Barnesiella intestinihominis (DSM 21032, JCM 15079, YIT 11860)

Name: Barnesiella intestinihominis (DSM 21032, JCM 15079, YIT 11860)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12519

Type strain

Culture col. no. DSM 21032 JCM 15079 YIT 11860

NCBI tax ID(s) 742726 487174

Special Collections DSMZ JCM Literature strains

Links

Barnesiella intestinihominis DSM 21032 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from human faeces.

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

Name and taxonomic classification

SI-ID 400531

JCM 15079,DSM 21032

@ref 20215

Last LPSN update 2025-12-16 09:49:52

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Barnesiellaceae

Genus Barnesiella

Species Barnesiella intestinihominis

Full scientific name Barnesiella intestinihominis Morotomi et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31196	negative	1.3-3 µm	0.4-1 µm	rod-shaped
125438	negative				97.267
125439	negative				99.2

Colony morphology

15518

Incubation period2-3 days

Pigmentation

31196

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15518	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)	Range
15518	positive	growth	37	mesophilic
31196	positive	growth	37	mesophilic
31196	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
31196	positive	optimum	7
31196	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
15518	anaerobe
31196	anaerobe
125439	anaerobe	98.8

Spore formation

@ref	Spore formation	Confidence
31196
125438		93.978
125439		99.7

Observation

31196

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
31196	17234 ChEBI	glucose	+	carbon source
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
31196	17716 ChEBI	lactose	+	carbon source
31196	17306 ChEBI	maltose	+	carbon source
31196	37684 ChEBI	mannose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
31196	acid phosphatase	+	3.1.3.2
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
31196	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
31196	alpha-galactosidase	+	3.2.1.22
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-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate 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	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	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
15518	-	-	+	+	-	+	+/-	-	-	+	-	-	+	+	-	-	+	-	-	+	+/-	-	-	+/-	+	+/-	-	-	-
15518	-	-	+/-	+	-	+	+/-	-	-	+	-	+/-	+	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-
15518	-	-	+	+	-	+	+	-	-	+	-	-	+	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15518	human faeces	Tokyo	Japan	JPN	Asia
67770	Human feces

Taxonmaps

69479

Global distribution of 16S sequence AB547647 (>99% sequence identity) for Barnesiella intestinihominis subclade from Microbeatlas

Aquatic Samples	1533
Soil Samples	278
Animal Samples	64067
Plant Samples	103
Total Samples	65981

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15518	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
67770	Barn_inte_YIT_11860_V1 assembly for Barnesiella intestinihominis YIT 11860	scaffold	GCA_000296465	742726.3	2529292932	742726	74.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Barnesiella intestinihominis gene for 16S ribosomal RNA, partial sequence, strain: JCM 15079	AB547647	1481		487174
15518	Barnesiella intestinihominis gene for 16S ribosomal RNA, partial sequence	AB370251	1484		742726

