Alistipes shahii (DSM 19121, ATCC BAA-1179, CCUG 48947)

Name: Alistipes shahii (DSM 19121, ATCC BAA-1179, CCUG 48947)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14032

Type strain

Culture col. no. DSM 19121 ATCC BAA-1179 CCUG 48947 KCTC 15238 WAL 8301 1 more

NCBI tax ID(s) 717959 328814

Special Collections DSMZ CCUG JCM KCTC Literature strains

History DSMZ <- CCUG <- Y. Song; WAL 8301 JCM <-- CCUG 48947 <-- Y. Song WAL 8301. KCTC <- CCUG <- Y Song, WAL 8301

Links

Alistipes shahii DSM 19121 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human appendix tissue.

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

Name and taxonomic classification

SI-ID 297120

KCTC 15238,ATCC BAA-1179,CCUG 48947,DSM 19121,JCM 16773

@ref 20215

Last LPSN update 2026-05-29 08:28:11

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes shahii

Full scientific name Alistipes shahii Song et al. 2006

BacDive ID	Other strains from **Alistipes shahii** (1)	Type strain
159529	A. shahii BL-389-WT-23F, DSM 107272

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31803	negative	0.6-4 µm	0.1-0.2 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative				99.889
125438	negative				96.781
125438					91.095

Colony morphology

58401

Incubation period1 day

Pigmentation

31803

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7920	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7920	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)
7920	positive	growth	37
31803	positive	growth	37
31803	positive	optimum	37
58401	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31803	positive	optimum	7
31803	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7920	anaerobe
31803	anaerobe
58401	anaerobe
67771	anaerobe
125439	obligate anaerobe	98.906

Spore formation

@ref	Spore formation	Confidence
31803
125438		95.898
125439		99.993

Observation

31803

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
31803	4853 ChEBI	esculin	+	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
31803	37684 ChEBI	mannose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
31803	16634 ChEBI	raffinose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31803	35581 ChEBI	indole
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31803	35581 ChEBI	indole	+
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
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
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
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
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
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

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
7920	-	-	+	+	-	+	+	-	-	+	-	-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-
7920	-	-	+	+	-	+	+	-	-	+	-	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human
#Host Body-Site	#Gastrointestinal tract

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
7920	human appendix tissue	Homo sapiens			USA	USA	North America
58401	Human appendix tissue	Homo sapiens	1989	Los Angeles	USA	USA	North America
67770	Human specimens	Homo sapiens
67771	From human appendix tissue	Homo sapiens			USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence FP929032 (>99% sequence identity) for Alistipes shahii subclade from Microbeatlas

Aquatic Samples	3715
Soil Samples	1190
Animal Samples	187778
Plant Samples	375
Total Samples	193058

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
7920	yes, in single cases	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
124043	ASM2514584v1 assembly for Alistipes shahii WAL 8301	complete	GCA_025145845	717959.412	8079346206	717959	96.38
67771	ASM21057v1 assembly for Alistipes shahii WAL 8301	chromosome	GCA_000210575	717959.3	650377904	717959	40.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7920	Alistipes shahii strain WAL 8301 16S ribosomal RNA gene, partial sequence	AY974072	1433		717959
67770	Alistipes shahii gene for 16S ribosomal RNA, partial sequence, strain: JCM 16773	AB554233	1486		328814

GC content

@ref	GC-content (mol%)	Method
7920	56
7920	57.6	sequence analysis
67770	56	high performance liquid chromatography (HPLC)
67770	57.2	genome sequence analysis
67771	56.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2514584v1 assembly for Alistipes shahii WAL 8301
BV-BRC: 717959.412

