Guo C, Tong Y, Li M, Liu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y.	Nat Commun	10.1038/s41467-019-09618-8	2019
	Disrupted gut harmony in attention-deficit/hyperactivity disorder: Dysbiosis and decreased short-chain fatty acids.	Steckler R, Magzal F, Kokot M, Walkowiak J, Tamir S.	Brain Behav Immun Health	10.1016/j.bbih.2024.100829	2024
Biotechnology	Synergy and oxygen adaptation for development of next-generation probiotics.	Khan MT, Dwibedi C, Sundh D, Pradhan M, Kraft JD, Caesar R, Tremaroli V, Lorentzon M, Backhed F.	Nature	10.1038/s41586-023-06378-w	2023
	Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP).	Matthews C, Walsh AM, Gordon SV, Markey B, Cotter PD, O' Mahony J.	Animals (Basel)	10.3390/ani13101652	2023
	Gut microbiota prevents small intestinal tumor formation due to bile acids in gnotobiotic mice.	Wortmann E, Wylensek D, Basic M, Hermeling S, Bleich A, Haller D, Tolba R, Liebisch G, Janssen KP, Clavel T.	Microbiome Res Rep	10.20517/mrr.2024.20	2024
	Designing synthetic microbial communities for enhanced anaerobic waste treatment.	Jourdain L, Gu W.	Appl Environ Microbiol	10.1128/aem.00404-25	2025
Genetics	Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing.	Correa F, Luise D, Palladino G, Estelle J, Turroni S, Scicchitano D, Babbi G, Rampelli S, Candela M, Martelli PL, Stefanelli C, Perez-Calvo E, Trevisi P.	Anim Microbiome	10.1186/s42523-025-00477-x	2025
	Multi-site microbiota alteration is a hallmark of kidney stone formation.	Al KF, Joris BR, Daisley BA, Chmiel JA, Bjazevic J, Reid G, Gloor GB, Denstedt JD, Razvi H, Burton JP.	Microbiome	10.1186/s40168-023-01703-x	2023
	Red palm olein biscuit supplementation modulates gut microbiota in vitamin A deficient rural Malaysian schoolchildren: a randomised controlled trial.	Tan PY, Loganathan R, Lee SC, Mohd Johari SN, Teng KT, Selvaduray KR, Lim YA.	Nat Commun	10.1038/s41467-025-64395-x	2025
Pathogenicity	Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.	Xu SY, Feng XR, Zhao W, Bi YL, Diao QY, Tu Y.	Microbiome	10.1186/s40168-024-01844-7	2024
Genetics	Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing.	Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M.	Animals (Basel)	10.3390/ani13142303	2023
Phylogeny	Comparative Analysis of Taxonomic and Functional Gut Microbiota Profiles in Relation to Seroconversion of Thyroid Peroxidase Antibodies in Euthyroid Participants.	Fenneman AC, Boulund U, Collard D, Galenkamp H, Zwinderman AH, van den Born BH, van der Spek AH, Fliers E, Rampanelli E, Blaser MJ, Nieuwdorp M.	Thyroid	10.1089/thy.2023.0346	2024
	Gut microbiota: an ideal biomarker and intervention strategy for aging	Xu X, Xu T, Wei J, Chen T.	Microbiome Res Rep		2024
Genetics	Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows.	Fu H, He M, Wu J, Zhou Y, Ke S, Chen Z, Liu Q, Liu M, Jiang H, Huang L, Chen C.	Front Microbiol	10.3389/fmicb.2021.729039	2021
	A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao.	Han Y, Quan X, Chuang Y, Liang Q, Li Y, Yuan Z, Bian Y, Wei L, Wang J, Zhao Y.	Clin Transl Med	10.1002/ctm2.909	2022
	Effects of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, short chain fatty acids, and microbiota in Eimeria-challenged broiler chickens fed high fiber diet.	Lin Y, Lourenco JM, Olukosi OA.	Anim Nutr	10.1016/j.aninu.2023.08.009	2023
	Faecalibacterium prausnitzii Supplementation Prevents Intestinal Barrier Injury and Gut Microflora Dysbiosis Induced by Sleep Deprivation.	Wang X, Li Y, Wang X, Wang R, Hao Y, Ren F, Wang P, Fang B.	Nutrients	10.3390/nu16081100	2024
	Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.	Vinogradova E, Mukhanbetzhanov N, Nurgaziyev M, Jarmukhanov Z, Aipova R, Sailybayeva A, Bekbossynova M, Kozhakhmetov S, Kushugulova A.	mSystems	10.1128/msystems.00585-24	2024
Metabolism	Activity and kinetic properties of phosphotransacetylase from intestinal sulfate-reducing bacteria.	Kushkevych IV.	Acta Biochim Pol	10.18388/abp.2014_845	2015
	Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats.	Leigh SJ, Kaakoush NO, Westbrook RF, Morris MJ.	Transl Psychiatry	10.1038/s41398-020-0774-1	2020
Transcriptome	Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model.	Kovatcheva-Datchary P, Shoaie S, Lee S, Wahlstrom A, Nookaew I, Hallen A, Perkins R, Nielsen J, Backhed F.	Cell Rep	10.1016/j.celrep.2019.02.090	2019
	Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization.	Horrocks V, King OG, Yip AYG, Marques IM, McDonald JAK.	Microbiology (Reading)	10.1099/mic.0.001377	2023
	Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition.	Lin YY, Chang PE, Shen SY, Wang SD.	Poult Sci	10.1016/j.psj.2023.102731	2023
Genetics	A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.	Xiong X, Rao Y, Ma J, Wang Z, He Q, Gong J, Sheng W, Xu J, Zhu X, Tan Y, Yang Y.	Poult Sci	10.1016/j.psj.2023.102931	2023
	Antibiotic-Resistant Desulfovibrio Produces H₂S from Supplements for Animal Farming.	Karnachuk OV, Beletsky AV, Rakitin AL, Ikkert OP, Avakyan MR, Zyusman VS, Napilov A, Mardanov AV, Ravin NV.	Microorganisms	10.3390/microorganisms11040838	2023
Pathogenicity	Phenotyping of Fecal Microbiota of Winnie, a Rodent Model of Spontaneous Chronic Colitis, Reveals Specific Metabolic, Genotoxic, and Pro-inflammatory Properties.	Tala A, Guerra F, Resta SC, Calcagnile M, Barca A, Tredici SM, De Donno MD, Vacca M, Liso M, Chieppa M, De Angelis M, Verri T, Bozzetti MG, Bucci C, Alifano P.	Inflammation	10.1007/s10753-022-01706-0	2022