GC content

@ref	GC-content (mol%)	Method
15518	45.5
15518	43.9	sequence analysis
67770	45.5	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: Barnesiella intestinihominis YIT 11860
NCBI: GCA_000296465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	no	65.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Barnesiella intestinihominis YIT 11860
PATRIC: 742726.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.27	no
125438	anaerobic	anaerobicⓘ	yes	89.53	no
125438	spore-forming	spore-formingⓘ	no	93.98	no
125438	aerobic	aerobicⓘ	no	94.52	yes
125438	thermophilic	thermophileⓘ	no	95.48	yes
125438	flagellated	motile2+ⓘ	no	87.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Barnesiella intestinihominis improves gut microbiota disruption and intestinal barrier integrity in mice with impaired glucose regulation.	Liu X, Wang L, Huang B, Jiao Y, Guan Y, Nuli R.	Front Pharmacol	10.3389/fphar.2025.1635579	2025
	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
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
	Maternal diet and gut microbiome composition modulate early-life immune development.	Grant ET, Boudaud M, Muller A, Muller A, Macpherson AJ, Desai MS.	EMBO Mol Med	10.15252/emmm.202217241	2023
Pathogenicity	Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk.	Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS.	STAR Protoc	10.1016/j.xpro.2021.100607	2021
	Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host.	Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC.	Cell Host Microbe	10.1016/j.chom.2024.03.001	2024
	Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome.	Steinway SN, Biggs MB, Loughran TP, Papin JA, Albert R.	PLoS Comput Biol	10.1371/journal.pcbi.1004338	2015
	A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.	Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC.	Cell	10.1016/j.cell.2016.10.043	2016
Phylogeny	Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation.	Laursen MF, Laursen RP, Larnkjaer A, Michaelsen KF, Bahl MI, Licht TR.	BMC Microbiol	10.1186/s12866-017-1090-7	2017
Metabolism	Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing.	Godwin S, Kang A, Gulino LM, Manefield M, Gutierrez-Zamora ML, Kienzle M, Ouwerkerk D, Dawson K, Klieve AV.	ISME J	10.1038/ismej.2014.25	2014
	Bupi Yishen formula against chronic kidney injury via Akkermansia muciniphila mediated group 3 innate lymphoid cells activation to repair intestinal barrier funciton.	Liu W, Zhang Y, Gu S, Zhang, Cai Y, Mo Y, Wu Y, Huang L, Liu X, Lu Z.	Phytomedicine	10.1016/j.phymed.2025.157412	2025
	Bifidobacterium breve B2798 and Its Heat-Killed Cells Alleviate Inflammation in Rats with DSS Model by Modulating Gut Microbiota.	Feng C, Zhao Y, He Q, Yu J, Sun Z.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10648-6	2025
	Molecular mechanisms of complex-type N-glycan breakdown and metabolism by the human intestinal bacterium Barnesiella intestinihominis.	Doi K, Mori K, Komatsu M, Shinoda A, Tashiro K, Higuchi Y, Nakayama J, Takegawa K.	J Biosci Bioeng	10.1016/j.jbiosc.2024.10.006	2025
	Characterization of novel endo-beta-N-acetylglucosaminidases from intestinal Barnesiella intestinihominis that hydrolyze multi-branched complex-type N-glycans.	Doi K, Mitani A, Nakakita SI, Higuchi Y, Takegawa K.	J Biosci Bioeng	10.1016/j.jbiosc.2023.12.004	2024
	Chelerythrine Protects Against Acetaminophen-Induced Acute Liver Injury: Insights from Gut Microbiota and Multi-Omics Analysis.	Liu J, Zhang Y, Wu H, Yang P, Wang W, Li C, Cao H, Wu J, Sun X.	Antioxidants (Basel)	10.3390/antiox14091063	2025
	Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota (Iron-saturated bovine lactoferrin impact on elderly gut microbiota).	Ruiz-Rico M, Ye H, O'Callaghan TF, O'Toole PW, McCarthy EK.	PLoS One	10.1371/journal.pone.0332631	2025
	Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.	Woodworth MH, Conrad RE, Haldopoulos M, Pouch SM, Babiker A, Mehta AK, Sitchenko KL, Wang CH, Strudwick A, Ingersoll JM, Philippe C, Lohsen S, Kocaman K, Lindner BG, Hatt JK, Jones RM, Miller C, Neish AS, Friedman-Moraco R, Karadkhele G, Liu KH, Jones DP, Mehta CC, Ziegler TR, Weiss DS, Larsen CP, Konstantinidis KT, Kraft CS.	Sci Transl Med	10.1126/scitranslmed.abo2750	2023
	Dietary Capsaicin Exacerbates Gut Microbiota Dysbiosis and Mental Disorders in Type 1 Diabetes Mice.	Zhang X, Hu H, Zhang Y, Hu S, Lu J, Peng W, Luo D.	Nutrients	10.3390/nu17030593	2025