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.91	no
125439	gram_stain	BacteriaNetⓘ	negative	99.89	no
125439	motility	BacteriaNetⓘ	yes	51.69	no
125439	spore_formation	BacteriaNetⓘ	no	99.99	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes shahii WAL 8301
PATRIC: 717959.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.78	yes
125438	anaerobic	anaerobicⓘ	yes	87.06	yes
125438	spore-forming	spore-formingⓘ	no	95.90	yes
125438	aerobic	aerobicⓘ	no	90.99	no
125438	thermophilic	thermophileⓘ	no	97.32	yes
125438	flagellated	motile2+ⓘ	no	91.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	RELMbeta sets the threshold for microbiome-dependent oral tolerance.	Stephen-Victor E, Kuziel GA, Martinez-Blanco M, Jugder BE, Benamar M, Wang Z, Chen Q, Lozano GL, Abdel-Gadir A, Cui Y, Fong J, Saint-Denis E, Chang I, Nadeau KC, Phipatanakul W, Zhang A, Farraj FA, Holder-Niles F, Zeve D, Breault DT, Schmitz-Abe K, Rachid R, Crestani E, Rakoff-Nahoum S, Chatila TA.	Nature	10.1038/s41586-024-08440-7	2025
	Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds.	Seveso A, Mazurkewich S, Banerjee S, Poulsen J-CN, Lo Leggio L, Larsbrink J.	Appl Environ Microbiol	10.1128/aem.01768-23	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
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
Metabolism	SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.	Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS.	Elife	10.7554/elife.82401	2023
Enzymology	Degradation of the low-calorie sugar substitute 5-ketofructose by different bacteria.	Schiessl J, Kosciow K, Garschagen LS, Hoffmann JJ, Heymuth J, Franke T, Deppenmeier U.	Appl Microbiol Biotechnol	10.1007/s00253-021-11168-3	2021
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
Metabolism	Chitosan Oligosaccharides Show Protective Effects in Coronary Heart Disease by Improving Antioxidant Capacity via the Increase in Intestinal Probiotics.	Jiang T, Xing X, Zhang L, Liu Z, Zhao J, Liu X.	Oxid Med Cell Longev	10.1155/2019/7658052	2019
Metabolism	Altered tryptophan metabolism and gut immune crosstalk in hypertensive middle-aged women.	Shah S, Mu C, Shen-Tu G, Schlicht K, Forkert ND, Laudes M, Kofeler HC, Shearer J.	Am J Physiol Heart Circ Physiol	10.1152/ajpheart.00395.2025	2025
	Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.	Li X, He N, Wang H, Wu Z, Wang M, Liang H, Xiao L, Yang Z, Li C, Xu P, Dai T, Li S, Zou Y.	J Appl Microbiol	10.1093/jambio/lxaf119	2025
Pathogenicity	Body mass index distinctly modulates the associations between Alistipes and CRP/IL-6 in metabolic and lupus inflammatory features.	Chero-Sandoval L, Higuera-Gomez A, de Cuevillas B, Castejon R, Martinez-Urbistondo M, Mellor-Pita S, Moreno-Torres V, de Luis D, Cuevas-Sierra A, Martinez JA.	PLoS One	10.1371/journal.pone.0335452	2025
	Microbiota-shaped neutrophil senescence regulates sexual dimorphism in bladder cancer.	Zhu Q, Zhang G, Cao M, Huang H, He D, Zang Z, Xing J, Zhan M, Pei S, Deng X, Li J, Meng G, Xu J, Dai D, Hu G, Zheng M, Liu C, Qin J, Xiao Y.	Nat Immunol	10.1038/s41590-025-02126-6	2025
	Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.	Zeng L, Yu B, Zeng P, Duoji Z, Zuo H, Lian J, Yang T, Dai Y, Feng Y, Yu P, Yang J, Yang S, Dou Q.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00721-x	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
	Effect of dark sweet cherry (Prunus avium) supplementation on the fecal microbiota, metabolic endotoxemia, and intestinal permeability in obese subjects: a single-blind randomized trial.	Arbizu S, Mertens-Talcott SU, Talcott S, Noratto GD.	Food Funct	10.1039/d4fo01650e	2024
	Gut commensal Alistipes shahii improves experimental colitis in mice with reduced intestinal epithelial damage and cytokine secretion.	Lin X, Xu M, Lan R, Hu D, Zhang S, Zhang S, Lu Y, Sun H, Yang J, Liu L, Xu J.	mSystems	10.1128/msystems.01607-24	2025
Enzymology	Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.	Kuzmichenko P, Fedorov D, Galeeva J, Postoeva A, Krieger E, Kudryavtsev A, Pavlenko A, Vvedensky A, Starikova E, Govorun V, Ilina E.	Sci Rep	10.1038/s41598-025-26617-6	2025
	Fiber from elicited butternut pumpkin (Cucurbita moschata D. cv. Ariel) modulates the human intestinal microbiota dysbiosis.	Nieto JA, Roses C, Garcia-Ibanez P, Perez B, Viadel B, Romo-Hualde A, Milagro FI, Barcelo A, Carvajal M, Gallego E, Agudelo A.	Int J Biol Macromol	10.1016/j.ijbiomac.2024.132130	2024
	MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics.	Bai D, Ma C, Xun J, Luo H, Yang H, Lyu H, Zhu Z, Gai A, Yousuf S, Peng K, Xu S, Gao Y, Wang Y, Liu YX.	Imeta	10.1002/imt2.70002	2025
	Palmitoleic Acid Inhibits Hepatotoxic Effects by Reducing Trimethylamine-N-Oxide (TMAO) Formation in High L-Carnitine-Treated Mice.	Han Q, Liu Y, Liu X, Geng Y, Wu Q, Xiao H.	Nutrients	10.3390/nu16213599	2024
	Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.	Wang H, Xue W, Cheng J, He Y, Song Y, Hu D, Peng A, Li C, Bao H.	Microbiol Spectr	10.1128/spectrum.03166-24	2025
	Association between seizure reduction during ketogenic diet treatment of epilepsy and changes in circulatory metabolites and gut microbiota composition.	Dahlin M, Wheelock CE, Prast-Nielsen S.	EBioMedicine	10.1016/j.ebiom.2024.105400	2024
	Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus.	Medina-Martinez I, Gil-Gutierrez R, Garcia-Garcia J, de la Hera-Fernandez FJ, Navarrete-Navarrete N, Zamora-Pasadas M, Ortego-Centeno N, Callejas-Rubio JL, Garcia-Garcia F, Galvez-Peralta J, Rodriguez-Nogales A, Correa-Rodriguez M, Rueda-Medina B.	Med Sci (Basel)	10.3390/medsci13030151	2025
Genetics	Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.	Li J, Zhu Y, Chang Q, Gong Y, Wan J, Xu S.	Pol J Microbiol	10.33073/pjm-2025-006	2025
	Hormonal Contraceptives and the Gut Microbiome in Female Athletes: Implications for Health, Performance, and Exercise-Related Physiological Adjustments	Pierudzka W, Slawatycki J, Klemenska P, Warczak K, Wasilewska P, Horwat P, Gorski J.	Cureus
Genetics	Mendelian randomization analyses support causal relationships between gut microbiome and longevity.	Chen S, Chen W, Wang X, Liu S.	J Transl Med	10.1186/s12967-024-05823-2	2024
Genetics	Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.	Cai X, Dai J, Xie Y, Xu S, Liu M.	Sci Rep	10.1038/s41598-024-71740-5	2024
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
	Effect of exercise on the human gut microbiota in individuals with overweight and obesity: a systematic review and meta-analysis of randomized controlled trials.	Kim YI, Choi W, Seo M, Ka S, Park J.	Phys Act Nutr	10.20463/pan.2025.0014	2025
	Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.	Wong MK, Armstrong E, Heirali AA, Schneeberger PHH, Chen H, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	mBio	10.1128/mbio.01904-25	2025
Genetics	Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.	Chen J, Luo Y, Hao Y, Wang Q, Wang Q.	Front Nutr	10.3389/fnut.2025.1676238	2025
	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
	The alpha-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket.	Wei X, Wang YL, Wen BT, Liu SJ, Wang L, Sun L, Gu TY, Li Z, Bao Y, Fan SL, Zhou H, Wang F, Xin F.	J Agric Food Chem	10.1021/acs.jafc.1c00940	2021
	Causal relationship between gut microbiota and pituitary neuroendocrine tumors: a bidirectional Mendelian randomization.	Wang W, Liu M, Wang Z, Ye W, Li X.	Discov Oncol	10.1007/s12672-025-02958-6	2025
Pathogenicity	Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.	Hong HH, Lee SY, Jang DH, Ju SE, Shim JE, Kim TH, Kang HS, Kim SM.	J Microbiol Biotechnol	10.4014/jmb.2507.07010	2025
Phylogeny	Exploring the Intestinal Microbiota Profile in Prostate Cancer Patients and Healthy Controls.	Cocomazzi G, Villani A, Mencarelli G, Contu V, De Ruvo D, Virgili E, Marino F, Baldini GM, Binda E, Parmegiani L, Ciampaglia W, Capone L, Perri F, Cisternino A, Pazienza V, Panebianco C.	Microorganisms	10.3390/microorganisms13092105	2025
Proteome	Proteomic and microbial assessments on the effect of Antrodia cinnamomea in C57BL/6 mice.	Tsai YT, Ruan JW, Chang CS, Ko ML, Chou HC, Lin CC, Lin CM, Huang CT, Wei YS, Liao EC, Chen HY, Lin LH, Lin MW, Kao CY, Chan HL.	Arch Biochem Biophys	10.1016/j.abb.2021.109058	2021
	Insights into Intrinsic Atopic Dermatitis: immunogenicity, Dysbiosis, and Imaging (Reflectance Confocal Microscopy, Optical Coherence Tomography).	Gavrilita E, Silion SI, Bitca ML, Tatu AL.	Clin Cosmet Investig Dermatol	10.2147/ccid.s459096	2024
	Gut microbiome metabolites, molecular mimicry, and species-level variation drive long-term efficacy and adverse event outcomes in lung cancer survivors.	Liu X, Lu B, Tang H, Jia X, Zhou Q, Zeng Y, Gao X, Chen M, Xu Y, Wang M, Tan B, Li J.	EBioMedicine	10.1016/j.ebiom.2024.105427	2024
	Roxadustat alleviates the inflammatory status in patients receiving maintenance hemodialysis with erythropoiesis-stimulating agent resistance by increasing the short-chain fatty acids producing gut bacteria.	Zhao XN, Liu SX, Wang ZZ, Zhang S, You LL.	Eur J Med Res	10.1186/s40001-023-01179-3	2023
	Preliminary Study to Understand the Role of Gut Microbiota in Coronary Slow Flow Phenomenon (CSFP).	Gurol T, Karaman T, Gurol Y, Sezerman OU, Oktem Okullu S.	Metabolites	10.3390/metabo15070475	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
Stress	Evaluation of the Safety and Impact of Heat-Treated Lactiplantibacillus plantarum KM2 Fermentation on Gut Microbiome Architecture.	Won S, Jeong Y, Kim JE, Kim JH, Song HS, Bae HH, Kwak MS, Kim DK, Sung MH, Kwak S.	J Microbiol Biotechnol	10.4014/jmb.2411.11069	2024
Pathogenicity	The Effects of Prebiotic Dietary Fibers, Probiotics, and Synbiotics on Gut Permeability and Immunity: A Systematic Review.	Maghsoumi-Norouzabad L, Bagherzadeh-Karimi A, Aliakbari Majd S, Hosseini L, Shahi F.	Iran J Med Sci	10.30476/ijms.2024.102363.3525	2025
	Fecal microbiota transplantation treatment for type 1 diabetes mellitus with malnutrition: a case report.	Xie YC, Jing XB, Chen X, Chen LZ, Zhang SH, Cai XB.	Ther Adv Chronic Dis	10.1177/20406223221117449	2022
Genetics	A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.	Kim S, Thapa I, Ali H.	BMC Microbiol	10.1186/s12866-024-03633-6	2024
	Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial.	Zhang Z, Mocanu V, Deehan EC, Hotte N, Zhu Y, Wei S, Kao DH, Karmali S, Birch DW, Walter J, Madsen KL.	Gut Microbes	10.1080/19490976.2024.2345134	2024
	Microbiota Diversity in Non-Small Cell Lung Cancer Gut and Mouth Cavity Microbiota Diversity in Non-Small Cell Lung Cancer Patients.	Brisudova A, Bielnikova-Krystofova H, Motyka O, Fritzova D, Katuchova V, Ponikelska N, Skanderova D, Raclavsky V, Michalek J, Mittak M, Svecova P, Jakubec P, Rozsivalova D, Szkorupa M, Klein J, Skarda J, Kolar Z, Skopelidou V.	Pol J Microbiol	10.33073/pjm-2023-044	2023