	Case-Control Study Examining the Composition of the Gut Microbiome in Individuals With and Without Immune-Mediated Dry Eye.	Goodman CF, Doan T, Mehra D, Betz J, Locatelli E, Mangwani-Mordani S, Kalahasty K, Hernandez M, Hwang J, Galor A.	Cornea	10.1097/ico.0000000000003195	2023
	Gastrointestinal Microbiota and Breast Cancer Chemotherapy Interactions: A Systematic Review.	Csendes D, Gutlapalli SD, Prakash K, Swarnakari KM, Bai M, Manoharan MP, Raja R, Jamil A, Desai A, Desai DM, Khan S.	Cureus	10.7759/cureus.31648	2022
	Dysbiosis in the Development of Type I Diabetes and Associated Complications: From Mechanisms to Targeted Gut Microbes Manipulation Therapies.	Gradisteanu Pircalabioru G, Corcionivoschi N, Gundogdu O, Chifiriuc MC, Marutescu LG, Ispas B, Savu O.	Int J Mol Sci	10.3390/ijms22052763	2021
	Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial.	de Groot P, Nikolic T, Pellegrini S, Sordi V, Imangaliyev S, Rampanelli E, Hanssen N, Attaye I, Bakker G, Duinkerken G, Joosten A, Prodan A, Levin E, Levels H, Potter van Loon B, van Bon A, Brouwer C, van Dam S, Simsek S, van Raalte D, Stam F, Gerdes V, Hoogma R, Diekman M, Gerding M, Rustemeijer C, de Bakker B, Hoekstra J, Zwinderman A, Bergman J, Holleman F, Piemonti L, De Vos W, Roep B, Nieuwdorp M.	Gut	10.1136/gutjnl-2020-322630	2021
	The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.	Wang J, Qie J, Zhu D, Zhang X, Zhang Q, Xu Y, Wang Y, Mi K, Pei Y, Liu Y, Ji G, Liu X.	Gut Microbes	10.1080/19490976.2022.2107288	2022
	Bacterial cysteate dissimilatory pathway involves a racemase and d-cysteate sulfo-lyase.	Liu C, Ma K, Jiang L, Liu X, Tong Y, Yang S, Jin X, Wei Y, Zhang Y.	J Biol Chem	10.1016/j.jbc.2024.107371	2024
	Metabolic network of the gut microbiota in inflammatory bowel disease	Sugihara K, Kamada N.	Inflamm Regen		2024
	Maternal diet and gut microbiome composition modulate early-life immune development.	Grant ET, Boudaud M, Muller A, Muller A, Macpherson AJ, Desai MS.	EMBO Mol Med	10.15252/emmm.202217241	2023
Genetics	Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments.	Guitart-Matas J, Ballester M, Fraile L, Darwich L, Giler-Baquerizo N, Tarres J, Lopez-Soria S, Ramayo-Caldas Y, Migura-Garcia L.	Anim Microbiome	10.1186/s42523-024-00307-6	2024
	Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study.	Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1181328	2023
Phylogeny	From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.	Huang F, Lyu B, Xie F, Li F, Xing Y, Han Z, Lai J, Ma J, Zou Y, Zeng H, Xu Z, Gao P, Luo Y, Bolund L, Tong G, Fengping X.	Front Microbiol	10.3389/fmicb.2024.1366744	2024
Metabolism	Analyzing Predominant Bacterial Species and Potential Short-Chain Fatty Acid-Associated Metabolic Routes in Human Gut Microbiome Using Integrative Metagenomics.	Kingkaw A, Raethong N, Patumcharoenpol P, Suratannon N, Nakphaichit M, Keawsompong S, Roytrakul S, Vongsangnak W.	Biology (Basel)	10.3390/biology12010021	2022
	Captivity Influences the Gut Microbiome of Rhinopithecus roxellana.	Wang X, Wang Z, Pan H, Qi J, Li D, Zhang L, Shen Y, Xiang Z, Li M.	Front Microbiol	10.3389/fmicb.2021.763022	2021
	Acetate kinase Activity and Kinetic Properties of the Enzyme in Desulfovibrio piger Vib-7 and Desulfomicrobium sp. Rod-9 Intestinal Bacterial Strains.	Kushkevych IV.	Open Microbiol J	10.2174/1874285801408010138	2014
	Model-based Characterization of the Parameters of Dissimilatory Sulfate Reduction Under the Effect of Different Initial Density of Desulfovibrio piger Vib-7 Bacterial Cells.	Kushkevych I, Bolis M, Bartos M.	Open Microbiol J	10.2174/1874285801509010055	2015
Phylogeny	Distinct gut microbiomes in Thai patients with colorectal polyps.	Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S.	World J Gastroenterol	10.3748/wjg.v30.i27.3336	2024
	Biotic methylation of mercury by intestinal and sulfate-reducing bacteria and their potential role in mercury accumulation in the tissue of the soil-living Eisenia foetida	Kaschak E, Knopf B, Petersen JH, Bings NH, Konig H.	Soil Biol Biochem	10.1016/j.soilbio.2013.11.004	2014
Metabolism	Metabolites of gut microbiome are associated with glucose metabolism in non-diabetic obese adults: a Chinese monozygotic twin study.	Yu K, Yu CG, Yin XQ, Wang ZW, Wang XB, Wang LL, Guo S, An YX, Zhao D.	Diabetol Metab Syndr	10.1186/s13098-021-00724-6	2021
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
Metabolism	Therapeutic Potential of Metabolites from Lactobacillus rhamnosus and Mare's Milk in the Treatment of Dysbiosis.	Kozhakhmetov S, Babenko D, Kozhakhmetova S, Tuyakova A, Nurgaziyev M, Nurgozhina A, Muhanbetganov N, Chulenbayeva L, Sergazy S, Gulyayev A, Aljofan M, Kushugulova A.	Biomed Res Int	10.1155/2022/3851478	2022
	Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging.	Sun L, Li Z, Hu C, Ding J, Zhou Q, Pang G, Wu Z, Yang R, Li S, Li J, Cai J, Sun Y, Li R, Zhen H, Sun S, Zhang J, Fang M, Chen Z, Lv Y, Cao Q, Sun Y, Gong R, Huang Z, Duan Y, Liu H, Dong J, Li J, Ruan J, Lu H, He B, Li N, Li T, Xue W, Li Y, Shen J, Yang F, Zhao C, Liang Q, Zhang M, Chen C, Gong H, Hou Y, Wang J, Zhang Y, Yang H, Zhu S, Xiao L, Jin Z, Guo H, Zhao P, Brix S, Xu X, Jia H, Kristiansen K, Yang Z, Nie C.	Aging Cell	10.1111/acel.14028	2023
Genetics	Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome.	Holman DB, Gzyl KE, Mou KT, Allen HK.	mSystems	10.1128/msystems.00682-21	2021
	Engineering Microbial Consortia as Living Materials: Advances and Prospectives.	Wang S, Zhan Y, Jiang X, Lai Y.	ACS Synth Biol	10.1021/acssynbio.4c00313	2024