	Potential Therapeutic Targets for Androgenetic Alopecia (AGA) in Obese Individuals as Revealed by a Gut Microbiome Analysis: A Mendelian Randomization Study.	Li Y, Liao X, Tang S, Wang Q, Lin H, Yu X, Xiao Y, Tao X, Zhong T.	Nutrients	10.3390/nu17111892	2025
Phylogeny	Case report: Tracing in parallel the salivary and gut microbiota profiles to assist Larotrectinib anticancer treatment for NTRK fusion-positive glioblastoma.	Turco L, Della Monica R, Giordano P, Cuomo M, Biazzo M, Mateu B, Di Liello R, Daniele B, Normanno N, De Luca A, Rachiglio AM, Chiaramonte C, Giugliano FM, Chiariotti L, Catapano G, Coretti L, Lembo F.	Front Oncol	10.3389/fonc.2024.1458990	2024
	Gut microbiota mediates the pro-pyroptosis effect of xierezhuyubuxu decoction in hepatocellular carcinoma.	Zeng Z, Feng M, He F, Zhang E, Li X, Cao Z.	Front Microbiol	10.3389/fmicb.2024.1481111	2024
	Mixed supplementation of dietary inorganic and organic selenium modulated systemic health parameters and fecal microbiota in weaned pigs.	Kyoung H, Shin I, Kim Y, Cho JH, Park KI, Kim Y, Ahn J, Nam J, Kim K, Kang Y, Kim HB, Song M.	Front Vet Sci	10.3389/fvets.2025.1531336	2025
	Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro.	Ye H, Meehan D, Timmons S, O'Toole PW.	J Agric Food Chem	10.1021/acs.jafc.5c00364	2025
	Gut Commensal Barnesiella Intestinihominis Ameliorates Hyperglycemia and Liver Metabolic Disorders.	Zhang Y, Xu D, Cai X, Xing X, Shao X, Yin A, Zhao Y, Wang M, Fan YN, Liu B, Yang H, Zhou W, Li P.	Adv Sci (Weinh)	10.1002/advs.202411181	2025
Phylogeny	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.	Blasco T, Balzerani F, Valcarcel LV, Larranaga P, Bielza C, Francino MP, Rufian-Henares JA, Planes FJ, Perez-Burillo S.	Bioinformatics	10.1093/bioinformatics/btae266	2024
	Gut microbiota and breast cancer risk: a Mendelian randomization study stratified by ER status	Yue J, Gu L, Chen S, Wen F, Huang G.	Discov Oncol		2025
	TIGIT⁺ NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.	Tsakmaklis A, Farowski F, Zenner R, Lesker TR, Strowig T, Schlosser H, Lehmann J, von Bergwelt-Baildon M, Mauch C, Schlaak M, Knuever J, Schweinsberg V, Heinzerling LM, Vehreschild MJGT.	BMC Cancer	10.1186/s12885-023-11551-5	2023
	Gut microbiome alterations in IgG4-related ophthalmic disease.	Ren T, Li J, Liu R, Wang N, Guo Q, Xu L, Yan H, Zhang Y, Ma J.	BMC Microbiol	10.1186/s12866-025-04350-4	2025
	A ferroptosis-related risk model for non-coding RNA AC002331.1 in colon cancer: construction via competing endogenous RNA network analysis.	Liu J, Zhang C, Ma B, Qi J, Zhang X, Zhao H.	Discov Oncol	10.1007/s12672-025-03351-z	2025
	Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways.	He Q, Zhang Y, Ma D, Zhang W, Zhang H.	Eur J Nutr	10.1007/s00394-021-02764-0	2022
	A Literature Review on the Impact of the Gut Microbiome on Cancer Treatment Efficacy, Disease Evolution and Toxicity: The Implications for Hematological Malignancies.	Dumitru IG, Todor SB, Ichim C, Helgiu C, Helgiu A.	J Clin Med	10.3390/jcm14092982	2025
	Cerebral small vessel disease burden is associated with decreased abundance of gut Barnesiella intestinihominis bacterium in the Framingham Heart Study.	Fongang B, Satizabal C, Kautz TF, Wadop YN, Muhammad JAS, Vasquez E, Mathews J, Gireud-Goss M, Saklad AR, Himali J, Beiser A, Cavazos JE, Mahaney MC, Maestre G, DeCarli C, Shipp EL, Vasan RS, Seshadri S.	Sci Rep	10.1038/s41598-023-40872-5	2023
Pathogenicity	The bacterial microbiome and cancer: development, diagnosis, treatment, and future directions.	Qasem HH, El-Sayed WM.	Clin Exp Med	10.1007/s10238-024-01523-9	2024
	Interplay of Gut Microbiota, Biologic Agents, and Postoperative Anastomotic Leakage in Inflammatory Bowel Disease: A Narrative Review	Menni A, Kyriazopoulou E, Karakike E, Tzikos G, Filidou E, Kotzampassi K.	Int J Mol Sci		2025
Genetics	Comparison Of The Gut Microbiota In Different Age Groups In China.	Yan H, Qin Q, Yan S, Chen J, Yang Y, Li T, Gao X, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.877914	2022
Pathogenicity	Matrine protects against DSS-induced murine colitis by improving gut barrier integrity, inhibiting the PPAR-alpha signaling pathway, and modulating gut microbiota.	Yao H, Shi Y, Yuan J, Sa R, Chen W, Wan X.	Int Immunopharmacol	10.1016/j.intimp.2021.108091	2021
	Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.	Marcos-Zambrano LJ, Lacruz-Pleguezuelos B, Aguilar-Aguilar E, Marcos-Pasero H, Valdes A, Loria-Kohen V, Cifuentes A, Ramirez de Molina A, Diaz-Ruiz A, Pancaldi V, Carrillo de Santa Pau E.	mSystems	10.1128/msystems.00143-25	2025