Genetics	Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia.	Lv L-J, Wen J-Y, Zhang Y, Guo R-C, Li H, Yi Z-T, He T-W, Chen M-C, Chen Y, Wu X-Y, Li S-h, Kang J, Hou Y-P, Yan Q-l, Yin A-H.	mSphere	10.1128/msphere.00676-23	2024
Genetics	Characteristics of the gut virome in patients with premalignant colorectal adenoma.	Zhang P, Tuo X, Jiang J, Zhang Y, Zhao J, Deng C, Zhao G, Cheng Y, Song L, Yang Y, Guo R, Zhang H, Zhao H, Ma S, Li L, Shi H.	J Transl Med	10.1186/s12967-025-06404-7	2025
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
	Sex-Specific Associations of Gut Microbiota Composition with Sarcopenia Defined by the Asian Working Group for Sarcopenia 2019 Consensus in Older Outpatients: Prospective Cross-Sectional Study in Japan.	Asaoka D, Toda K, Yoshimoto S, Katsumata N, Odamaki T, Iwabuchi N, Tanaka M, Xiao JZ, Nishikawa Y, Nomura O, Takeda T, Nagahara A, Koido S, Ohkusa T, Sato N.	Nutrients	10.3390/nu17101746	2025
	Sex chromosomes/hormones and the tumor microenvironment of non-reproductive cancers.	Zhang CM, Ge ZB, Zhou HH, Wei MX, Ding XY, Lin ZZ, Wang MY, Bai CJ.	Front Immunol	10.3389/fimmu.2025.1642956	2025
Phylogeny	Fecal Microbial Dysbiosis Is Associated with Colorectal Cancer Risk in a Korean Population.	Kim J, Gunathilake M, Yeo HY, Oh JH, Kim BC, Han N, Kim B, Pyun H, Lim MY, Nam YD, Chang HJ.	Cancer Res Treat	10.4143/crt.2024.382	2025
	Selection for environmental variance shifted the gut microbiome composition driving animal resilience.	Casto-Rebollo C, Argente MJ, Garcia ML, Pena RN, Blasco A, Ibanez-Escriche N.	Microbiome	10.1186/s40168-023-01580-4	2023
	Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease.	Yu J, Meng J, Qin Z, Yu Y, Liang Y, Wang Y, Min D.	J Neuroinflammation	10.1186/s12974-023-02782-1	2023
Phylogeny	Exploring the Characteristics of Gut Microbiota Associated with Depression via the Depression Assessment Scales.	Won S, Kim EJ, Park SE, Lee MH, Pak J, Kim K, Son HS, Kim JH, Kwak S.	J Microbiol Biotechnol	10.4014/jmb.2408.08042	2024
	Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.	Rasoulimehrabani H, Khadem S, Hodzic A, Philipp M, Gallo R, Nikolov G, Seneca J, Ramesmayer J, Sivulic P, Berry D.	Microbiome Res Rep	10.20517/mrr.2025.29	2025
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
	Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.	Ye X, Sahana G, Lund MS, Li B, Cai Z.	Anim Microbiome	10.1186/s42523-025-00386-z	2025
Genetics	Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.	Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N.	Nat Commun	10.1038/s41467-024-52097-9	2024
	Sturgeon-derived peptide LLLE alleviates colitis via regulating gut microbiota and its metabolites.	Lin J, Yang J, Cui L, Nagpal R, Singh P, Salazar G, Rao Q, Peng Y, Sun Q.	Curr Res Food Sci	10.1016/j.crfs.2024.100898	2024
Genetics	Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.	Yang J, Wang H, Lin X, Liu J, Feng Y, Bai Y, Liang H, Hu T, Wu Z, Lai J, Liu J, Zou Y, Wei S, Yan P.	mSystems	10.1128/msystems.01366-24	2024
Phylogeny	Gut microbial predictors of first-line immunotherapy efficacy in advanced NSCLC patients.	Grenda A, Iwan E, Kuznar-Kaminska B, Bomba A, Bielinska K, Krawczyk P, Chmielewska I, Frak M, Szczyrek M, Rolska-Kopinska A, Jankowski T, Kieszko R, Milanowski J.	Sci Rep	10.1038/s41598-025-89406-1	2025
	Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.	Feng C, Li N, Gao G, He Q, Kwok LY, Zhang H.	Int J Mol Sci	10.3390/ijms25073768	2024
	Functional recovery outcomes following acute stroke is associated with abundance of gut microbiota related to inflammation, butyrate and secondary bile acid.	Hammond TC, Powell E, Green SJ, Chlipala G, Frank J, Yackzan AT, Yanckello LM, Chang YH, Xing X, Heil S, Springer JE, Pennypacker K, Stromberg A, Sawaki L, Lin AL.	Front Rehabil Sci	10.3389/fresc.2022.1017180	2022
	Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population.	Liu Y, Zhu J, Wang H, Lu W, Lee YK, Zhao J, Zhang H.	BMC Genomics	10.1186/s12864-022-09087-2	2022
Genetics	Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.	Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS, Kim SY.	BMC Microbiol	10.1186/s12866-023-03084-5	2023
	Alterations in microbiome associated with acute pancreatitis.	Yazici C, Priyadarshini M, Boulay B, Dai Y, Layden BT.	Curr Opin Gastroenterol	10.1097/mog.0000000000001046	2024
Pathogenicity	Assembled human microbiome and metabolome in chronic kidney disease: Dysbiosis a double-edged sword interlinking Circ-YAP1, Circ-APOE & Circ-SLC8A1.	Zaki EA, Afifi SM, Ammar NM, Kadry MO.	Toxicol Rep	10.1016/j.toxrep.2025.102058	2025
	Consumption of only wild foods induces large scale, partially persistent alterations to the gut microbiome.	Rampelli S, Pomstra D, Barone M, Fabbrini M, Turroni S, Candela M, Henry AG.	Sci Rep	10.1038/s41598-025-00319-5	2025
Genetics	Pharmacological and Nutritional Modulation of Metabolome and Metagenome in Cardiometabolic Disorders.	Witkowska AM, Salem JE.	Biomolecules	10.3390/biom13091340	2023
	Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach.	Romanov VA, Karasev IA, Klimenko NS, Koshechkin SI, Tyakht AV, Malikhova OA.	Cancers (Basel)	10.3390/cancers14215207	2022
Pathogenicity	Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus.	MacCann R, Li J, Leon AAG, Negi R, Alalwan D, Tinago W, McGettrick P, Cotter AG, Landay A, Sabin C, O'Toole PW, Mallon PWG, Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group .	J Infect Dis	10.1093/infdis/jiaf043	2025
Phylogeny	Correlation between invasive microbiota in margin-surrounding mucosa and anastomotic healing in patients with colorectal cancer.	Li YD, He KX, Zhu WF.	World J Gastrointest Oncol	10.4251/wjgo.v11.i9.717	2019
Phylogeny	Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus).	Neha SA, Salazar-Bravo J.	BMC Microbiol	10.1186/s12866-023-02778-0	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
	Plant-based diets and the gut microbiome: findings from the Baltimore Longitudinal Study of Aging.	Shen X, Tilves C, Kim H, Tanaka T, Spira AP, Chia CW, Talegawkar SA, Ferrucci L, Mueller NT.	Am J Clin Nutr	10.1016/j.ajcnut.2024.01.006	2024
	Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.	Zhang F, Luan J, Suo L, Wang H, Zhao Y, Sun T, Ni Y, Cao H, Zou X, Liu B.	Microbiol Spectr	10.1128/spectrum.02639-24	2025
Phylogeny	Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis.	Horvath A, Durdevic M, Leber B, di Vora K, Rainer F, Krones E, Douschan P, Spindelboeck W, Durchschein F, Zollner G, Stauber RE, Fickert P, Stiegler P, Stadlbauer V.	Nutrients	10.3390/nu12061874	2020
	Distinct exercise modalities on GUT microbiome in sarcopenic older adults: study protocol of a pilot randomized controlled trial.	Merelim AS, Zacca R, Moreira-Goncalves D, Costa PP, Baptista LC.	Front Med (Lausanne)	10.3389/fmed.2025.1504786	2025
	Assessing the Role of Dark Sweet Cherry (Prunus avium L.) Consumption on Cognitive Function, Neuropeptides, and Circadian Rhythm in Obesity: Results from a Randomized Controlled Trial.	Arbizu S, Mertens-Talcott SU, Talcott S, Riviere A, Riechman SE, Noratto GD.	Nutrients	10.3390/nu17050784	2025
	Prebiotic-Engineered Oral Nanoplatform against Ulcerative Colitis via Photodynamic Remodeling of Gut Microbiota and Macrophage Polarization.	He N, Jiang H, Dai T, Kim GS, Liu P, Zhao Y, Li S, Cao J, Li Z.	Biomater Res	10.34133/bmr.0283	2025
	Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.	Nomura K, Ishikawa D, Okahara K, Ito S, Haga K, Takahashi M, Arakawa A, Shibuya T, Osada T, Kuwahara-Arai K, Kirikae T, Nagahara A.	J Clin Med	10.3390/jcm10081749	2021
Genetics	Non-small cell lung cancer patients treated with Anti-PD1 immunotherapy show distinct microbial signatures and metabolic pathways according to progression-free survival and PD-L1 status.	Dora D, Ligeti B, Kovacs T, Revisnyei P, Galffy G, Dulka E, Krizsan D, Kalcsevszki R, Megyesfalvi Z, Dome B, Weiss GJ, Lohinai Z.	Oncoimmunology	10.1080/2162402x.2023.2204746	2023
Phylogeny	Impact of Ketogenic and Mediterranean Diets on Gut Microbiota Profile and Clinical Outcomes in Drug-Naïve Patients with Diabesity: A 12-Month Pilot Study.	Palmas V, Deledda A, Heidrich V, Sanna G, Cambarau G, Fosci M, Puglia L, Cappai EA, Lai A, Loviselli A, Manzin A, Velluzzi F.	Metabolites	10.3390/metabo15010022	2025
Metabolism	Coenzyme A metabolism: a key driver of gut microbiota dynamics and metabolic profiles.	Bottcher J, Sibon OCM, El Aidy S.	FEMS Microbiol Rev	10.1093/femsre/fuaf051	2025
	Physical Therapy for Knee Pain Relief Induces Changes in Gut Microbiome Composition: A Secondary Analysis of Data From a Randomized Controlled Trial.	Kouraki A, Vijay A, Gohir S, Millar B, Kelly A, Valdes AM.	Sports Health	10.1177/19417381241283812	2025
	Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model.	Cuisiniere T, Hajjar R, Oliero M, Calve A, Fragoso G, Rendos HV, Gerkins C, Taleb N, Gagnon-Konamna M, Dagbert F, Loungnarath R, Sebajang H, Schwenter F, Wassef R, Ratelle R, De Broux E, Richard C, Santos MM.	Microbiome	10.1186/s40168-025-02101-1	2025
	Integrated Microbiome and Metabolome Analysis Reveals Hypothalamic-Comorbidities Related Signatures in Craniopharyngioma.	Lin B, Ye Z, Cao Z, Ye Z, Yu Y, Jiang W, Guo S, Melnikov V, Zhou P, Ji C, Shi C, Wu Z, Chen Z, Xu Y, Zhang Q, Ma Z, Qiao N, Chen L, Shou X, Cao X, Zhou X, Zhang L, He M, Wang Y, Ye H, Li Y, Zhang Z, Wang M, Gao R, Zhang Y.	Adv Sci (Weinh)	10.1002/advs.202400684	2024
	Polyphenols and Microbiota Modulation: Insights from Swine and Other Animal Models for Human Therapeutic Strategies.	Anghel AC, Taranu I, Ortan A, Marcu Spinu S, Dragoi Cudalbeanu M, Rosu PM, Babeanu NE.	Molecules	10.3390/molecules29246026	2024
Genetics	Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.	Hu X, Yu C, He Y, Zhu S, Wang S, Xu Z, You S, Jiao Y, Liu SL, Bao H.	BMC Microbiol	10.1186/s12866-024-03278-5	2024
	Intratumorally specific microbial-derived lipopolysaccharide contributes to non-small cell lung cancer progression.	Sha G, Wu Z, Wang B, Ding Y, Xiao Z, Zhang W, Zhou J, Zhou Y, Ji G, Tian Z, Zhang W, Zhao X.	Virulence	10.1080/21505594.2025.2548626	2025
Phylogeny	Dysregulation of saliva and fecal microbiota as novel biomarkers of colorectal cancer.	Rong J, Chen X, Li Z, Li B, Sun Y, Miao Y.	Front Oncol	10.3389/fonc.2024.1498328	2024
	Are Faecal Microbiota Analyses on Species-Level Suitable Clinical Biomarkers? A Pilot Study in Subjects with Morbid Obesity.	Farup PG, Maseng MG.	Microorganisms	10.3390/microorganisms9030664	2021
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
	Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs.	Ren H, Shi Z, Yang F, Wang S, Yuan F, Li T, Li M, Zhu J, Li J, Wu K, Zhang Y, Ning G, Kristiansen K, Wang W, Gu Y, Zhong H.	Imeta	10.1002/imt2.179	2024