	Gut bacterial species in late trimester of pregnant sows influence the occurrence of stillborn piglet through pro-inflammation response.	Chen Z, Yang H, Fu H, Wu L, Liu M, Jiang H, Liu Q, Wang Y, Xiong S, Zhou M, Sun X, Chen C, Huang L.	Front Immunol	10.3389/fimmu.2022.1101130	2022
	Bacteroides thetaiotaomicron enhances H₂S production in Bilophila wadsworthia.	Davies J, Mayer MJ, Juge N, Narbad A, Sayavedra L.	Gut Microbes	10.1080/19490976.2024.2431644	2024
	Entamoeba muris mitigates metabolic consequences of high-fat diet in mice.	Roy M, Dumay A, Adiba S, Rozes S, Kobayashi S, Paradis V, Postic C, Rainteau D, Ogier-Denis E, Le Gall M, Meinzer U, Viennois E, Casado-Bedmar M, Mosca A, Hugot JP.	Gut Microbes	10.1080/19490976.2024.2409210	2024
	Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs.	Ortiz Sanjuan JM, Arguello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG.	Anim Microbiome	10.1186/s42523-024-00306-7	2024
	Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity.	Wilson BC, Vatanen T, Jayasinghe TN, Leong KSW, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Holland DJ, Cutfield WS, O'Sullivan JM.	Microbiome	10.1186/s40168-021-01060-7	2021
	Biotics and bacterial function: impact on gut and host health.	Kandari A, Odat MA, Alzaid F, Scott KP.	ISME J	10.1093/ismejo/wrae226	2024
	Multiomics Analysis Reveals Gut Virome-Bacteria-Metabolite Interactions and Their Associations with Symptoms in Patients with IBS-D.	Xie P, Luo M, Fan J, Xiong L.	Viruses	10.3390/v16071054	2024
	Short-Term Tolerability, Safety, and Gut Microbial Composition Responses to a Multi-Strain Probiotic Supplement: An Open-Label Study in Healthy Adults.	Ryan JJ, Patno NM.	Integr Med (Encinitas)		2021
	Diversity and Comparison of Intestinal Desulfovibrio in Patients with Liver Cirrhosis and Healthy People.	Lu G, Zhang Y, Ren Y, Shi JS, Xu ZH, Geng Y.	Microorganisms	10.3390/microorganisms11020276	2023
	Microbiota and epigenetics: promising therapeutic approaches?	El-Sayed A, Aleya L, Kamel M.	Environ Sci Pollut Res Int	10.1007/s11356-021-15623-6	2021
Metabolism	Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome.	Steimle A, Neumann M, Grant ET, Turner JD, Desai MS.	Int J Mol Sci	10.3390/ijms22136855	2021
	TCM syndrome differentiation in colorectal cancer patients assisted by differences in gut microbiota: An exploratory study.	Ming-Bin G, Ya-Nan W, Yong-Ting X, Min Z, Hao T, Lian-Ping Q, Feng G.	Heliyon	10.1016/j.heliyon.2023.e21057	2023
Metabolism	Isolation and characterization of porins from Desulfovibrio piger and Bilophila wadsworthia: structure and gene sequencing.	Avidan O, Kaltageser E, Pechatnikov I, Wexler HM, Shainskaya A, Nitzan Y.	Arch Microbiol	10.1007/s00203-008-0416-0	2008
Phylogeny	Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease.	Jia W, Whitehead RN, Griffiths L, Dawson C, Bai H, Waring RH, Ramsden DB, Hunter JO, Cauchi M, Bessant C, Fowler DP, Walton C, Turner C, Cole JA.	FEMS Immunol Med Microbiol	10.1111/j.1574-695x.2012.00935.x	2012
	Gut microbiota markers associated with obesity and overweight in Italian adults.	Palmas V, Pisanu S, Madau V, Casula E, Deledda A, Cusano R, Uva P, Vascellari S, Loviselli A, Manzin A, Velluzzi F.	Sci Rep	10.1038/s41598-021-84928-w	2021
Enzymology	First isolation of Desulfovibrio from the human vaginal flora.	Ichiishi S, Tanaka K, Nakao K, Izumi K, Mikamo H, Watanabe K.	Anaerobe	10.1016/j.anaerobe.2010.02.002	2010
Genetics	Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial.	Pickering H, Hart JD, Burr S, Stabler R, Maleta K, Kalua K, Bailey RL, Holland MJ.	Gut Pathog	10.1186/s13099-021-00478-6	2022
	Gut-microbiota in children and adolescents with obesity: inferred functional analysis and machine-learning algorithms to classify microorganisms.	Squillario M, Bonaretti C, La Valle A, Di Marco E, Piccolo G, Minuto N, Patti G, Napoli F, Bassi M, Maghnie M, d'Annunzio G, Biassoni R.	Sci Rep	10.1038/s41598-023-36533-2	2023
Genetics	Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.	Holman DB, Kommadath A, Tingley JP, Abbott DW.	Microbiol Spectr	10.1128/spectrum.02380-22	2022
Metabolism	Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants.	Pham VT, Lacroix C, Braegger CP, Chassard C.	Sci Rep	10.1038/s41598-017-11509-1	2017
Genetics	Diversity and host interaction of the gut microbiota in specific pathogen-free pigs.	Wen M, Chen S, Zhang Y, Liu Y, Tang C, Zhang J, Sun J, Li X, Ding Y, Lu L, Long K, Nie Y, Li X, Li M, Ge L, Ma J.	Front Microbiol	10.3389/fmicb.2024.1402807	2024
	Predicting microbial interactions with approaches based on flux balance analysis: an evaluation.	Joseph C, Zafeiropoulos H, Bernaerts K, Faust K.	BMC Bioinformatics	10.1186/s12859-024-05651-7	2024
Transcriptome	Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood.	Liu Y, Ma L, Riqing D, Qu J, Chen J, Zhandu D, Li B, Jiang M.	Animals (Basel)	10.3390/ani14091365	2024
	The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive, and Gut Microbiome Parameters Are Preserved in Adult Rat Offspring of Mothers Fed a High-Fat, High-Sugar Diet.	Kendig MD, Hasebe K, Tajaddini A, Kaakoush NO, Westbrook RF, Morris MJ.	Mol Nutr Food Res	10.1002/mnfr.202200318	2023
	Genesis of fecal floatation is causally linked to gut microbial colonization in mice.	Aalam SMM, Crasta DN, Roy P, Miller AL, Gamb SI, Johnson S, Till LM, Chen J, Kashyap P, Kannan N.	Sci Rep	10.1038/s41598-022-22626-x	2022
	Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.	Liu X, Wu J, Tang J, Xu Z, Zhou B, Liu Y, Hu F, Zhang G, Cheng R, Xia X, Chen Y, Wu H, Wang D, Yue J, Dong B, Fu J, Yu H, Dong B.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13313	2023
	Gut bacterial microbiota in patients with myasthenia gravis: results from the MYBIOM study.	Totzeck A, Ramakrishnan E, Schlag M, Stolte B, Kizina K, Bolz S, Thimm A, Stettner M, Marchesi JR, Buer J, Kleinschnitz C, Verhasselt HL, Hagenacker T.	Ther Adv Neurol Disord	10.1177/17562864211035657	2021
Pathogenicity	Gut Microbiota Markers and Dietary Habits Associated with Extreme Longevity in Healthy Sardinian Centenarians.	Palmas V, Pisanu S, Madau V, Casula E, Deledda A, Cusano R, Uva P, Loviselli A, Velluzzi F, Manzin A.	Nutrients	10.3390/nu14122436	2022
	Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile.	Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Im H, Vivas EI, Simcox J, Venturelli OS.	Cell Host Microbe	10.1016/j.chom.2024.12.001	2025
	Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals.	Scanlan PD, Shanahan F, Marchesi JR.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2009.00709.x	2009
	Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges.	Rodriguez J, Cordaillat-Simmons M, Badalato N, Berger B, Breton H, de Lahondes R, Deschasaux-Tanguy M, Desvignes C, D'Humieres C, Kampshoff S, Lavelle A, Metwaly A, Quijada NM, Seegers JFML, Udocor A, Zwart H, Human Microbiome Action Consortium, Maguin E, Dore J, Druart C.	Microbiome	10.1186/s40168-024-01991-x	2024
Metabolism	The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance.	Yoshimura T, McLean MH, Dzutsev AK, Yao X, Chen K, Huang J, Gong W, Zhou J, Xiang Y, H Badger J, O'hUigin C, Thovarai V, Tessarollo L, Durum SK, Trinchieri G, Bian XW, Wang JM.	J Immunol	10.4049/jimmunol.1602073	2018
	Diversity and community pattern of sulfate-reducing bacteria in piglet gut.	Ran S, Mu C, Zhu W.	J Anim Sci Biotechnol	10.1186/s40104-019-0346-5	2019
Phylogeny	Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.	Kumar H, Jang YN, Kim K, Park J, Jung MW, Park JE.	Animals (Basel)	10.3390/ani10081372	2020
Genetics	Changes in Gut Microbiota of Patients with Atopic Dermatitis During Balneotherapy.	Thirion F, Guilly S, Fromentin S, Plaza Onate F, Alvarez AS, Le Chatelier E, Pons N, Levenez F, Quinquis B, Ehrlich S, Dore J, Martin R, Seite S.	Clin Cosmet Investig Dermatol	10.2147/ccid.s342104	2022
	Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape.	Grant ET, Parrish A, Boudaud M, Hunewald O, Hirayama A, Ollert M, Fukuda S, Desai MS.	Microbiome	10.1186/s40168-024-01898-7	2024
	Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics.	Hromada S, Venturelli OS.	PLoS Biol	10.1371/journal.pbio.3002100	2023
	Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.	Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS.	Nat Commun	10.1038/s41467-023-39121-0	2023
	Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail.	Ma JE, Xiong XW, Xu JG, Gong JS, Li J, Xu Q, Li YF, Yang YB, Zhou M, Zhu XN, Tan YW, Sheng WT, Wang ZF, Tu XT, Zeng CY, Zhang XQ, Rao YS.	Front Vet Sci	10.3389/fvets.2021.693755	2021
Genetics	Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning.	Ortiz Sanjuan JM, Manzanilla EG, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Arguello H.	Microbiol Spectr	10.1128/spectrum.01597-22	2022
Metabolism	Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.	Thakur P, Alaba MO, Rauniyar S, Singh RN, Saxena P, Bomgni A, Gnimpieba EZ, Lushbough C, Goh KM, Sani RK.	Microorganisms	10.3390/microorganisms11010119	2023
	Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction.	Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N.	Cell Rep	10.1016/j.celrep.2022.111093	2022
	Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database.	Chen H, Jiao J, Wei M, Jiang X, Yang R, Yu X, Zhang G, Zhou X.	Gut Pathog	10.1186/s13099-022-00527-8	2022
Genetics	Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis.	Schwarzerova J, Zeman M, Babak V, Jureckova K, Nykrynova M, Varga M, Weckwerth W, Dolejska M, Provaznik V, Rychlik I, Cejkova D.	Microbiol Spectr	10.1128/spectrum.01964-23	2024
Metabolism	MMinte: an application for predicting metabolic interactions among the microbial species in a community.	Mendes-Soares H, Mundy M, Soares LM, Chia N.	BMC Bioinformatics	10.1186/s12859-016-1230-3	2016
	T cell-mediated regulation of the microbiota protects against obesity.	Petersen C, Bell R, Klag KA, Lee SH, Soto R, Ghazaryan A, Buhrke K, Ekiz HA, Ost KS, Boudina S, O'Connell RM, Cox JE, Villanueva CJ, Stephens WZ, Round JL.	Science	10.1126/science.aat9351	2019
	Ginsenosides Rb3 and Rd reduce polyps formation while reinstate the dysbiotic gut microbiota and the intestinal microenvironment in Apc^Min/+ mice.	Huang G, Khan I, Li X, Chen L, Leong W, Ho LT, Hsiao WLW.	Sci Rep	10.1038/s41598-017-12644-5	2017
	Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations.	Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS.	Nat Ecol Evol	10.1038/s41559-022-01930-9	2023
	Effects of Glucosinolate-Enriched Red Radish (Raphanus sativus) on In Vitro Models of Intestinal Microbiota and Metabolic Syndrome-Related Functionalities.	Roses C, Garcia-Ibanez P, Agudelo A, Viadel B, Tomas-Cobos L, Gallego E, Carvajal M, Milagro FI, Barcelo A.	ACS Omega	10.1021/acsomega.2c08128	2023
	Gut microbiota diversity in human strongyloidiasis differs little in two different regions in endemic areas of Thailand.	Rodpai R, Sanpool O, Janwan P, Boonroumkaew P, Sadaow L, Thanchomnang T, Intapan PM, Maleewong W.	PLoS One	10.1371/journal.pone.0279766	2022