Phylogeny	The gut microbiota in experimental abdominal aortic aneurysm.	Xiao J, Wei Z, Yang C, Dai S, Wang X, Shang Y.	Front Cardiovasc Med	10.3389/fcvm.2023.1051648	2023
Pathogenicity	High carbohydrate diet decreases microbial diversity and increases IL-1beta levels in mice colon.	Ulutas MS, Aydin E, Cebeci A.	Food Sci Biotechnol	10.1007/s10068-024-01581-5	2024
Genetics	Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.	Al Radi ZMA, Prins FM, Collij V, Vich Vila A, Festen EAM, Dijkstra G, Weersma RK, Klaassen MAY, Gacesa R.	Inflamm Bowel Dis	10.1093/ibd/izae064	2024
	Effect of the gut microbiome, skin microbiome, plasma metabolome, white blood cells subtype, immune cells, inflammatory proteins, and inflammatory cytokines on asthma: a two-sample Mendelian randomized study and mediation analysis.	Guo W, Hong E, Ma H, Wang J, Wang Q.	Front Immunol	10.3389/fimmu.2025.1436888	2025
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
	Species-level enterosignatures predict clinical phenotypes in chronic hepatitis B and causal triangulation of gut-metabolite-CHB interactions.	Yuan T, Chen J, Yang J, Li L, Lu S, Pu J, Sun Y, Lin W, Lu Y, Zhu Z, Zheng H, Xu J.	Front Microbiol	10.3389/fmicb.2025.1683451	2025
	Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.	Lim MY, Hong S, Nam YD.	Front Immunol	10.3389/fimmu.2024.1512683	2024
	Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies.	Drago L, De La Motte LR, Deflorio L, Sansico DF, Salvatici M, Micaglio E, Biazzo M, Giarritiello F.	Front Microbiol	10.3389/fmicb.2025.1540943	2025
	Concomitant decrease of double-positive lymphocyte population CD4CD8alphaalpha and Faecalibacterium prausnitzii in patients with colorectal cancer.	Touchefeu Y, Duchalais E, Bruley des Varannes S, Alameddine J, Mirallie E, Matysiak-Budnik T, Le Bastard Q, Javaudin F, Rimbert M, Jotereau F, Montassier E.	Eur J Gastroenterol Hepatol	10.1097/meg.0000000000001842	2021
	Gut Microbiome rewiring via fecal transplants: Uncovering therapeutic avenues in Alzheimer's disease models.	Upadhyay P, Kumar S, Tyagi A, Tyagi AR, Barbhuyan T, Gupta S.	BMC Neurosci	10.1186/s12868-025-00953-9	2025
Pathogenicity	Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model.	Ye H, Ghosh TS, Hueston CM, Vlckova K, Golubeva AV, Hyland NP, O'Toole PW.	Gut Microbes	10.1080/19490976.2023.2282796	2023
Genetics	Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.	Fan KC, Lin CC, Chiu YL, Koh SH, Liu YC, Chuang YF.	Alzheimers Res Ther	10.1186/s13195-025-01769-9	2025
	Pharmaco-psychiatry and gut microbiome: a systematic review of effects of psychotropic drugs for bipolar disorder.	Bui TA, O'Croinin BR, Dennett L, Winship IR, Greenshaw AJ.	Microbiology (Reading)	10.1099/mic.0.001568	2025
	Rapeseed Meal as an Alternative Protein Source in Fish Feed and Its Impact on Growth Parameters, Digestive Tract, and Gut Microbiota.	Karolina WA, Justyna N.	Animals (Basel)	10.3390/ani15091264	2025
	Analysis of the Gut Microbiome and Dietary Habits in Metastatic Melanoma Patients with a Complete and Sustained Response to Immunotherapy.	Golcic M, Simetic L, Herceg D, Blazicevic K, Kendel Jovanovic G, Drazic I, Belancic A, Skocibusic N, Palcevski D, Rubinic I, Vlahovic-Palcevski V, Majnaric T, Dobrila-Dintinjana R, Plestina S.	Cancers (Basel)	10.3390/cancers15113052	2023
	What Is the Role of the Gut Microbiota in Anastomotic Leakage After Colorectal Resection? A Scoping Review of Clinical and Experimental Studies.	Lianos GD, Frountzas M, Kyrochristou ID, Sakarellos P, Tatsis V, Kyrochristou GD, Bali CD, Gazouli M, Mitsis M, Schizas D.	J Clin Med	10.3390/jcm13226634	2024
	Self-Initiated Dietary Adjustments Alter Microbiota Abundances: Implications for Perceived Health.	Willems A, Sura-de Jong M, Klaassens E, van den Bogert B, van Beek A, van Dijk G.	Nutrients	10.3390/nu16203544	2024
	Impact of occupational pesticide exposure on the human gut microbiome.	Gois MFB, Fernandez-Pato A, Huss A, Gacesa R, Wijmenga C, Weersma RK, Fu J, Vermeulen RCH, Zhernakova A, Lenters VC, Kurilshikov A.	Front Microbiol	10.3389/fmicb.2023.1223120	2023
Pathogenicity	Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.	Ryu HM, Islam SMS, Riaz B, Sayeed HM, Choi B, Sohn S.	Int J Mol Sci	10.3390/ijms25168571	2024
	Community metabolic modeling of host-microbiota interactions through multi-objective optimization.	Lambert A, Budinich M, Mahe M, Chaffron S, Eveillard D.	iScience	10.1016/j.isci.2024.110092	2024
	Role of preoperative gut microbiota on colorectal anastomotic leakage: preliminary results.	Palmisano S, Campisciano G, Iacuzzo C, Bonadio L, Zucca A, Cosola D, Comar M, de Manzini N.	Updates Surg	10.1007/s13304-020-00720-x	2020