Metabolism	Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma.	Lin B, Wang M, Gao R, Ye Z, Yu Y, He W, Qiao N, Ma Z, Ji C, Shi C, Zhou X, Wang Y, Zeng F, Zhang L, Gong W, Cao Z, Zhou P, Melnikov V, Ye H, Li Y, Zhang Z, He M, Qin H, Zhang Y.	Microbiol Spectr	10.1128/spectrum.00425-21	2022
Genetics	Microbial characterization based on multifractal analysis of metagenomes.	Xie XH, Huang YJ, Han GS, Yu ZG, Ma YL.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1117421	2023
	Clinical effectiveness of fecal microbial transplantation for metabolic syndrome: Advances in clinical efficacy and multi-omics research.	Wang H, Tian J, Mi J.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100415	2025
Pathogenicity	Enterococcus faecium R0026 Combined with Bacillus subtilis R0179 Prevent Obesity-Associated Hyperlipidemia and Modulate Gut Microbiota in C57BL/6 Mice.	Huang J, Huang J, Yin T, Lv H, Zhang P, Li H.	J Microbiol Biotechnol	10.4014/jmb.2009.09005	2021
	Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift.	Chanda D, De D.	Gut Microbes	10.1080/19490976.2024.2304900	2024
	Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions.	Gnanasekaran T, Sarathi A, Fang Q, Azarm A, Assis Geraldo J, Nigro E, Arumugam M.	mSystems	10.1128/msystems.01249-22	2023
	alpha-synuclein overexpression and the microbiome shape the gut and brain metabolome in mice.	Morais LH, Boktor JC, MahmoudianDehkordi S, Kaddurah-Daouk R, Mazmanian SK.	NPJ Parkinsons Dis	10.1038/s41531-024-00816-w	2024
Metabolism	Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.	Park S, Li C, Wu X, Zhang T.	Int J Mol Sci	10.3390/ijms241713329	2023
Phylogeny	Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.	Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE.	Cell Host Microbe	10.1016/j.chom.2024.08.016	2024
	Exercise and microbiome: From big data to therapy.	Meng D, Ai S, Spanos M, Shi X, Li G, Cretoiu D, Zhou Q, Xiao J.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.10.034	2023
Pathogenicity	Intestinal Microbiota Influence Doxorubicin Responsiveness in Triple-Negative Breast Cancer.	Bawaneh A, Wilson AS, Levi N, Howard-McNatt MM, Chiba A, Soto-Pantoja DR, Cook KL.	Cancers (Basel)	10.3390/cancers14194849	2022
	The gut microbiota-mediated ferroptosis pathway: a key mechanism of ginsenoside Rd against metabolism-associated fatty liver disease.	Liu W, Zhou X, Xiao L, Huang X, Chang D, Zhong X, Zeng M, Xian Y, Zheng Y, Huang W, Huang R, Huang M.	Chin Med	10.1186/s13020-025-01121-1	2025
	The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Kim EH, Choi J, Choi Y, Yoon H, Lee SM, Seok YJ.	Gut Liver	10.5009/gnl230385	2024
Pathogenicity	Oral administration of the probiotic strain Lactobacillus helveticus BGRA43 reduces high-fat diet-induced hepatic steatosis in mice and restores gut microbiota composition.	Teofilovic A, Vrataric M, Bursac B, Gligorovska L, Vojnovic Milutinovic D, Stanisavljevic N, Strahinic I, Misic D, Nikolic F, Pavlovic B, Joncic Savic K, Aydogan C, Djordjevic A.	Front Pharmacol	10.3389/fphar.2025.1688777	2025
Genetics	Probiotics Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 prevent high blood pressure via modulating the gut microbiota composition and host metabolic products.	Zhang Y, Zheng T, Ma D, Shi P, Zhang H, Li J, Sun Z.	mSystems	10.1128/msystems.00331-23	2023
Phylogeny	Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis.	Budzinski L, Sempert T, Lietz L, Maier R, Kang GU, von Stuckrad ASL, Goetzke CC, Roth M, Shah A, Abbas A, Lehman K, Necke K, Bartsch S, Hoffmann U, Mashreghi MF, Biesen R, Kallinich T, Chang HD.	Mol Cell Pediatr	10.1186/s40348-024-00186-6	2024
Metabolism	Treatment-Related Mechanisms of Tibetan Medicine Terminalia chebula (TC) Aqueous Extract Against Mouse Gastroenteritis Caused by Yak-Origin Salmonella Determined Using Intestinal Microbiome Analysis and Metabolomics.	Li D, Zhang K, Xue X, Bai Z, Yang, Qi J, Suolang S.	Animals (Basel)	10.3390/ani15050755	2025
	Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.	Sanchez-Terron G, Martinez R, Morcuende D, Estevez M.	J Agric Food Chem	10.1021/acs.jafc.5c02799	2025
	The involvement of oral bacteria in inflammatory bowel disease.	Xiang B, Hu J, Zhang M, Zhi M.	Gastroenterol Rep (Oxf)	10.1093/gastro/goae076	2024
	Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.	Li D, Li M, Gao H, Hu K, Xie R, Fan J, Huang M, Liao C, Han C, Guo Z, Chen X, Li M.	Front Microbiol	10.3389/fmicb.2024.1475984	2024
Genetics	The crosstalk between microbiota and metabolites in AP mice: an analysis based on metagenomics and untargeted metabolomics.	Zhou Q, Tao X, Guo F, Zhu Y, Wu Y, Xiang H, Shang D.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1134321	2023
Pathogenicity	The regulation of intestinal flora on host's genes may play an essential role in the development of endometrial hyperplastic processes in yang deficiency individuals.	Zhang HX, Zhao XL, Wu HX, Luo ZQ, Wang LM, Lv SR, Huang XR, Dong N, Li DZ, Bao C, Su LD, Liu YX, Hu HQ, Bu ZX, Zhang HR, Liu Y, Chang SJ, He ZY, Sai L, Wang HW, Guo HM, Huang XH, Cao X.	Int J Clin Exp Pathol	10.62347/hbkg3920	2024
	Predicting Adverse Recanalization Therapy Outcomes in Acute Ischemic Stroke Patients Using Characteristic Gut Microbiota.	Chou PS, Hung WC, Yang IH, Kuo CM, Wu MN, Lin TC, Fong YO, Juan CH, Lai CL.	Microorganisms	10.3390/microorganisms11082016	2023
	Engineering the Active Site Pocket to Enhance the Catalytic Efficiency of a Novel Feruloyl Esterase Derived From Human Intestinal Bacteria Dorea formicigenerans.	Shen Y, Wang Y, Wei X, Wen B, Liu S, Tan H, Zhang J, Shao S, Xin F.	Front Bioeng Biotechnol	10.3389/fbioe.2022.936914	2022
Genetics	Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors.	Matsukawa H, Iida N, Kitamura K, Terashima T, Seishima J, Makino I, Kannon T, Hosomichi K, Yamashita T, Sakai Y, Honda M, Yamashita T, Mizukoshi E, Kaneko S.	Am J Cancer Res		2021
	An Analysis of the Gut Microbiota and Related Metabolites following PCSK9 Inhibition in Statin-Treated Patients with Elevated Levels of Lipoprotein(a).	Caparros-Martin JA, Maher P, Ward NC, Saladie M, Agudelo-Romero P, Stick SM, Chan DC, Watts GF, O'Gara F.	Microorganisms	10.3390/microorganisms12010170	2024
	Fecal Lcn-2 level is a sensitive biological indicator for gut dysbiosis and intestinal inflammation in multiple sclerosis.	Yadav SK, Ito N, Mindur JE, Kumar H, Youssef M, Suresh S, Kulkarni R, Rosario Y, Balashov KE, Dhib-Jalbut S, Ito K.	Front Immunol	10.3389/fimmu.2022.1015372	2022
	Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.	Qu Q, Dou Q, Xiang Z, Yu B, Chen L, Fan Z, Zhao X, Yang S, Zeng P.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00661-6	2025
	Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.	Mah JC, Lohmueller KE, Garud NR.	Mol Biol Evol	10.1093/molbev/msaf010	2025
Genetics	Metagenome-based characterization of the gut bacteriome, mycobiome, and virome in patients with chronic hepatitis B-related liver fibrosis.	Chen W, Liang F, Zhang Y, Zhang Y, Lv J, Jin X, Ran Y, Li S, Sun W.	Front Microbiol	10.3389/fmicb.2024.1449090	2024
Phylogeny	Gut Microbiota Profile Changes in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease: A Metagenomic Study.	De Caro C, Spagnuolo R, Quirino A, Mazza E, Carrabetta F, Maurotti S, Cosco C, Bennardo F, Roberti R, Russo E, Giudice A, Giudice A, Pujia A, Doldo P, Matera G, Marascio N.	Int J Mol Sci	10.3390/ijms25105453	2024
	Lipid complexation reduces rice starch digestibility and boosts short-chain fatty acid production via gut microbiota.	Shen Y, An Z, Huyan Z, Shu X, Wu D, Zhang N, Pellegrini N, Rubert J.	NPJ Sci Food	10.1038/s41538-023-00230-1	2023
	The gut microbiota in persistent post-operative pain following breast cancer surgery.	Masaud K, Collins JM, Rubio RC, Corrigan M, Cotter PD, O'Brien N, Bluett R, Jimenez CK, O'Mahony SM, Shorten GD.	Sci Rep	10.1038/s41598-024-62397-1	2024
	The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing.	Ticinesi A, Mancabelli L, Tagliaferri S, Nouvenne A, Milani C, Del Rio D, Lauretani F, Maggio MG, Ventura M, Meschi T.	Int J Mol Sci	10.3390/ijms21238946	2020
	Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity.	Jiao B, Ouyang Z, Liu Q, Xu T, Wan M, Ma G, Zhou L, Guo J, Wang J, Tang B, Zhao Z, Shen L.	Gut Microbes	10.1080/19490976.2024.2331434	2024
	Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.	Aljuraiban GS, Alfhili MA, Aldhwayan MM, Aljazairy EA, Al-Musharaf S.	Biomolecules	10.3390/biom13040640	2023
	Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men.	Li J, Li Y, Ivey KL, Wang DD, Wilkinson JE, Franke A, Lee KH, Chan A, Huttenhower C, Hu FB, Rimm EB, Sun Q.	Gut	10.1136/gutjnl-2020-322473	2022
Enzymology	Druggable proteins of Alistipes reveal promising antimicrobial targets against chronic intestinal inflammation.	Sohail S, Wisal A, Rana S, Abid Khan RM, Ullah A, Khan FA, Irfan M, Imran M, Carvalho PVSD, Rozental R, Shaheen F, Hassan SS.	Front Pharmacol	10.3389/fphar.2025.1555062	2025
Pathogenicity	Integrative metagenomic and metabolomic analyses reveal gut microbiota-derived multiple hits connected to development of gestational diabetes mellitus in humans.	Ye D, Huang J, Wu J, Xie K, Gao X, Yan K, Zhang P, Tao Y, Li Y, Zang S, Rong X, Li J, Guo J.	Gut Microbes	10.1080/19490976.2022.2154552	2023
	Ex Vivo Colonic Fermentation of NUTRIOSE^® Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects.	Perreau C, Thabuis C, Verstrepen L, Ghyselinck J, Marzorati M.	Nutrients	10.3390/nu15194229	2023
	Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains.	Koo H, Morrow CD.	PLoS One	10.1371/journal.pone.0274633	2022
Genetics	Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.	Li P, Jiang J, Li Y, Lan Y, Yang F, Wang J, Xie Y, Xiong F, Wu J, Liu H, Fan Z.	BMC Genomics	10.1186/s12864-023-09805-4	2023
	Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance.	Leigh RJ, Corrigan A, Murphy RA, Taylor-Pickard J, Moran CA, Walsh F.	Anim Microbiome	10.1186/s42523-024-00295-7	2024
	Gut dysbiosis conveys psychological stress to activate LRP5/beta-catenin pathway promoting cancer stemness.	Cui B, Luo H, He B, Liu X, Lv D, Zhang X, Su K, Zheng S, Lu J, Wang C, Yang Y, Zhao Z, Liu X, Wang X, Zhao Y, Nie X, Jiang Y, Zhang Z, Liu C, Chen X, Cai A, Lv Z, Liu Z, An F, Zhang Y, Yan Q, Kelley KW, Xu G, Xu L, Liu Q, Peng F.	Signal Transduct Target Ther	10.1038/s41392-025-02159-1	2025
Genetics	Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.	Kulecka M, Czarnowski P, Balabas A, Turkot M, Kruczkowska-Tarantowicz K, Zeber-Lubecka N, Dabrowska M, Paszkiewicz-Kozik E, Walewski J, Lugowska I, Kosela-Paterczyk H, Rutkowski P, Kluska A, Piatkowska M, Jagiello-Gruszfeld A, Tenderenda M, Gawinski C, Wyrwicz L, Borucka M, Krzakowski M, Zajac L, Kaminski M, Mikula M, Ostrowski J.	Int J Mol Sci	10.3390/ijms25158026	2024