Metabolism	Gut microbiota promotes cholesterol gallstone formation by modulating bile acid composition and biliary cholesterol secretion.	Hu H, Shao W, Liu Q, Liu N, Wang Q, Xu J, Zhang X, Weng Z, Lu Q, Jiao L, Chen C, Sun H, Jiang Z, Zhang X, Gu A.	Nat Commun	10.1038/s41467-021-27758-8	2022
Metabolism	Design of synthetic human gut microbiome assembly and butyrate production.	Clark RL, Connors BM, Stevenson DM, Hromada SE, Hamilton JJ, Amador-Noguez D, Venturelli OS.	Nat Commun	10.1038/s41467-021-22938-y	2021
Metabolism	Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats.	Kushkevych I, Hyzova B, Vitezova M, Rittmann SKR.	Int J Mol Sci	10.3390/ijms22084007	2021
Phylogeny	Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity.	Kozhieva M, Naumova N, Alikina T, Boyko A, Vlassov V, Kabilov MR.	BMC Microbiol	10.1186/s12866-019-1685-2	2019
Phylogeny	Taxonomic and Functional Fecal Microbiota Signatures Associated With Insulin Resistance in Non-Diabetic Subjects With Overweight/Obesity Within the Frame of the PREDIMED-Plus Study.	Atzeni A, Bastiaanssen TFS, Cryan JF, Tinahones FJ, Vioque J, Corella D, Fito M, Vidal J, Moreno-Indias I, Gomez-Perez AM, Torres-Collado L, Coltell O, Castaner O, Bullo M, Salas-Salvado J.	Front Endocrinol (Lausanne)	10.3389/fendo.2022.804455	2022
Genetics	Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections.	Hocquart M, Pham T, Kuete E, Tomei E, Lagier JC, Raoult D.	Open Forum Infect Dis	10.1093/ofid/ofz398	2019
	How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding.	Berkhout MD, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwab105	2022
	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
	Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes.	Sulaiman JE, Thompson J, Qian Y, Vivas EI, Diener C, Gibbons SM, Safdar N, Venturelli OS.	Nat Commun	10.1038/s41467-024-51062-w	2024
Genetics	Enhanced intestinal protein fermentation in schizophrenia.	Liang Y, Shi X, Shen Y, Huang Z, Wang J, Shao C, Chu Y, Chen J, Yu J, Kang Y.	BMC Med	10.1186/s12916-022-02261-z	2022
	Evaluation of Physiological Parameters of Intestinal Sulfate-Reducing Bacteria Isolated from Patients Suffering from IBD and Healthy People.	Kushkevych I, Castro Sangrador J, Dordevic D, Rozehnalova M, Cerny M, Fafula R, Vitezova M, Rittmann SKR.	J Clin Med	10.3390/jcm9061920	2020
Metabolism	Metabolic niche of a prominent sulfate-reducing human gut bacterium.	Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1312524110	2013
	Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough.	Trotter VV, Shatsky M, Price MN, Juba TR, Zane GM, De Leon KB, Majumder EL, Gui Q, Ali R, Wetmore KM, Kuehl JV, Arkin AP, Wall JD, Deutschbauer AM, Chandonia JM, Butland GP.	Front Microbiol	10.3389/fmicb.2023.1095191	2023
Phylogeny	Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador.	Soto-Giron MJ, Pena-Gonzalez A, Hatt JK, Montero L, Paez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K.	Am J Trop Med Hyg	10.4269/ajtmh.20-0831	2021
Genetics	Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics.	Dukes HE, Tinker KA, Ottesen EA.	Front Microbiol	10.3389/fmicb.2023.1156809	2023
Metabolism	Impacts of Cigarette Smoking Status on Metabolomic and Gut Microbiota Profile in Male Patients With Coronary Artery Disease: A Multi-Omics Study.	Hu X, Fan Y, Li H, Zhou R, Zhao X, Sun Y, Zhang S.	Front Cardiovasc Med	10.3389/fcvm.2021.766739	2021
Genetics	Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer.	Wolf PG, Cowley ES, Breister A, Matatov S, Lucio L, Polak P, Ridlon JM, Gaskins HR, Anantharaman K.	Microbiome	10.1186/s40168-022-01242-x	2022
	Versatile Triad Alliance: Bile Acid, Taurine and Microbiota.	Duszka K.	Cells	10.3390/cells11152337	2022
	Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases.	Loubinoux J, Bronowicki JP, Pereira IA, Mougenel JL, Faou AE.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2002.tb00942.x	2002
	Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.	Pieper R, Dadi TH, Pieper L, Vahjen W, Franke A, Reinert K, Zentek J.	ISME J	10.1038/s41396-020-0730-3	2020
Pathogenicity	Hydrogen sulfide suppresses ghrelin secretion in vitro and delays postprandial ghrelin secretion while reducing appetite in mice.	Slade E, Williams L, Gagnon J.	Physiol Rep	10.14814/phy2.13870	2018
Metabolism	Altered microRNA regulation of short chain fatty acid receptors in the hypertensive kidney is normalized with hydrogen sulfide supplementation.	Weber GJ, Foster J, Pushpakumar SB, Sen U.	Pharmacol Res	10.1016/j.phrs.2018.06.012	2018
Metabolism	New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.	Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS.	J Bacteriol	10.1128/jb.00679-13	2013
Enzymology	Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense.	Zhou Y, Wei Y, Nanjaraj Urs AN, Lin L, Xu T, Hu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y.	Biosci Rep	10.1042/bsr20190715	2019
	Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma.	Bjork JR, Bolte LA, Maltez Thomas A, Lee KA, Rossi N, Wind TT, Smit LM, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Spector TD, Bataille V, Segata N, Hospers GAP, Weersma RK.	Nat Med	10.1038/s41591-024-02803-3	2024
	Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice.	Parrish A, Boudaud M, Grant ET, Willieme S, Neumann M, Wolter M, Craig SZ, De Sciscio A, Cosma A, Hunewald O, Ollert M, Desai MS.	Nat Microbiol	10.1038/s41564-023-01464-1	2023
	Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium.	Neumann M, Steimle A, Grant ET, Wolter M, Parrish A, Willieme S, Brenner D, Martens EC, Desai MS.	Gut Microbes	10.1080/19490976.2021.1966263	2021