Genetics	Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.	Yang J, Wang L, Liang Q, Wang Y, Yang X, Wu X, Pei X.	BMC Microbiol	10.1186/s12866-025-04115-z	2025
Phylogeny	Compositional alterations of the gut microbiota in acute myocardial infarction patients with type 2 diabetes mellitus.	Lei C, Zhang X, Chen E, Lin L, Zhou Z, Wang Z, Liu T, Liu Z.	Ann Transl Med	10.21037/atm-22-3521	2023
Pathogenicity	Potential roles of the interactions between gut microbiota and metabolites in LPS-induced intrauterine inflammation (IUI) and associated preterm birth (PTB).	Jia B, Tang L, Liu H, Chen W, Chen Q, Zhong M, Yin A.	J Transl Med	10.1186/s12967-023-04603-8	2024
	Microbiota boost immunotherapy? A meta-analysis dives into fecal microbiota transplantation and immune checkpoint inhibitors.	Lin A, Huang L, Jiang A, Zhu L, Mou W, Li Y, Zhang C, Liu Z, Zhang J, Cheng Q, Wei T, Luo P.	BMC Med	10.1186/s12916-025-04183-y	2025
Phylogeny	Cellulase activity and age-based variation of intestinal microbiota in Hezuo pigs.	Liang Y, Wang F, Jia R, Li J, Wang L, Li Y, Li Y, Gun S, Yang Q.	Front Microbiol	10.3389/fmicb.2025.1599847	2025
Genetics	Metabolic response of intestinal microbiota to guar gum consumption.	Barber C, Sabater C, Guarner F, Margolles A, Azpiroz F.	Front Nutr	10.3389/fnut.2023.1160694	2023
	Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines.	Finazzi M, Bovio F, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Microorganisms	10.3390/microorganisms13010192	2025
	Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma.	Dizman N, Hsu J, Bergerot PG, Gillece JD, Folkerts M, Reining L, Trent J, Highlander SK, Pal SK.	Cancer Med	10.1002/cam4.3569	2021
	Modulating Gut Microbiota with Dietary Components: A Novel Strategy for Cancer-Depression Comorbidity Management.	Dai H, Yang H, Wang R, Wang X, Zhang X.	Nutrients	10.3390/nu17091505	2025
Metabolism	Effect of Lactobacillus plantarum Extracellular Vesicles on Lipid Metabolism in Mice Fed a High-Fat Diet.	Xu SS, Yu CJ, Qin MY, Zhang Y, Jiang JP, Liu W, Pan Y, Zhang S, Zhao XY.	Mol Nutr Food Res	10.1002/mnfr.70183	2025
	Ginsenoside Rh4 inhibits colorectal cancer via the modulation of gut microbiota-mediated bile acid metabolism.	Bai X, Duan Z, Deng J, Zhang Z, Fu R, Zhu C, Fan D.	J Adv Res	10.1016/j.jare.2024.06.028	2025
	Ginsenoside Rk3 modulates gut microbiota and regulates immune response of group 3 innate lymphoid cells to against colorectal tumorigenesis.	Bai X, Fu R, Liu Y, Deng J, Fei Q, Duan Z, Zhu C, Fan D.	J Pharm Anal	10.1016/j.jpha.2023.09.010	2024
	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
	Age and aging process alter the gut microbes.	Zhanbo Q, Jing Z, Shugao H, Yinhang W, Jian C, Xiang Y, Feimin Z, Jian L, Xinyue W, Wei W, Shuwen H.	Aging (Albany NY)	10.18632/aging.205728	2024
Phylogeny	The intensive physical activity causes changes in the composition of gut and oral microbiota.	Urban S, Chmura O, Wator J, Panek P, Zapala B.	Sci Rep	10.1038/s41598-024-71684-w	2024
	The science behind TCM and Gut microbiota interaction-their combinatorial approach holds promising therapeutic applications.	Xia W, Liu B, Tang S, Yasir M, Khan I.	Front Cell Infect Microbiol	10.3389/fcimb.2022.875513	2022
Pathogenicity	The Gut Microbiome Role in Multiple Myeloma: Emerging Insights and Therapeutic Opportunities.	George MY, Gamal NK, Mansour DE, Famurewa AC, Bose D, Messiha PA, Cerchione C.	Hematol Rep	10.3390/hematolrep17060056	2025
	Potential application of pig (Sus scrofa domestica) skin peptide-iron chelates in the treatment of iron deficiency anemia and regulation of intestinal flora metabolism.	Huang S, Deng H, Liang K, Zhao X, Zhang J.	Front Nutr	10.3389/fnut.2025.1553668	2025
	Gut microbiome is associated with radiotherapy response in lung cancer patients with brain metastases.	Liang F, Sun Y, Yang J, Shen Z, Wang G, Zhu J, Zhou C, Xia Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1562831	2025
	Bifidobacterium as a Potential Biomarker of Sarcopenia in Elderly Women.	Wang Z, Xu X, Deji Y, Gao S, Wu C, Song Q, Shi Z, Xiang X, Zang J, Su J.	Nutrients	10.3390/nu15051266	2023
	Attempting to Identify Bacterial Allies in Immunotherapy of NSCLC Patients.	Grenda A, Iwan E, Krawczyk P, Frak M, Chmielewska I, Bomba A, Giza A, Rolska-Kopinska A, Szczyrek M, Kieszko R, Kucharczyk T, Jarosz B, Wasyl D, Milanowski J.	Cancers (Basel)	10.3390/cancers14246250	2022
	Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome.	Chang B, Zhang W, Wang Y, Zhang Y, Zhong S, Gao P, Wang L, Zhao Z.	BMC Microbiol	10.1186/s12866-024-03211-w	2024
	Synergistic Effects of Probiotics and Lifestyle Interventions on Intestinal Microbiota Composition and Clinical Outcomes in Obese Adults.	Florencio GP, Xavier AR, Natal ACC, Sadoyama LP, Pena GDG, Menezes RP, Sadoyama Leal G, Patrizzi LJ, Roder DVDB.	Metabolites	10.3390/metabo15020070	2025
	B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients.	Vietsch EE, Latifi D, Verheij M, van der Oost EWA, de Wilde RF, Haen R, van den Boom AL, Koerkamp BG, Doornebosch PG, van Verschuer VMT, Ooms AHAG, Mohammad F, Willemsen M, Aerts JGJV, Krog RT, de Miranda NFCC, van den Bosch TPP, Mueller YM, Katsikis PD, van Eijck CHJ.	Front Immunol	10.3389/fimmu.2023.1230306	2023
	Probiotics supplementation or probiotic-fortified products on sarcopenic indices in older adults: systematic review and meta-analysis from recent randomized controlled trials.	Handajani YS, Turana Y, Hengky A, Hamid G, Schroeder-Butterfill E, Kristian K.	Front Aging	10.3389/fragi.2024.1307762	2024
	Gut Microbiota and Metabolites: Biomarkers and Therapeutic Targets for Diabetes Mellitus and Its Complications	Yan K, Sun X, Wang X, Zheng J, Yu H.	Nutrients		2025
	Matrine Protects Intestinal Barrier Function via MicroRNA-155 Through ROCK1-Signaling Pathway.	Yu D, Su D, Liu Z.	Turk J Gastroenterol	10.5152/tjg.2023.21884	2023
	Current Insights: The Impact of Gut Microbiota on Postoperative Complications in Visceral Surgery-A Narrative Review.	Lederer AK, Chikhladze S, Kohnert E, Huber R, Muller A.	Diagnostics (Basel)	10.3390/diagnostics11112099	2021
Phylogeny	Chinese herbal medicine, Tongxieyaofang, alleviates diarrhea via gut microbiota remodeling: evidence from network pharmacology and full-length 16S rRNA gene sequencing.	Shao H, Wang L, Zhang H.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1502373	2024
	The Interplay Between the Gut Microbiota and Colorectal Cancer: A Review of the Literature.	Cintoni M, Palombaro M, Zoli E, D'Agostino G, Pulcini G, Leonardi E, Raoul P, Rinninella E, De Maio F, Capristo E, Gasbarrini A, Mele MC.	Microorganisms	10.3390/microorganisms13061410	2025
Genetics	The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.	Wang X, Dong Q, Huang P, Yang S, Gao M, Zhang C, Zhang C, Deng Y, Huang Z, Ma B, Jiao Y, Zhou Y, Wu T, Zou H, Shi J, Sheng Y, Wang Y, Consortium C, Tang L, Hu S, Duan Y, Sun W, Chen W, Zhai Q, Kong X, Chen L.	Microbiome	10.1186/s40168-025-02185-9	2025
	Effects of exercise and physical activity on gut microbiota composition and function in older adults: a systematic review.	Aya V, Jimenez P, Munoz E, Ramirez JD.	BMC Geriatr	10.1186/s12877-023-04066-y	2023
	Guardians in the Gut: Mechanistic Insights into a Hidden Ally Against Triple-Negative Breast Cancer.	Jaye K, Alsherbiny MA, Chang D, Li CG, Bhuyan DJ.	Cancers (Basel)	10.3390/cancers17193248	2025
	Collagenase-producing bacteria are common in anastomotic leakage after colorectal surgery: a systematic review.	Jorgensen AB, Jonsson I, Friis-Hansen L, Brandstrup B.	Int J Colorectal Dis	10.1007/s00384-023-04562-y	2023
	The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy.	Susic DF, Wang L, Roberts LM, Bai M, Gia A, McGovern E, Jiang XT, Davis GK, El-Omar E, Henry A.	Front Cell Infect Microbiol	10.3389/fcimb.2022.646165	2022
	Modulation of the Gut Microbiota by the Plantaricin-Producing Lactiplantibacillus plantarum D13, Analysed in the DSS-Induced Colitis Mouse Model.	Butorac K, Novak J, Banic M, Lebos Pavunc A, Culjak N, Orsolic N, Odeh D, Perica J, Suskovic J, Kos B.	Int J Mol Sci	10.3390/ijms242015322	2023
Phylogeny	Changes in the Gut and Oral Microbiome in Children with Phenylketonuria in the Context of Dietary Restrictions-A Preliminary Study.	Ostrowska M, Nowosad K, Mikoluc B, Szczerba H, Komon-Janczara E.	Nutrients	10.3390/nu16223915	2024
	Predicting cancer-related mycobiome aspects in gastrointestinal cancers: a systematic review.	Szklenarik G, Kiraly P, Szegvari G, Dora D, Lohinai Z.	Front Med (Lausanne)	10.3389/fmed.2024.1488377	2024
Pathogenicity	Modulation of the Gut-Lung Axis by Water Kefir and Kefiran and Their Impact on Toll-like Receptor 3-Mediated Respiratory Immunity.	Dentice Maidana S, Arganaraz Aybar JN, Albarracin L, Imamura Y, Arellano-Arriagada L, Namai F, Suda Y, Nishiyama K, Villena J, Kitazawa H.	Biomolecules	10.3390/biom14111457	2024
	Exploring the role of gut microbiota in advancing personalized medicine.	Huang G, Khan R, Zheng Y, Lee PC, Li Q, Khan I.	Front Microbiol	10.3389/fmicb.2023.1274925	2023