	Gut-microbiome Taxonomic Profiling as Non-invasive Biomarkers for the Early Detection of Alcoholic Hepatocellular Carcinoma.	Seok J, Suk KT.	J Liver Cancer	10.17998/jlc.20.1.32	2020
	Specific microbiome patterns and their association with breast cancer: the intestinal microbiota as a potential biomarker and therapeutic strategy.	Amaro-da-Cruz A, Rubio-Tomas T, Alvarez-Mercado AI.	Clin Transl Oncol	10.1007/s12094-024-03554-w	2025
	Non-alcoholic fatty liver disease: pathophysiological concepts and treatment options.	Grander C, Grabherr F, Tilg H.	Cardiovasc Res	10.1093/cvr/cvad095	2023
	The gut microbiota and diabetic nephropathy: an observational study review and bidirectional Mendelian randomization study.	Han YZ, Wang YZY, Zhu XY, Du BX, Wang YX, Zhang XQ, Jia JM, Liu WJ, Zheng HJ.	Trials	10.1186/s13063-025-08755-4	2025
Pathogenicity	Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.	Gaber M, Wilson AS, Millen AE, Hovey KM, LaMonte MJ, Wactawski-Wende J, Ochs-Balcom HM, Cook KL.	Microbiome	10.1186/s40168-024-01901-1	2024
	Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.	Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.	Sci Rep	10.1038/s41598-024-54769-4	2024
	Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.	Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E.	Microbiol Spectr	10.1128/spectrum.00336-23	2023
	Flexibility of Gut Microbiota in Ageing Individuals during Dietary Fiber Long-Chain Inulin Intake.	Kiewiet MBG, Elderman ME, El Aidy S, Burgerhof JGM, Visser H, Vaughan EE, Faas MM, de Vos P.	Mol Nutr Food Res	10.1002/mnfr.202000390	2021
	Breaking the Cycle: Can Vitamin D Bridge the Gap Between Gut Microbiota and Immune Dynamics in Multiple Sclerosis?	Gencer Bingol F, Kocyigit E, Celik E, Agagunduz D, Budan F.	Int J Mol Sci	10.3390/ijms26125464	2025
Pathogenicity	The effects of fermented vegetables on the gut microbiota for prevention of cardiovascular disease.	Baron M, Zuo B, Chai J, Zhao J, Jahan-Mihan A, Ochrietor J, Arikawa AY.	Gut Microbiome (Camb)	10.1017/gmb.2024.4	2024
Genetics	Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.	Lotankar M, Houttu N, Mokkala K, Laitinen K.	Nutr Rev	10.1093/nutrit/nuae192	2025
	Does the ketogenic diet improve neurological disorders by influencing gut microbiota? A systematic review.	Mazandarani M, Lashkarbolouk N, Ejtahed HS, Qorbani M.	Nutr J	10.1186/s12937-023-00893-2	2023
	Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids.	Zhou C, Wang Y, Li C, Xie Z, Dai L.	Microbiol Spectr	10.1128/spectrum.03330-22	2023
Metabolism	Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis.	Wang Z, Guo M, Li J, Jiang C, Yang S, Zheng S, Li M, Ai X, Xu X, Zhang W, He X, Wang Y, Chen Y.	Microbiol Spectr	10.1128/spectrum.00829-23	2023
	Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages.	Shridhar SV, Beghini F, Alexander M, Singh A, Juarez RM, Brito IL, Christakis NA.	Cell Rep	10.1016/j.celrep.2024.114442	2024
	Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review.	Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.804644	2022
Pathogenicity	The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.	Liu X, van Beek N, Cepic A, Andreani NA, Chung CJ, Hermes BM, Yilmaz K, Benoit S, Drenovska K, Gerdes S, Glaser R, Goebeler M, Gunther C, von Georg A, Hammers CM, Holtsche MM, Hubner F, Kiritsi D, Schauer F, Linnenmann B, Huilaja L, Tasanen-Maatta K, Vassileva S, Zillikens D, Sadik CD, Schmidt E, Ibrahim S, Baines JF.	Front Immunol	10.3389/fimmu.2023.1212551	2023
	Novel systems modeling methodology in comparative microbial metabolomics: identifying key enzymes and metabolites implicated in autism spectrum disorders.	Heberling C, Dhurjati P.	Int J Mol Sci	10.3390/ijms16048949	2015
	Gut Microbiota Disruption in Hematologic Cancer Therapy: Molecular Insights and Implications for Treatment Efficacy.	Guevara-Ramirez P, Cadena-Ullauri S, Paz-Cruz E, Ruiz-Pozo VA, Tamayo-Trujillo R, Cabrera-Andrade A, Zambrano AK.	Int J Mol Sci	10.3390/ijms251910255	2024
	Gut-dependent inflammation and alterations of the intestinal microbiota in individuals with perinatal HIV exposure and different HIV serostatus.	Tincati C, Ficara M, Ferrari F, Augello M, Dotta L, Tagliabue C, Diana A, Camelli V, Iughetti L, Badolato R, Cellini M, Marchetti G, on behalf of MIRROR Study Group (MIcRobiota study in pediatRic pOpulation gRoup) .	AIDS	10.1097/qad.0000000000003324	2022
	Lactobacillus plantarum-Derived Postbiotics Ameliorate Acute Alcohol-Induced Liver Injury by Protecting Cells from Oxidative Damage, Improving Lipid Metabolism, and Regulating Intestinal Microbiota.	Ye W, Chen Z, He Z, Gong H, Zhang J, Sun J, Yuan S, Deng J, Liu Y, Zeng A.	Nutrients	10.3390/nu15040845	2023
	Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion.	Fulcher JA, Li F, Tobin NH, Zabih S, Elliott J, Clark JL, D'Aquila R, Mustanski B, Kipke MD, Shoptaw S, Gorbach PM, Aldrovandi GM.	EBioMedicine	10.1016/j.ebiom.2022.104286	2022
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
	Microbiome- and Host Inflammasome-Targeting Inhibitor Nanoligomers Are Therapeutic in the Murine Colitis Model.	Sharma S, Gilberto VS, Levens CL, Chatterjee A, Kuhn KA, Nagpal P.	ACS Pharmacol Transl Sci	10.1021/acsptsci.4c00102	2024
	Unveiling the Pathogenic Bacteria Causing Descending Necrotizing Mediastinitis.	Sun Q, Li Z, Wang P, Zhao J, Chen S, Sun M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.873161	2022
Metabolism	The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.	Lyu L, Fan Y, Vogt JK, Clos-Garcia M, Bonnefond A, Pedersen HK, Dutta A, Koivula R, Sharma S, Allin KH, Brorsson C, Cederberg H, Chabanova E, De Masi F, Dermitzakis E, Elders PJ, Blom MT, Hollander M, Eriksen R, Forgie I, Frost G, Giordano GN, Grallert H, Haid M, Hansen TH, Jablonka B, Kokkola T, Mahajan A, Mari A, McDonald TJ, Musholt PB, Pavo I, Prehn C, Ridderstrale M, Ruetten H, Hart LM', Schwenk JM, Stankevic E, Thomsen HS, Vangipurapu J, Vestergaard H, Vinuela A, Walker M, Hansen T, Linneberg A, Nielsen HB, Brunak S, McCarthy MI, Froguel P, Adamski J, Franks PW, Laakso M, Beulens JWJ, Pearson E, Pedersen O.	Genome Med	10.1186/s13073-025-01508-7	2025
	Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial.	Shin SY, Park S, Moon JM, Kim K, Kim JW, Chun J, Lee TH, Choi CH, Microbiome Research Group of the Korean Society for Neurogastroenterology and Motility.	J Neurogastroenterol Motil	10.5056/jnm21202	2022
	Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study.	Khattab RH, Abo-Hammam RH, Salah M, Hanora AM, Shabayek S, Zakeer S.	BMC Microbiol	10.1186/s12866-023-02991-x	2023
	MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks.	Nagpal S, Singh R, Yadav D, Mande SS.	Nucleic Acids Res	10.1093/nar/gkaa254	2020
Genetics	Gut Microbial Genes and Metabolism for Methionine and Branched-Chain Amino Acids in Diabetic Nephropathy.	Kim JE, Nam H, Park JI, Cho H, Lee J, Kim HE, Kim DK, Joo KW, Kim YS, Kim BS, Park S, Lee H.	Microbiol Spectr	10.1128/spectrum.02344-22	2023
	Consistent signatures in the human gut microbiome of longevous populations.	Chen S, Zhang Z, Liu S, Chen T, Lu Z, Zhao W, Mou X, Liu S.	Gut Microbes	10.1080/19490976.2024.2393756	2024
Genetics	Metagenomics Study Reveals Changes in Gut Microbiota in Centenarians: A Cohort Study of Hainan Centenarians.	Luan Z, Sun G, Huang Y, Yang Y, Yang R, Li C, Wang T, Tan D, Qi S, Jun C, Wang C, Wang S, Zhao Y, Jing Y.	Front Microbiol	10.3389/fmicb.2020.01474	2020
	Poly-omic risk scores predict inflammatory bowel disease diagnosis.	Arehart CH, Sterrett JD, Garris RL, Quispe-Pilco RE, Gignoux CR, Evans LM, Stanislawski MA.	mSystems	10.1128/msystems.00677-23	2024
Pathogenicity	Gut Microbiota Characteristics of People with Obesity by Meta-Analysis of Existing Datasets.	Gong J, Shen Y, Zhang H, Cao M, Guo M, He J, Zhang B, Xiao C.	Nutrients	10.3390/nu14142993	2022
Genetics	Gut microbial composition and functionality of school-age Mexican population with metabolic syndrome and type-2 diabetes mellitus using shotgun metagenomic sequencing.	Carrizales-Sanchez AK, Tamez-Rivera O, Garcia-Gamboa R, Garcia-Cayuela T, Rodriguez-Gutierrez NA, Elizondo-Montemayor L, Garcia-Rivas G, Pacheco A, Hernandez-Brenes C, Senes-Guerrero C.	Front Pediatr	10.3389/fped.2023.1193832	2023
	Early life gut microbiome and its impact on childhood health and chronic conditions.	Nunez H, Nieto PA, Mars RA, Ghavami M, Sew Hoy C, Sukhum K.	Gut Microbes	10.1080/19490976.2025.2463567	2025
	Gut microbial structural variation associates with immune checkpoint inhibitor response.	Liu R, Zou Y, Wang WQ, Chen JH, Zhang L, Feng J, Yin JY, Mao XY, Li Q, Luo ZY, Zhang W, Wang DM.	Nat Commun	10.1038/s41467-023-42997-7	2023
Genetics	MMINP: A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm.	Tang W, Zheng H, Xu S, Li P, Zhan L, Luo X, Dai Z, Wang Q, Yu G.	Gut Microbes	10.1080/19490976.2023.2223349	2023
	The gut microbiome regulates the clinical efficacy of sulfasalazine therapy for IBD-associated spondyloarthritis.	Lima SF, Pires S, Rupert A, Oguntunmibi S, Jin WB, Marderstein A, Funez-dePagnier G, Maldarelli G, Viladomiu M, Putzel G, Yang W, Tran N, Xiang G, Grier A, Guo CJ, Lukin D, Mandl LA, Scherl EJ, Longman RS.	Cell Rep Med	10.1016/j.xcrm.2024.101431	2024
	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
	Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year.	Shahi F, Forrester S, Redeker K, Chong JPJ, Barlow G.	Wellcome Open Res	10.12688/wellcomeopenres.17450.3	2022
	The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection.	Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1335450	2024
Metabolism	Combination Therapy of TGF-beta Blockade and Commensal-derived Probiotics Provides Enhanced Antitumor Immune Response and Tumor Suppression.	Shi L, Sheng J, Wang M, Luo H, Zhu J, Zhang B, Liu Z, Yang X.	Theranostics	10.7150/thno.35131	2019
Genetics	Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.	Lim JJ, Diener C, Wilson J, Valenzuela JJ, Baliga NS, Gibbons SM.	Nat Commun	10.1038/s41467-023-41424-1	2023
	Sex Differences in Association Between Gut Microbiome and Essential Hypertension Based on Ambulatory Blood Pressure Monitoring.	Virwani PD, Qian G, Hsu MSS, Pijarnvanit TKKTS, Cheung CN, Chow YH, Tang LK, Tse YH, Xian JW, Lam SS, Lee CPI, Lo CCW, Liu RKC, Ho TL, Chow BY, Leung KS, Tsang HW, Lo EKK, Tung KTS, Chung SK, Yuen MF, Leung SY, Ip P, Hung IF, Louie JCY, El-Nezami H, Ho JWK, Lau KK.	Hypertension	10.1161/hypertensionaha.122.20752	2023
	Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome.	Feng P, Yang J, Zhao S, Ling Z, Han R, Wu Y, Salama ES, Kakade A, Khan A, Jin W, Zhang W, Jeon BH, Fan J, Liu M, Mamtimin T, Liu P, Li X.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00326-8	2022