Metabolism	Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms.	Willemin MS, Hamelin R, Armand F, Holliger C, Maillard J.	Front Microbiol	10.3389/fmicb.2023.1058127	2023
Metabolism	Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough.	Zeng L, Wooton E, Stahl DA, Walian PJ.	J Bacteriol	10.1128/jb.00286-17	2017
	Deciphering microbial interactions in synthetic human gut microbiome communities.	Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.	Mol Syst Biol	10.15252/msb.20178157	2018
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Phylogeny	Impact of a Moderately Hypocaloric Mediterranean Diet on the Gut Microbiota Composition of Italian Obese Patients.	Pisanu S, Palmas V, Madau V, Casula E, Deledda A, Cusano R, Uva P, Vascellari S, Boi F, Loviselli A, Manzin A, Velluzzi F.	Nutrients	10.3390/nu12092707	2020
Genetics	Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.	Bratburd JR, Keller C, Vivas E, Gemperline E, Li L, Rey FE, Currie CR.	mBio	10.1128/mbio.02032-18	2018
	Gastrointestinal Helminth Infection Improves Insulin Sensitivity, Decreases Systemic Inflammation, and Alters the Composition of Gut Microbiota in Distinct Mouse Models of Type 2 Diabetes.	Khudhair Z, Alhallaf R, Eichenberger RM, Whan J, Kupz A, Field M, Krause L, Wilson DT, Daly NL, Giacomin P, Sotillo J, Loukas A.	Front Endocrinol (Lausanne)	10.3389/fendo.2020.606530	2020
Pathogenicity	A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.	Van den Abbeele P, Verstrepen L, Ghyselinck J, Albers R, Marzorati M, Mercenier A.	Nutrients	10.3390/nu12071917	2020
Metabolism	Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for Immunomodulation.	Peterson CT, Iablokov SN, Uchitel S, Chopra D, Perez-Santiago J, Rodionov DA, Peterson SN.	Front Genet	10.3389/fgene.2021.584197	2021
	Electrophysiology of the Facultative Autotrophic Bacterium Desulfosporosinus orientis.	Agostino V, Lenic A, Bardl B, Rizzotto V, Phan ANT, Blank LM, Rosenbaum MA.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00457	2020
	Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome.	Koopen AM, Almeida EL, Attaye I, Witjes JJ, Rampanelli E, Majait S, Kemper M, Levels JHM, Schimmel AWM, Herrema H, Scheithauer TPM, Frei W, Dragsted L, Hartmann B, Holst JJ, O'Toole PW, Groen AK, Nieuwdorp M.	Front Microbiol	10.3389/fmicb.2021.662159	2021
Enzymology	Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon.	Nava GM, Carbonero F, Croix JA, Greenberg E, Gaskins HR.	ISME J	10.1038/ismej.2011.90	2012
	Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization.	Nishiyama K, Yokoi T, Sugiyama M, Osawa R, Mukai T, Okada N.	Front Microbiol	10.3389/fmicb.2021.754819	2021
Enzymology	A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia.	Peck SC, Denger K, Burrichter A, Irwin SM, Balskus EP, Schleheck D.	Proc Natl Acad Sci U S A	10.1073/pnas.1815661116	2019
Phylogeny	Dietary Inulin and Trichuris suis Infection Promote Beneficial Bacteria Throughout the Porcine Gut.	Stolzenbach S, Myhill LJ, Andersen LO, Krych L, Mejer H, Williams AR, Nejsum P, Stensvold CR, Nielsen DS, Thamsborg SM.	Front Microbiol	10.3389/fmicb.2020.00312	2020
	Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes.	Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M.	Microorganisms	10.3390/microorganisms9050931	2021
	Effects of Intranasal Pseudorabies Virus AH02LA Infection on Microbial Community and Immune Status in the Ileum and Colon of Piglets.	Zhang C, Liu Y, Chen S, Qiao Y, Zheng Y, Xu M, Wang Z, Hou J, Wang J, Fan H.	Viruses	10.3390/v11060518	2019
	Negative interactions determine Clostridioides difficile growth in synthetic human gut communities.	Hromada S, Qian Y, Jacobson TB, Clark RL, Watson L, Safdar N, Amador-Noguez D, Venturelli OS.	Mol Syst Biol	10.15252/msb.202110355	2021
	Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles.	Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cardenas P, Baldeon ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G.	Nat Neurosci	10.1038/s41593-023-01361-0	2023
	Evidence for a multi-level trophic organization of the human gut microbiome.	Wang T, Goyal A, Dubinkina V, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1007524	2019
Enzymology	Isolation of sulfate-reducing bacteria from human thoracoabdominal pus.	Loubinoux J, Jaulhac B, Piemont Y, Monteil H, Le Faou AE.	J Clin Microbiol	10.1128/jcm.41.3.1304-1306.2003	2003
Genetics	Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs.	Tan Z, Yang T, Wang Y, Xing K, Zhang F, Zhao X, Ao H, Chen S, Liu J, Wang C.	Front Microbiol	10.3389/fmicb.2017.01546	2017
	Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.	Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R.	Microbiome	10.1186/s40168-017-0233-2	2017
Pathogenicity	In vitro activity of tomopenem (CS-023/RO4908463) against anaerobic bacteria.	Tanaka K, Mikamo H, Nakao K, Ichiishi T, Goto T, Yamagishi Y, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00595-08	2009
	Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection.	Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE.	PLoS Pathog	10.1371/journal.ppat.1007611	2019
Genetics	Genomic and Experimental Evidence Suggests that Verrucomicrobium spinosum Interacts with Eukaryotes.	Sait M, Kamneva OK, Fay DS, Kirienko NV, Polek J, Shirasu-Hiza MM, Ward NL.	Front Microbiol	10.3389/fmicb.2011.00211	2011