Metabolism	Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.	Zou S, Yang C, Zhang J, Zhong D, Meng M, Zhang L, Chen H, Fang L.	J Transl Med	10.1186/s12967-024-04984-4	2024
	Microbiota and Hematological Diseases.	D'Angelo G.	Int J Hematol Oncol Stem Cell Res	10.18502/ijhoscr.v16i3.10139	2022
	Characterization and Evaluation of Lactobacillus plantarum LC5.2 Isolated from Thai Native Pigs for its Probiotic Potential in Gut Microbiota Modulation and Immune Enhancement.	Khongkool K, Taweechotipatr M, Payungporn S, Sawaswong V, Lertworapreecha M.	J Microbiol Biotechnol	10.4014/jmb.2503.03028	2025
Enzymology	Gut microbiota modulation and immunity enhancement by Bacillus amyloliquefaciens NL1.2: A fiber-degrading probiotic isolated from native Thai swine.	Khongkool K, Taweechotipatr M, Payungporn S, Sawaswong V, Lertworapreecha M.	Vet World	10.14202/vetworld.2025.1487-1507	2025
Metabolism	Targeting the Gut Microbiome to Improve Immunotherapy Outcomes: A Review.	David A, Lev-Ari S.	Integr Cancer Ther	10.1177/15347354241269870	2024
	Enterococcus hirae and Barnesiella intestinihominis Facilitate Cyclophosphamide-Induced Therapeutic Immunomodulatory Effects.	Daillere R, Vetizou M, Waldschmitt N, Yamazaki T, Isnard C, Poirier-Colame V, Duong CPM, Flament C, Lepage P, Roberti MP, Routy B, Jacquelot N, Apetoh L, Becharef S, Rusakiewicz S, Langella P, Sokol H, Kroemer G, Enot D, Roux A, Eggermont A, Tartour E, Johannes L, Woerther PL, Chachaty E, Soria JC, Golden E, Formenti S, Plebanski M, Madondo M, Rosenstiel P, Raoult D, Cattoir V, Boneca IG, Chamaillard M, Zitvogel L.	Immunity	10.1016/j.immuni.2016.09.009	2016
	Impact of broad-spectrum antibiotics on the gut-microbiota-spleen-brain axis.	Wan X, Eguchi A, Sakamoto A, Fujita Y, Yang Y, Qu Y, Hatano M, Mori C, Hashimoto K.	Brain Behav Immun Health	10.1016/j.bbih.2022.100573	2023
	Microbial Features Linked to Medication Strategies in Cardiometabolic Disease Management.	Shearer J, Shah S, Shen-Tu G, Schlicht K, Laudes M, Mu C.	ACS Pharmacol Transl Sci	10.1021/acsptsci.3c00261	2024
	Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults.	Fielding RA, Reeves AR, Jasuja R, Liu C, Barrett BB, Lustgarten MS.	Exp Gerontol	10.1016/j.exger.2019.110722	2019
	The Hazards of Probiotics on Gut-Derived Pseudomonas aeruginosa Sepsis in Mice Undergoing Chemotherapy.	Huang FC, Huang SC.	Biomedicines	10.3390/biomedicines12020253	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	A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans.	Wang S, Li N, Li N, Zou H, Wu M.	Biomed Res Int	10.1155/2019/6361320	2019
	Alterations of gut microbiota in biopsy-proven diabetic nephropathy and a long history of diabetes without kidney damage.	Lu X, Ma J, Li R.	Sci Rep	10.1038/s41598-023-39444-4	2023
Pathogenicity	Blueberry Supplementation and Skin Health.	Ivarsson J, Pecorelli A, Lila MA, Valacchi G.	Antioxidants (Basel)	10.3390/antiox12061261	2023
	The gut microbiota modulates responses to anti-PD-1 and chemotherapy combination therapy and related adverse events in patients with advanced solid tumors.	Wu Z, Zhang S, Li L, Huang Z, Huang D, Hu Y.	Front Oncol	10.3389/fonc.2022.887383	2022
Pathogenicity	Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice.	Smith BJ, Miller RA, Schmidt TM.	mSphere	10.1128/msphere.00851-21	2021
	Gastrointestinal complaints after Roux-en-Y gastric bypass surgery. Impact of microbiota and its metabolites.	Custers E, van der Burgh YGR, Vreeken D, Schuren F, van den Broek TJ, Verschuren L, de Blaauw I, Bouwens M, Kleemann R, Kiliaan AJ, Hazebroek EJ.	Heliyon	10.1016/j.heliyon.2024.e39899	2024
	Oral vancomycin treatment suppresses gut trypsin activity and preserves intestinal barrier function during EAE.	Bianchimano P, Iwanowski K, Smith EM, Cantor A, Leone P, Bongers G, Gonzalez CG, Hongsup Y, Elias J, Weiner HL, Clemente JC, Tankou SK.	iScience	10.1016/j.isci.2023.108143	2023
Genetics	Gut resistome of NSCLC patients treated with immunotherapy.	Iwan E, Grenda A, Bomba A, Bielinska K, Wasyl D, Kieszko R, Rolska-Kopinska A, Chmielewska I, Krawczyk P, Rybczynska-Tkaczyk K, Olejnik M, Milanowski J.	Front Genet	10.3389/fgene.2024.1378900	2024
	Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota.	Leigh RJ, Corrigan A, Murphy RA, Walsh F.	Anim Microbiome	10.1186/s42523-022-00208-6	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