Genetics	Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics.	Xia Y, Yang C, Zhang T.	Biotechnol Biofuels	10.1186/s13068-018-1042-y	2018
Metabolism	Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism.	Xu T, Wang X, Chen Y, Li H, Zhao L, Ding X, Zhang C.	mBio	10.1128/mbio.03487-22	2023
	Metagenomic assessment of gut microbial communities and risk of severe COVID-19.	Nguyen LH, Okin D, Drew DA, Battista VM, Jesudasen SJ, Kuntz TM, Bhosle A, Thompson KN, Reinicke T, Lo CH, Woo JE, Caraballo A, Berra L, Vieira J, Huang CY, Das Adhikari U, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg MB, Kwon DS, Huttenhower C, Chan AT, Lai PS.	Genome Med	10.1186/s13073-023-01202-6	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
	Dynamics of bacterial recombination in the human gut microbiome.	Liu Z, Good BH.	PLoS Biol	10.1371/journal.pbio.3002472	2024
	Crosstalk between gut microbiota and host immune system and its response to traumatic injury.	Ullah H, Arbab S, Tian Y, Chen Y, Liu CQ, Li Q, Li K.	Front Immunol	10.3389/fimmu.2024.1413485	2024
	Protective Effect of Vegan Microbiota on Liver Steatosis Is Conveyed by Dietary Fiber: Implications for Fecal Microbiota Transfer Therapy.	Daskova N, Heczkova M, Modos I, Hradecky J, Hudcovic T, Kuzma M, Pelantova H, Buskova I, Sticova E, Funda D, Golias J, Drabonova B, Jarkovska J, Kralova M, Cibulkova I, Gojda J, Cahova M.	Nutrients	10.3390/nu15020454	2023
Pathogenicity	Inflammaging: The Next Challenge-Exploring the Role of Gut Microbiota, Environmental Factors, and Sex Differences.	Caldarelli M, Rio P, Marrone A, Giambra V, Gasbarrini A, Gambassi G, Cianci R.	Biomedicines	10.3390/biomedicines12081716	2024
Genetics	When old metagenomic data meet newly sequenced genomes, a case study.	Li X, Naser SA, Khaled A, Hu H, Li X.	PLoS One	10.1371/journal.pone.0198773	2018
	Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines.	Peng Y, Zhang L, Mok CKP, Ching JYL, Zhao S, Wong MKL, Zhu J, Chen C, Wang S, Yan S, Qin B, Liu Y, Zhang X, Cheung CP, Cheong PK, Ip KL, Fung ACH, Wong KKY, Hui DSC, Chan FKL, Ng SC, Tun HM.	Signal Transduct Target Ther	10.1038/s41392-023-01629-8	2023
Genetics	Expanded microbiome niches of RAG-deficient patients.	Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, NISC Comparative Sequencing Program, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA.	Cell Rep Med	10.1016/j.xcrm.2023.101205	2023
	Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity.	Thomas AM, Asnicar F, Kroemer G, Segata N.	Appl Environ Microbiol	10.1128/aem.00471-21	2021
Genetics	Association of distinct microbial signatures with premalignant colorectal adenomas.	Lee JWJ, Plichta DR, Asher S, Delsignore M, Jeong T, McGoldrick J, Staller K, Khalili H, Xavier RJ, Chung DC.	Cell Host Microbe	10.1016/j.chom.2023.04.007	2023
	Efficacy of Bifidobacterium animalis subsp. lactis BL-99 in the treatment of functional dyspepsia: a randomized placebo-controlled clinical trial.	Zhang Q, Li G, Zhao W, Wang X, He J, Zhou L, Zhang X, An P, Liu Y, Zhang C, Zhang Y, Liu S, Zhao L, Liu R, Li Y, Jiang W, Wang X, Wang Q, Fang B, Zhao Y, Ren Y, Niu X, Li D, Shi S, Hung WL, Wang R, Liu X, Ren F.	Nat Commun	10.1038/s41467-023-44292-x	2024
	Obesity, Gut Microbiota, and Metabolome: From Pathophysiology to Nutritional Interventions.	Puljiz Z, Kumric M, Vrdoljak J, Martinovic D, Ticinovic Kurir T, Krnic MO, Urlic H, Puljiz Z, Zucko J, Dumanic P, Mikolasevic I, Bozic J.	Nutrients	10.3390/nu15102236	2023
	Bacteroides vulgatus attenuates experimental mice colitis through modulating gut microbiota and immune responses.	Liu L, Xu M, Lan R, Hu D, Li X, Qiao L, Zhang S, Lin X, Yang J, Ren Z, Xu J.	Front Immunol	10.3389/fimmu.2022.1036196	2022
	Associations between self-reported psychological symptom severity and gut microbiota: further support for the microgenderome.	Ganci M, Suleyman E, Butt H, Ball M.	BMC Psychiatry	10.1186/s12888-022-03947-7	2022
	Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.	Gao W, Gao X, Zhu L, Gao S, Sun R, Feng Z, Wu D, Liu Z, Zhu R, Jiao N.	Gut Microbes	10.1080/19490976.2023.2245562	2023
	Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.	Belda E, Capeau J, Zucker JD, Chatelier EL, Pons N, Onate FP, Quinquis B, Alili R, Fellahi S, Katlama C, Clement K, Feve B, Jaureguiberry S, Goujard C, Lambotte O, Dore J, Prifti E, Bastard JP.	BMC Med Genomics	10.1186/s12920-024-01978-5	2024
Genetics	Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes.	Obon-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Diez-Villanueva A, Moratalla-Navarro F, Guino E, Ibanez-Sanz G, Rodriguez-Alonso L, Mulet-Margalef N, Mata A, Garcia-Rodriguez A, Duell EJ, Pimenoff VN, Moreno V.	Cancers (Basel)	10.3390/cancers14174214	2022
	Breast Cancer Survivors and Healthy Women: Could Gut Microbiota Make a Difference?-"BiotaCancerSurvivors": A Case-Control Study.	Caleca T, Ribeiro P, Vitorino M, Menezes M, Sampaio-Alves M, Mendes AD, Vicente R, Negreiros I, Faria A, Costa DA.	Cancers (Basel)	10.3390/cancers15030594	2023
	The DAV132 colon-targeted adsorbent does not interfere with plasma concentrations of antibiotics but prevents antibiotic-related dysbiosis: a randomized phase I trial in healthy volunteers.	Messaoudene M, Ferreira S, Saint-Lu N, Ponce M, Truntzer C, Boidot R, Le Bescop C, Loppinet T, Corbel T, Feger C, Bertrand K, Elkrief A, Isaksen M, Vitry F, Sablier-Gallis F, Andremont A, Bod L, Ghiringhelli F, de Gunzburg J, Routy B.	Nat Commun	10.1038/s41467-024-52373-8	2024
Metabolism	Bifidobacterium longum mediated tryptophan metabolism to improve atopic dermatitis via the gut-skin axis.	Fang Z, Pan T, Li L, Wang H, Zhu J, Zhang H, Zhao J, Chen W, Lu W.	Gut Microbes	10.1080/19490976.2022.2044723	2022
Metabolism	Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents.	Wang X, Yang S, Li S, Zhao L, Hao Y, Qin J, Zhang L, Zhang C, Bian W, Zuo L, Gao X, Zhu B, Lei XG, Gu Z, Cui W, Xu X, Li Z, Zhu B, Li Y, Chen S, Guo H, Zhang H, Sun J, Zhang M, Hui Y, Zhang X, Liu X, Sun B, Wang L, Qiu Q, Zhang Y, Li X, Liu W, Xue R, Wu H, Shao D, Li J, Zhou Y, Li S, Yang R, Pedersen OB, Yu Z, Ehrlich SD, Ren F.	Gut	10.1136/gutjnl-2019-319766	2020
	Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades.	Koo H, Hakim JA, Crossman DK, Lefkowitz EJ, Morrow CD.	PLoS One	10.1371/journal.pone.0226111	2019
Metabolism	Effects of Fecal Microbiota Transplantation on Composition in Mice with CKD.	Barba C, Soulage CO, Caggiano G, Glorieux G, Fouque D, Koppe L.	Toxins (Basel)	10.3390/toxins12120741	2020
	Trust Your Gut: The Association of Gut Microbiota and Liver Disease.	Manzoor R, Ahmed W, Afify N, Memon M, Yasin M, Memon H, Rustom M, Al Akeel M, Alhajri N.	Microorganisms	10.3390/microorganisms10051045	2022
	Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission.	Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A, Ellul P.	Microbiol Spectr	10.1128/spectrum.00616-22	2022
Metabolism	Dynamic Alterations of the Gut Microbial Pyrimidine and Purine Metabolism in the Development of Liver Cirrhosis.	Xiong Y, Wu L, Shao L, Wang Y, Huang Z, Huang X, Li C, Wu A, Liu Z, Fan X, Zhou P.	Front Mol Biosci	10.3389/fmolb.2021.811399	2021
	Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review.	Imade EE, Obayagbona NO.	Gut Microbiome (Camb)	10.1017/gmb.2024.3	2024
	A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis.	McGregor BA, Razmjou E, Hooshyar H, Seeger DR, Golovko SA, Golovko MY, Singer SM, Hur J, Solaymani-Mohammadi S.	Parasit Vectors	10.1186/s13071-023-05821-1	2023
	Gut Microbiota Secondary Metabolites: Key Roles in GI Tract Cancers and Infectious Diseases.	Anwer EKE, Ajagbe M, Sherif M, Musaibah AS, Mahmoud S, ElBanbi A, Abdelnaser A.	Biomedicines	10.3390/biomedicines13010100	2025
	Effects of Jian Pi Qu Shi Formula on intestinal bacterial flora in patients with idiopathic membranous nephropathy: A prospective randomized controlled trial.	Lang R, Wang XH, Li AF, Liang Y, Zhu BC, Shi B, Zheng YQ, Yu RH.	Chronic Dis Transl Med	10.1016/j.cdtm.2020.04.004	2020
	A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases.	Liu X, Tang S, Zhong H, Tong X, Jie Z, Ding Q, Wang D, Guo R, Xiao L, Xu X, Yang H, Wang J, Zong Y, Liu W, Liu X, Zhang Y, Brix S, Kristiansen K, Hou Y, Jia H, Zhang T.	Cell Discov	10.1038/s41421-020-00239-w	2021
Transcriptome	The Colorectal Cancer Gut Environment Regulates Activity of the Microbiome and Promotes the Multidrug Resistant Phenotype of ESKAPE and Other Pathogens.	Lamaudiere MTF, Arasaradnam R, Weedall GD, Morozov IY.	mSphere	10.1128/msphere.00626-22	2023
Metabolism	Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation.	Chen Q, Fan Y, Zhang B, Yan C, Zhang Q, Ke Y, Chen Z, Wang L, Shi H, Hu Y, Huang Q, Su J, Xie C, Zhang X, Zhou L, Ren J, Xu H.	Microbiol Spectr	10.1128/spectrum.04152-22	2023
Genetics	Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.	Vasco K, Guevara N, Mosquera J, Zapata S, Zhang L.	Anim Microbiome	10.1186/s42523-022-00218-4	2022
	Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.	Zeybel M, Altay O, Arif M, Li X, Yang H, Fredolini C, Akyildiz M, Saglam B, Gonenli MG, Ural D, Kim W, Schwenk JM, Zhang C, Shoaie S, Nielsen J, Uhlen M, Boren J, Mardinoglu A.	Mol Syst Biol	10.15252/msb.202110459	2021
Metabolism	Omega-3-Supplemented Fat Diet Drives Immune Metabolic Response in Visceral Adipose Tissue by Modulating Gut Microbiota in a Mouse Model of Obesity.	Portela ND, Galvan C, Sanmarco LM, Bergero G, Aoki MP, Cano RC, Pesoa SA.	Nutrients	10.3390/nu15061404	2023
Genetics	A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota.	Zhang XX, Lv QB, Yan QL, Zhang Y, Guo RC, Meng JX, Ma H, Qin SY, Zhu QH, Li CQ, Liu R, Liu G, Li SH, Sun DB, Ni HB.	Microbiol Spectr	10.1128/spectrum.02211-22	2022
	Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways.	Lacunza E, Fink V, Salas ME, Canzoneri R, Naipauer J, Williams S, Coso O, Sued O, Cahn P, Mesri EA, Abba MC.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00413-4	2023
Pathogenicity	Maternal PBDE exposure disrupts gut microbiome and promotes hepatic proinflammatory signaling in humanized PXR-transgenic mouse offspring over time.	Kim S, Li H, Jin Y, Armad J, Gu H, Mani S, Cui JY.	Toxicol Sci	10.1093/toxsci/kfad056	2023
	Modulation of gut mucosal microbiota as a mechanism of probiotics-based adjunctive therapy for ulcerative colitis.	Chen P, Xu H, Tang H, Zhao F, Yang C, Kwok LY, Cong C, Wu Y, Zhang W, Zhou X, Zhang H.	Microb Biotechnol	10.1111/1751-7915.13661	2020
	The Microbiome-Gut-Brain axis regulates social cognition & craving in young binge drinkers.	Carbia C, Bastiaanssen TFS, Iannone LF, Garcia-Cabrerizo R, Boscaini S, Berding K, Strain CR, Clarke G, Stanton C, Dinan TG, Cryan JF.	EBioMedicine	10.1016/j.ebiom.2023.104442	2023
	Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome.	Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB.	BMC Microbiol	10.1186/s12866-022-02495-0	2022
	The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health.	Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A.	Front Immunol	10.3389/fimmu.2020.00906	2020
Phylogeny	Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis.	Huh JW, Roh TY.	BMC Microbiol	10.1186/s12866-020-01887-4	2020
	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
Metabolism	A Soluble Fiber Diet Increases Bacteroides fragilis Group Abundance and Immunoglobulin A Production in the Gut.	Nakajima A, Sasaki T, Itoh K, Kitahara T, Takema Y, Hiramatsu K, Ishikawa D, Shibuya T, Kobayashi O, Osada T, Watanabe S, Nagahara A.	Appl Environ Microbiol	10.1128/aem.00405-20	2020
	Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events.	Ng SC, Peng Y, Zhang L, Mok CK, Zhao S, Li A, Ching JY, Liu Y, Yan S, Chan DLS, Zhu J, Chen C, Fung AC, Wong KK, Hui DS, Chan FK, Tun HM.	Gut	10.1136/gutjnl-2021-326563	2022
Metabolism	Relation of Gut Microbes and L-Thyroxine Through Altered Thyroxine Metabolism in Subclinical Hypothyroidism Subjects.	Yao Z, Zhao M, Gong Y, Chen W, Wang Q, Fu Y, Guo T, Zhao J, Gao L, Bo T.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00495	2020
	Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients.	Sun Z, Song ZG, Liu C, Tan S, Lin S, Zhu J, Dai FH, Gao J, She JL, Mei Z, Lou T, Zheng JJ, Liu Y, He J, Zheng Y, Ding C, Qian F, Zheng Y, Chen YM.	BMC Med	10.1186/s12916-021-02212-0	2022
	Gut Microbiota is Associated with Aging-Related Processes of a Small Mammal Species under High-Density Crowding Stress.	Xu X, Li G, Zhang D, Zhu H, Liu GH, Zhang Z.	Adv Sci (Weinh)	10.1002/advs.202205346	2023
Metabolism	Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD.	Jiao N, Loomba R, Yang ZH, Wu D, Fang S, Bettencourt R, Lan P, Zhu R, Zhu L.	Physiol Genomics	10.1152/physiolgenomics.00011.2021	2021
Enzymology	The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome.	Haran JP, Ward DV, Bhattarai SK, Loew E, Dutta P, Higgins A, McCormick BA, Bucci V.	Gut Microbes	10.1080/19490976.2021.1897209	2021
Pathogenicity	Probiotic-directed modulation of gut microbiota is basal microbiome dependent.	Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H.	Gut Microbes	10.1080/19490976.2020.1736974	2020
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
	Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis.	Damman CJ, Brittnacher MJ, Westerhoff M, Hayden HS, Radey M, Hager KR, Marquis SR, Miller SI, Zisman TL.	PLoS One	10.1371/journal.pone.0133925	2015
	Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress.	Sari Z, Miko E, Kovacs T, Janko L, Csonka T, Lente G, Sebo E, Toth J, Toth D, Arkosy P, Boratko A, Ujlaki G, Torok M, Kovacs I, Szabo J, Kiss B, Mehes G, Goedert JJ, Bai P.	Cancers (Basel)	10.3390/cancers12092411	2020
	CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis.	Lam TJ, Ye Y.	CRISPR J	10.1089/crispr.2018.0046	2019
	Diagnostic and prognostic potential of the microbiome in ovarian cancer treatment response.	Asangba AE, Chen J, Goergen KM, Larson MC, Oberg AL, Casarin J, Multinu F, Kaufmann SH, Mariani A, Chia N, Walther-Antonio MRS.	Sci Rep	10.1038/s41598-023-27555-x	2023
Phylogeny	An insight into intestinal mucosal microbiota disruption after stroke.	Stanley D, Moore RJ, Wong CHY.	Sci Rep	10.1038/s41598-017-18904-8	2018
	Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.	Thomas AM, Fidelle M, Routy B, Kroemer G, Wargo JA, Segata N, Zitvogel L.	Nat Rev Clin Oncol	10.1038/s41571-023-00785-8	2023
	Effects of Fecal Microbiome Transfer in Adolescents With Obesity: The Gut Bugs Randomized Controlled Trial.	Leong KSW, Jayasinghe TN, Wilson BC, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Vatanen T, Holland DJ, O'Sullivan JM, Cutfield WS.	JAMA Netw Open	10.1001/jamanetworkopen.2020.30415	2020
Genetics	Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.	Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C.	Cell Host Microbe	10.1016/j.chom.2020.03.005	2020
Pathogenicity	Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet.	Virwani PD, Cai L, Yeung PKK, Qian G, Chen Y, Zhou L, Wong JWH, Wang Y, Ho JWK, Lau KK, Qian PY, Chung SK.	Microbiome	10.1186/s40168-022-01366-0	2022
	The Debate between the Human Microbiota and Immune System in Treating Aerodigestive and Digestive Tract Cancers: A Review.	Domingues C, Cabral C, Jarak I, Veiga F, Dourado M, Figueiras A.	Vaccines (Basel)	10.3390/vaccines11030492	2023
	Effect of Diet Change on Gut Microbiota: Observational Pilot Study of Four Urban Couples.	Roh Y, Lee J, Kim WG, Yi G, Kim BK, Oh B.	J Obes Metab Syndr	10.7570/jomes.2017.26.4.257	2017
Genetics	A metagenome-wide association study of gut microbiome and visceral fat accumulation.	Nie X, Chen J, Ma X, Ni Y, Shen Y, Yu H, Panagiotou G, Bao Y.	Comput Struct Biotechnol J	10.1016/j.csbj.2020.09.026	2020
Genetics	Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage.	Zhang J, Zhao J, Jin H, Lv R, Shi H, De G, Yang B, Sun Z, Zhang H.	Gut Microbes	10.1080/19490976.2020.1722054	2020
Genetics	Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.	Yu D, Shu XO, Howard EF, Long J, English WJ, Flynn CR.	Surg Obes Relat Dis	10.1016/j.soard.2020.06.032	2020
Genetics	Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort.	Benitez-Paez A, Olivares M, Szajewska H, Piescik-Lech M, Polanco I, Castillejo G, Nunez M, Ribes-Koninckx C, Korponay-Szabo IR, Koletzko S, Meijer CR, Mearin ML, Sanz Y.	Front Microbiol	10.3389/fmicb.2020.01335	2020
Pathogenicity	The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2.	Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN.	Trends Mol Med	10.1016/j.molmed.2021.09.009	2021
Genetics	Variation and transmission of the human gut microbiota across multiple familial generations.	Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G.	Nat Microbiol	10.1038/s41564-021-01021-8	2022
	Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae's.	Mazzio E, Barnes A, Badisa R, Fierros-Romero G, Williams H, Council S, Soliman KFA.	J Funct Foods	10.1016/j.jff.2023.105687	2023
	Influence of probiotic bacteria on gut microbiota composition and gut wall function in an in-vitro model in patients with Parkinson's disease.	Ghyselinck J, Verstrepen L, Moens F, Van Den Abbeele P, Bruggeman A, Said J, Smith B, Barker LA, Jordan C, Leta V, Chaudhuri KR, Basit AW, Gaisford S.	Int J Pharm X	10.1016/j.ijpx.2021.100087	2021
Pathogenicity	Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.	Dahlin M, Singleton SS, David JA, Basuchoudhary A, Wickstrom R, Mazumder R, Prast-Nielsen S.	EBioMedicine	10.1016/j.ebiom.2022.104061	2022
Metabolism	Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease.	Wu IW, Gao SS, Chou HC, Yang HY, Chang LC, Kuo YL, Dinh MCV, Chung WH, Yang CW, Lai HC, Hsieh WP, Su SC.	Theranostics	10.7150/thno.41725	2020
	Drivers and determinants of strain dynamics following fecal microbiota transplantation.	Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P.	Nat Med	10.1038/s41591-022-01913-0	2022
	Association of fecal microbial diversity and taxonomy with selected enzymatic functions.	Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ.	PLoS One	10.1371/journal.pone.0039745	2012
Pathogenicity	Intestinal vitamin D receptor protects against extraintestinal breast cancer tumorigenesis.	Zhang YG, Xia Y, Zhang J, Deb S, Garrett S, Sun J.	Gut Microbes	10.1080/19490976.2023.2202593	2023
	DeepMicrobes: taxonomic classification for metagenomics with deep learning.	Liang Q, Bible PW, Liu Y, Zou B, Wei L.	NAR Genom Bioinform	10.1093/nargab/lqaa009	2020
	Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.	Zhang L, Jonscher KR, Zhang Z, Xiong Y, Mueller RS, Friedman JE, Pan C.	Nat Commun	10.1038/s41467-022-31227-1	2022
Genetics	Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.	Shao L, Ling Z, Chen D, Liu Y, Yang F, Li L.	Front Microbiol	10.3389/fmicb.2018.03166	2018
	Akkermansia muciniphila upregulates genes involved in maintaining the intestinal barrier function via ADP-heptose-dependent activation of the ALPK1/TIFA pathway.	Martin-Gallausiaux C, Garcia-Weber D, Lashermes A, Larraufie P, Marinelli L, Teixeira V, Rolland A, Beguet-Crespel F, Brochard V, Quatremare T, Jamet A, Dore J, Gray-Owen SD, Blottiere HM, Arrieumerlou C, Lapaque N.	Gut Microbes	10.1080/19490976.2022.2110639	2022
	Integrated gut virome and bacteriome dynamics in COVID-19 patients.	Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J, Yang P.	Gut Microbes	10.1080/19490976.2021.1887722	2021
	Harnessing the intestinal microbiome for optimal therapeutic immunomodulation.	Viaud S, Daillere R, Boneca IG, Lepage P, Pittet MJ, Ghiringhelli F, Trinchieri G, Goldszmid R, Zitvogel L.	Cancer Res	10.1158/0008-5472.can-14-0987	2014
Phylogeny	Dynamics of Gut Microbiota and Clinical Variables after Ketogenic and Mediterranean Diets in Drug-Naïve Patients with Type 2 Diabetes Mellitus and Obesity.	Deledda A, Palmas V, Heidrich V, Fosci M, Lombardo M, Cambarau G, Lai A, Melis M, Loi E, Loviselli A, Manzin A, Velluzzi F.	Metabolites	10.3390/metabo12111092	2022
Metabolism	Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes.	Wei Y, Zhou H, Zhang J, Zhang L, Geng A, Liu F, Zhao G, Wang S, Zhou Z, Yan X.	PLoS One	10.1371/journal.pone.0129921	2015
	Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts.	Luo G, Li B, Yang C, Wang Y, Bian X, Li W, Liu F, Huo G.	Front Microbiol	10.3389/fmicb.2019.00712	2019
	Role of the Gut Microbiota and Its Metabolites in Tumorigenesis or Development of Colorectal Cancer.	Qu R, Zhang Y, Ma Y, Zhou X, Sun L, Jiang C, Zhang Z, Fu W.	Adv Sci (Weinh)	10.1002/advs.202205563	2023
Metabolism	Microbiome and ischemic stroke: A systematic review.	Lee YT, Mohd Ismail NI, Wei LK.	PLoS One	10.1371/journal.pone.0245038	2021
Phylogeny	Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models.	Jiang P, Wu S, Luo Q, Zhao XM, Chen WH, Chen WH.	mSystems	10.1128/msystems.00112-21	2021
	Gut Microbiota in Human Systemic Lupus Erythematosus and a Mouse Model of Lupus.	Luo XM, Edwards MR, Mu Q, Yu Y, Vieson MD, Reilly CM, Ahmed SA, Bankole AA.	Appl Environ Microbiol	10.1128/aem.02288-17	2018
	Diet quality and anxiety: a critical overview with focus on the gut microbiome.	Basso M, Zorzan I, Johnstone N, Barberis M, Cohen Kadosh K.	Front Nutr	10.3389/fnut.2024.1346483	2024
Phylogeny	Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe.	Gough EK, Edens TJ, Geum HM, Baharmand I, Gill SK, Robertson RC, Mutasa K, Ntozini R, Smith LE, Chasekwa B, Majo FD, Tavengwa NV, Mutasa B, Francis F, Carr L, Tome J, Stoltzfus RJ, Moulton LH, Prendergast AJ, Humphrey JH, Manges AR, Team ST.	EBioMedicine	10.1016/j.ebiom.2021.103421	2021