Metabolism	Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate.	Liu J, Wei Y, Lin L, Teng L, Yin J, Lu Q, Chen J, Zheng Y, Li Y, Xu R, Zhai W, Liu Y, Liu Y, Cao P, Ang EL, Zhao H, Yuchi Z, Zhang Y.	Proc Natl Acad Sci U S A	10.1073/pnas.2003434117	2020
Enzymology	Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale.	Aminov RI, Walker AW, Duncan SH, Harmsen HJ, Welling GW, Flint HJ.	Appl Environ Microbiol	10.1128/aem.00701-06	2006
Enzymology	Diversity in gut bacterial community of school-age children in Asia.	Nakayama J, Watanabe K, Jiang J, Matsuda K, Chao SH, Haryono P, La-Ongkham O, Sarwoko MA, Sujaya IN, Zhao L, Chen KT, Chen YP, Chiu HH, Hidaka T, Huang NX, Kiyohara C, Kurakawa T, Sakamoto N, Sonomoto K, Tashiro K, Tsuji H, Chen MJ, Leelavatcharamas V, Liao CC, Nitisinprasert S, Rahayu ES, Ren FZ, Tsai YC, Lee YK.	Sci Rep	10.1038/srep08397	2015
	Metabolic Basis for Mutualism between Gut Bacteria and Its Impact on the Drosophila melanogaster Host.	Sommer AJ, Newell PD.	Appl Environ Microbiol	10.1128/aem.01882-18	2019
	Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment.	Lam BR, Barr CR, Rowe AR, Nealson KH.	Front Microbiol	10.3389/fmicb.2019.01979	2019
Phylogeny	Desulfovibrio desulfuricans bacteremia in a dog.	Shukla SK, Reed KD.	J Clin Microbiol	10.1128/jcm.38.4.1701-1702.2000	2000
Genetics	Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.	Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1000071108	2011
Pathogenicity	Responses in gut microbiota and fat metabolism to a halogenated methane analogue in Sprague Dawley rats.	Su Y, Luo YH, Zhang LL, Smidt H, Zhu WY.	Microb Biotechnol	10.1111/1751-7915.12256	2015
	Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries.	Rawat PS, Seyed Hameed AS, Meng X, Liu W.	Gut Microbes	10.1080/19490976.2022.2068367	2022
Metabolism	Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease.	Mohan M, Chow CT, Ryan CN, Chan LS, Dufour J, Aye PP, Blanchard J, Moehs CP, Sestak K.	Nutrients	10.3390/nu8110684	2016
Enzymology	An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress.	da Silva SM, Amaral C, Neves SS, Santos C, Pimentel C, Rodrigues-Pousada C.	FEBS Open Bio	10.1016/j.fob.2015.07.001	2015
Metabolism	Gasotransmitter hydrogen sulfide signaling in neuronal health and disease.	Paul BD, Snyder SH.	Biochem Pharmacol	10.1016/j.bcp.2017.11.019	2018
Metabolism	A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.	Samuel BS, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.0602187103	2006
	A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.	Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC.	Cell	10.1016/j.cell.2016.10.043	2016
Metabolism	16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.	Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.	PLoS One	10.1371/journal.pone.0213869	2019
Phylogeny	Diversity and distribution of sulfate-reducing bacteria in permanently frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica.	Karr EA, Sattley WM, Rice MR, Jung DO, Madigan MT, Achenbach LA.	Appl Environ Microbiol	10.1128/aem.71.10.6353-6359.2005	2005
Genetics	Baseline human gut microbiota profile in healthy people and standard reporting template.	King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R.	PLoS One	10.1371/journal.pone.0206484	2019
	Intestinal methane production in obese individuals is associated with a higher body mass index.	Basseri RJ, Basseri B, Pimentel M, Chong K, Youdim A, Low K, Hwang L, Soffer E, Chang C, Mathur R.	Gastroenterol Hepatol (N Y)		2012
Enzymology	Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea.	Hermann-Bank ML, Skovgaard K, Stockmarr A, Strube ML, Larsen N, Kongsted H, Ingerslev HC, Molbak L, Boye M.	BMC Vet Res	10.1186/s12917-015-0419-4	2015
	On the relationship between sialomucin and sulfomucin expression and hydrogenotrophic microbes in the human colonic mucosa.	Croix JA, Carbonero F, Nava GM, Russell M, Greenberg E, Gaskins HR.	PLoS One	10.1371/journal.pone.0024447	2011
Genetics	Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity.	Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M.	PLoS One	10.1371/journal.pone.0059361	2013
Genetics	B-Vitamin Sharing Promotes Stability of Gut Microbial Communities.	Sharma V, Rodionov DA, Leyn SA, Tran D, Iablokov SN, Ding H, Peterson DA, Osterman AL, Peterson SN.	Front Microbiol	10.3389/fmicb.2019.01485	2019
	Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease?	Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Hunter JO, Cole JA.	FEMS Microbiol Lett	10.1111/j.1574-6968.2010.02057.x	2010
Metabolism	The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary beta-mannans.	La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MO, Pope PB, Martens EC, Hachem MA, Westereng B.	Nat Commun	10.1038/s41467-019-08812-y	2019
	Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies.	Noecker C, Chiu HC, McNally CP, Borenstein E.	mSystems	10.1128/msystems.00579-19	2019
Phylogeny	Alterations in the gut microbiota associated with HIV-1 infection.	Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE.	Cell Host Microbe	10.1016/j.chom.2013.08.006	2013
Metabolism	Roles of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas.	Morais-Silva FO, Santos CI, Rodrigues R, Pereira IA, Rodrigues-Pousada C.	J Bacteriol	10.1128/jb.00411-13	2013
Metabolism	Diversity of the metal-transporting P1B-type ATPases.	Smith AT, Smith KP, Rosenzweig AC.	J Biol Inorg Chem	10.1007/s00775-014-1129-2	2014
Metabolism	Exopolysaccharides produced by intestinal Bifidobacterium strains act as fermentable substrates for human intestinal bacteria.	Salazar N, Gueimonde M, Hernandez-Barranco AM, Ruas-Madiedo P, de los Reyes-Gavilan CG.	Appl Environ Microbiol	10.1128/aem.00325-08	2008