Genetics	Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.	Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wullner U.	Genome Med	10.1186/s13073-017-0428-y	2017
Genetics	Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.	Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG.	BMC Bioinformatics	10.1186/s12859-015-0875-7	2016
	Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.	Arias MC, Danchin EG, Coutinho P, Henrissat B, Ball S.	Mob Genet Elements	10.4161/mge.20375	2012
Genetics	Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.	Stewart DB, Wright JR, Fowler M, McLimans CJ, Tokarev V, Amaniera I, Baker O, Wong HT, Brabec J, Drucker R, Lamendella R.	mSphere	10.1128/msphere.00454-19	2019
	Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease.	Chen Z, Xie Y, Zhou F, Zhang B, Wu J, Yang L, Xu S, Stedtfeld R, Chen Q, Liu J, Zhang X, Xu H, Ren J.	Front Microbiol	10.3389/fmicb.2020.00383	2020
Metabolism	An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.	Antharam VC, McEwen DC, Garrett TJ, Dossey AT, Li EC, Kozlov AN, Mesbah Z, Wang GP.	PLoS One	10.1371/journal.pone.0148824	2016
Pathogenicity	Commensals and Foodborne Pathogens can Arbitrate Epithelial-carcinogenesis.	Woappi Y, Singh OV.	Br Microbiol Res J	10.9734/bmrj/2016/26690	2016
Metabolism	Donor metabolic characteristics drive effects of faecal microbiota transplantation on recipient insulin sensitivity, energy expenditure and intestinal transit time.	de Groot P, Scheithauer T, Bakker GJ, Prodan A, Levin E, Khan MT, Herrema H, Ackermans M, Serlie MJM, de Brauw M, Levels JHM, Sales A, Gerdes VE, Stahlman M, Schimmel AWM, Dallinga-Thie G, Bergman JJ, Holleman F, Hoekstra JBL, Groen A, Backhed F, Nieuwdorp M.	Gut	10.1136/gutjnl-2019-318320	2020
Pathogenicity	The Role of Intestinal Bacteria and Gut-Brain Axis in Hepatic Encephalopathy.	Chen Z, Ruan J, Li D, Wang M, Han Z, Qiu W, Wu G.	Front Cell Infect Microbiol	10.3389/fcimb.2020.595759	2020
	Gut microbes contribute to variation in solid organ transplant outcomes in mice.	McIntosh CM, Chen L, Shaiber A, Eren AM, Alegre ML.	Microbiome	10.1186/s40168-018-0474-8	2018
Metabolism	Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire.	Zhang C, Bjorkman A, Cai K, Liu G, Wang C, Li Y, Xia H, Sun L, Kristiansen K, Wang J, Han J, Hammarstrom L, Pan-Hammarstrom Q.	Front Immunol	10.3389/fimmu.2018.00908	2018
	Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease.	Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, Singh N, Damman CJ, Hager KR, Nielson H, Miller SI.	Inflamm Bowel Dis	10.1097/mib.0000000000000307	2015
	Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples.	Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F.	mSystems	10.1128/msystems.00289-19	2019
	Carcinogenesis and therapeutics: the microbiota perspective.	Tsilimigras MC, Fodor A, Jobin C.	Nat Microbiol	10.1038/nmicrobiol.2017.8	2017
Phylogeny	Biochemical Characterization of a Family 15 Carbohydrate Esterase from a Bacterial Marine Arctic Metagenome.	De Santi C, Willassen NP, Williamson A.	PLoS One	10.1371/journal.pone.0159345	2016
	Microbiome signature and diversity regulates the level of energy production under anaerobic condition.	Rahman MS, Hoque MN, Puspo JA, Islam MR, Das N, Siddique MA, Hossain MA, Sultana M.	Sci Rep	10.1038/s41598-021-99104-3	2021
	The Glutaminase-Dependent Acid Resistance System: Qualitative and Quantitative Assays and Analysis of Its Distribution in Enteric Bacteria.	Pennacchietti E, D'Alonzo C, Freddi L, Occhialini A, De Biase D.	Front Microbiol	10.3389/fmicb.2018.02869	2018
Genetics	Strain/species identification in metagenomes using genome-specific markers.	Tu Q, He Z, Zhou J.	Nucleic Acids Res	10.1093/nar/gku138	2014
Metabolism	Interleukin-36 cytokines alter the intestinal microbiome and can protect against obesity and metabolic dysfunction.	Giannoudaki E, Hernandez-Santana YE, Mulfaul K, Doyle SL, Hams E, Fallon PG, Mat A, O'Shea D, Kopf M, Hogan AE, Walsh PT.	Nat Commun	10.1038/s41467-019-11944-w	2019
Enzymology	Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei.	Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, Lopez-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudino-Pinera E, Sotelo-Mundo RR, Brieba LG.	Biochim Biophys Acta	10.1016/j.bbapap.2016.09.002	2016
	Therapeutic Strategies to Modulate Gut Microbial Health: Approaches for Chronic Metabolic Disorder Management.	Rondanelli M, Borromeo S, Cavioni A, Gasparri C, Gattone I, Genovese E, Lazzarotti A, Minonne L, Moroni A, Patelli Z, Razza C, Sivieri C, Valentini EM, Barrile GC.	Metabolites	10.3390/metabo15020127	2025
	Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.	Aron-Wisnewsky J, Prifti E, Belda E, Ichou F, Kayser BD, Dao MC, Verger EO, Hedjazi L, Bouillot JL, Chevallier JM, Pons N, Le Chatelier E, Levenez F, Ehrlich SD, Dore J, Zucker JD, Clement K.	Gut	10.1136/gutjnl-2018-316103	2019
	Changes of Colonic Bacterial Composition in Parkinson's Disease and Other Neurodegenerative Diseases.	Gerhardt S, Mohajeri MH.	Nutrients	10.3390/nu10060708	2018
Enzymology	Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet.	Roager HM, Licht TR, Poulsen SK, Larsen TM, Bahl MI.	Appl Environ Microbiol	10.1128/aem.03549-13	2014
Transcriptome	Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data.	Ye Y, Zhang Q.	RNA	10.1261/rna.055988.116	2016
	Overcoming resistance to anti-PD1 and anti-PD-L1 treatment in gastrointestinal malignancies.	Puccini A, Battaglin F, Iaia ML, Lenz HJ, Salem ME.	J Immunother Cancer	10.1136/jitc-2019-000404	2020
Genetics	The gut microbiome in atherosclerotic cardiovascular disease.	Jie Z, Xia H, Zhong SL, Feng Q, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, Zhang D, Su Z, Fang Z, Lan Z, Li J, Xiao L, Li J, Li R, Li X, Li F, Ren H, Huang Y, Peng Y, Li G, Wen B, Dong B, Chen JY, Geng QS, Zhang ZW, Yang H, Wang J, Wang J, Zhang X, Madsen L, Brix S, Ning G, Xu X, Liu X, Hou Y, Jia H, He K, Kristiansen K.	Nat Commun	10.1038/s41467-017-00900-1	2017
	Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome.	Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J, Spector TD, Jia H.	Cell Syst	10.1016/j.cels.2016.10.004	2016
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
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
Enzymology	State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.	Tidjani Alou M, Naud S, Khelaifia S, Bonnet M, Lagier JC, Raoult D.	Clin Microbiol Rev	10.1128/cmr.00129-19	2020
	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.	Carr R, Shen-Orr SS, Borenstein E.	PLoS Comput Biol	10.1371/journal.pcbi.1003292	2013
Metabolism	Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes.	McBride MJ, Zhu Y.	J Bacteriol	10.1128/jb.01962-12	2013
Pathogenicity	Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology.	Rangan P, Choi I, Wei M, Navarrete G, Guen E, Brandhorst S, Enyati N, Pasia G, Maesincee D, Ocon V, Abdulridha M, Longo VD.	Cell Rep	10.1016/j.celrep.2019.02.019	2019
	Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.	Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, Weese S, Wong A, Low DE, Pillai DR.	mBio	10.1128/mbio.00338-12	2012
	Diverse CRISPRs evolving in human microbiomes.	Rho M, Wu YW, Tang H, Doak TG, Ye Y.	PLoS Genet	10.1371/journal.pgen.1002441	2012
Genetics	Inter-individual differences in the gene content of human gut bacterial species.	Zhu A, Sunagawa S, Mende DR, Bork P.	Genome Biol	10.1186/s13059-015-0646-9	2015
	Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases.	Loh JS, Mak WQ, Tan LKS, Ng CX, Chan HH, Yeow SH, Foo JB, Ong YS, How CW, Khaw KY.	Signal Transduct Target Ther	10.1038/s41392-024-01743-1	2024
Metabolism	Gut microbiome structure and metabolic activity in inflammatory bowel disease.	Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.	Nat Microbiol	10.1038/s41564-018-0306-4	2019
Phylogeny	Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.	Li ZP, Liu HL, Li GY, Bao K, Wang KY, Xu C, Yang YF, Yang FH, Wright AD.	BMC Microbiol	10.1186/1471-2180-13-151	2013
	Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.	Garud NR, Good BH, Hallatschek O, Pollard KS.	PLoS Biol	10.1371/journal.pbio.3000102	2019
Phylogeny	Microbiome as an Immunological Modifier.	Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S.	Methods Mol Biol	10.1007/978-1-4939-9773-2_27	2020
Genetics	Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice.	Li J, Sung CY, Lee N, Ni Y, Pihlajamaki J, Panagiotou G, El-Nezami H.	Proc Natl Acad Sci U S A	10.1073/pnas.1518189113	2016
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
	Comparative evaluation of establishing a human gut microbial community within rodent models.	Wos-Oxley M, Bleich A, Oxley AP, Kahl S, Janus LM, Smoczek A, Nahrstedt H, Pils MC, Taudien S, Platzer M, Hedrich HJ, Medina E, Pieper DH.	Gut Microbes	10.4161/gmic.19934	2012
	Role of the microbiota in immunity and inflammation.	Belkaid Y, Hand TW.	Cell	10.1016/j.cell.2014.03.011	2014
Metabolism	Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.	Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ.	J Biol Chem	10.1074/jbc.m110.163154	2010
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
	Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima.	Pope PB, Vivekanand V, Eijsink VG, Horn SJ.	3 Biotech	10.1007/s13205-012-0097-x	2013
Genetics	Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov.	Mourembou G, Rathored J, Ndjoyi-Mbiguino A, Lekana-Douki JB, Fenollar F, Robert C, Fournier PE, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2015.11.002	2016
Genetics	Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.	Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3336746	2013
Genetics	Genome sequence and description of Alistipes senegalensis sp. nov.	Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.2625821	2012
Phylogeny	Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.	Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003778	2020
Phylogeny	Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.	Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YL	Int J Syst Evol Microbiol	10.1099/ijs.0.063917-0	2014
Phylogeny	Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin.	Song Y, Kononen E, Rautio M, Liu C, Bryk A, Eerola E, Finegold SM	Int J Syst Evol Microbiol	10.1099/ijs.0.64318-0	2006

References

#7920	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19121
#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 )
#28072	IJSEM 1985 2006 ( DOI 10.1099/ijs.0.64318-0 , PubMed 16902041 )
#31803	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28072
#58401	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48947
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Alistipes shahii (DSM 19121, ATCC BAA-1179, CCUG 48947)

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