	A straightforward and efficient analytical pipeline for metaproteome characterization.	Tanca A, Palomba A, Pisanu S, Deligios M, Fraumene C, Manghina V, Pagnozzi D, Addis MF, Uzzau S.	Microbiome	10.1186/s40168-014-0049-2	2014
Genetics	High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.	Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L.	BMC Microbiol	10.1186/1471-2180-11-7	2011
Phylogeny	Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.	Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M.	Environ Microbiol	10.1111/1462-2920.12086	2013
Metabolism	The response of Caenorhabditis elegans to hydrogen sulfide and hydrogen cyanide.	Budde MW, Roth MB.	Genetics	10.1534/genetics.111.129841	2011
Genetics	Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.	Cross KL, Chirania P, Xiong W, Beall CJ, Elkins JG, Giannone RJ, Griffen AL, Guss AM, Hettich RL, Joshi SS, Mokrzan EM, Martin RK, Zhulin IB, Leys EJ, Podar M.	mBio	10.1128/mbio.02061-17	2018
Metabolism	The Qrc membrane complex, related to the alternative complex III, is a menaquinone reductase involved in sulfate respiration.	Venceslau SS, Lino RR, Pereira IA.	J Biol Chem	10.1074/jbc.m110.124305	2010
Metabolism	Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth.	Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin AP, Stahl DA.	J Bacteriol	10.1128/jb.01959-12	2013
	Methanogenic Archaea and oral infections - ways to unravel the black box.	Horz HP, Conrads G.	J Oral Microbiol	10.3402/jom.v3i0.5940	2011
	Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.	Koumandou VL, Kossida S.	PLoS Comput Biol	10.1371/journal.pcbi.1003821	2014
	A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities.	Harrington CR, Lucchini S, Ridgway KP, Wegmann U, Eaton TJ, Hinton JC, Gasson MJ, Narbad A.	BMC Microbiol	10.1186/1471-2180-8-195	2008
Metabolism	Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments.	Ravenschlag K, Sahm K, Knoblauch C, Jorgensen BB, Amann R.	Appl Environ Microbiol	10.1128/aem.66.8.3592-3602.2000	2000
Metabolism	Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.	Sharma M, Pudlo N, Jarva MA, Kaur A, John A, Burchill L, Lingford JP, Epa R, Abayakoon P, Scott NE, Turkenburg JP, Davies GJ, Martens EC, Goddard-Borger ED, Williams SJ.	J Biol Chem	10.1016/j.jbc.2025.108320	2025
	Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.	Gonzalez V, Abarca-Hurtado J, Arancibia A, Claverias F, Guevara MR, Orellana R.	Microorganisms	10.3390/microorganisms12091796	2024
Pathogenicity	Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk.	Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS.	STAR Protoc	10.1016/j.xpro.2021.100607	2021
Phylogeny	DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.	Sun Y, Kong L, Wu G, Cao B, Pang X, Deng Z, Dedon PC, Zhang C, You D.	Biomolecules	10.3390/biom10081175	2020
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Metabolism	Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.	Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.	J Bacteriol	10.1128/jb.01977-12	2013
Enzymology	Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico.	Tamura T, Tsunekawa N, Nemoto M, Inagaki K, Hirano T, Sato F.	Sci Rep	10.1038/srep19742	2016
	Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome.	Marchesi JR.	Bioeng Bugs	10.4161/bbug.2.6.17235	2011
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
Metabolism	An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction.	Biddle AS, Black SJ, Blanchard JL.	PLoS One	10.1371/journal.pone.0077599	2013
	Sulfite oxidation in chlorobaculum tepidum.	Rodriguez J, Hiras J, Hanson TE.	Front Microbiol	10.3389/fmicb.2011.00112	2011
Metabolism	Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.	Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO, Venturelli OS.	Elife	10.7554/elife.73870	2022
Genetics	A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.	D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N.	BMC Genomics	10.1186/s12864-015-2194-9	2016
Phylogeny	Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.	Shlykov MA, Zheng WH, Chen JS, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2011.12.005	2012
Metabolism	Synthetic Microbiomes on the Rise-Application in Deciphering the Role of Microbes in Host Health and Disease.	Bolsega S, Bleich A, Basic M.	Nutrients	10.3390/nu13114173	2021
Genetics	Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.	Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T	Sci Rep	10.1038/s41598-022-10762-3	2022
Metabolism	Lactate has the potential to promote hydrogen sulphide formation in the human colon.	Marquet P, Duncan SH, Chassard C, Bernalier-Donadille A, Flint HJ	FEMS Microbiol Lett	10.1111/j.1574-6968.2009.01750.x	2009
Phylogeny	Reclassification of the only species of the genus Desulfomonas, Desulfomonas pigra, as Desulfovibrio piger comb. nov.	Loubinoux J, Valente FM, Pereira IA, Costa A, Grimont PA, Le Faou AE	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1305	2002
Cultivation	[Rapid identification of Bilophila wadsworthia].	Sawamura H, Kato N, Sawa K, Watanabe K, Ueno K	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi1970.71.614	1997

References

#422	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 749
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Desulfovibrio piger (DSM 749, ATCC 29098, JCM 12224)

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