	Impact of Combined Prebiotic Galacto-Oligosaccharides and Bifidobacterium breve-Derived Postbiotic on Gut Microbiota and HbA1c in Prediabetic Adults: A Double-Blind, Randomized, Placebo-Controlled Study.	Beteri B, Barone M, Turroni S, Brigidi P, Tzortzis G, Vulevic J, Sekulic K, Motei DE, Costabile A.	Nutrients	10.3390/nu16142205	2024
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
	Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.	Choi JY, Shim B, Park Y, Kang YA.	Korean J Intern Med	10.3904/kjim.2023.097	2023
	Global research trends on the links between gut microbiota and cancer immunotherapy: A bibliometric analysis (2012-2021).	Yang S, Zhao S, Ye Y, Jia L, Lou Y.	Front Immunol	10.3389/fimmu.2022.952546	2022
	Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.	Luan M, Niu M, Yang P, Han D, Zhang Y, Li W, He Q, Zhao Y, Mao B, Chen J, Mou K, Li P.	BMC Microbiol	10.1186/s12866-023-03020-7	2023
Phylogeny	Characteristics of gut microbiota in people with obesity.	Duan M, Wang Y, Zhang Q, Zou R, Guo M, Zheng H.	PLoS One	10.1371/journal.pone.0255446	2021
	Assessing the gut microbiota composition in older adults: connections to physical activity and healthy ageing.	Ramos C, Magistro D, Walton GE, Whitham A, Camp N, Poveda C, Gibson GR, Hough J, Kinnear W, Hunter K.	Geroscience	10.1007/s11357-025-01605-w	2025
	Eco-evolutionary feedbacks in the human gut microbiome.	Good BH, Rosenfeld LB.	Nat Commun	10.1038/s41467-023-42769-3	2023
	Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.	Vinogradova E, Mukhanbetzhanov N, Nurgaziyev M, Jarmukhanov Z, Aipova R, Sailybayeva A, Bekbossynova M, Kozhakhmetov S, Kushugulova A.	mSystems	10.1128/msystems.00585-24	2024
	Monascus red pigments alleviate high-fat and high-sugar diet-induced NAFLD in mice by modulating the gut microbiota and metabolites.	Gao W, Chen X, Wu S, Jin L, Chen X, Mao G, Wan X, Xing W.	Food Sci Nutr	10.1002/fsn3.4208	2024
	Identification of Muscle Strength-Related Gut Microbes through Human Fecal Microbiome Transplantation.	Ahn JS, Koo BC, Choi YJ, Jung WW, Kim HS, Lee SJ, Hong ST, Chung HJ.	Int J Mol Sci	10.3390/ijms25010662	2024
	Akkermansia muciniphila alleviates abdominal aortic aneurysms via restoring CITED2 activated by EPAS1.	Wang S, Shi H, Cheng Y, Jiang L, Lou Y, Kumar M, Sun M, Shao X, Zhao X, Wang B.	Infect Immun	10.1128/iai.00172-24	2024
Pathogenicity	The Influence of Probiotic Supplementation on the Obesity Indexes, Neuroinflammatory and Oxidative Stress Markers, Gut Microbial Diversity, and Working Memory in Obese Thai Children.	Khongtan S, Sivamaruthi BS, Thangaleela S, Kesika P, Bharathi M, Sirilun S, Choeisoongnern T, Peerajan S, Sittiprapaporn P, Chaiyasut C.	Foods	10.3390/foods12213890	2023
	Beneficial effects of Lactobacillus plantarum on growth performance, immune status, antioxidant function and intestinal microbiota in broilers.	Xiao X, Cui T, Qin S, Wang T, Liu J, Sa L, Wu Y, Zhong Y, Yang C.	Poult Sci	10.1016/j.psj.2024.104280	2024
	Effects of Designed Herbal Formula on Growth Performance, Blood Indices, Organ Traits, and Cecum Microbiology in Broilers.	Sun Y, Zhang M, Shi D, Dai X, Li X.	Vet Sci	10.3390/vetsci11030107	2024
	Evidence from Animal Models: Is a Restricted or Conventional Intestinal Microbiota Composition Predisposing to Risk for High-LET Radiation Injury?	Maier I, Schiestl RH.	Radiat Res	10.1667/rr13837.1	2015
	Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma.	Limeta A, Ji B, Levin M, Gatto F, Nielsen J.	JCI Insight	10.1172/jci.insight.140940	2020
	Characterization of Novel Exopolysaccharides from Enterococcus hirae WEHI01 and Its Immunomodulatory Activity.	Jia K, Wei M, He Y, Wang Y, Wei H, Tao X.	Foods	10.3390/foods11213538	2022
	The Role of Gut Microbiota in Modulating Tumor Growth and Anticancer Agent Efficacy.	Kim J, Lee HK.	Mol Cells	10.14348/molcells.2021.0032	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
	Vitamin C improves gut Bifidobacteria in humans.	Hazan S, Dave S, Papoutsis AJ, Deshpande N, Howell MC, Martin LM.	Future Microbiol	10.2217/fmb-2022-0209	2025
	Increasing buffering capacity enhances rumen fermentation characteristics and alters rumen microbiota composition of high-concentrate fed Hanwoo steers.	Ramos SC, Kim SH, Jeong CD, Mamuad LL, Son AR, Kang SH, Cho YI, Kim TG, Lee JS, Cho KK, Lee SS, Lee SS.	Sci Rep	10.1038/s41598-022-24777-3	2022
	Holstein and Jersey Steers Differ in Rumen Microbiota and Enteric Methane Emissions Even Fed the Same Total Mixed Ration.	Islam M, Kim SH, Ramos SC, Mamuad LL, Son AR, Yu Z, Lee SS, Cho YI, Lee SS.	Front Microbiol	10.3389/fmicb.2021.601061	2021
	The Role of Tumor and Host Microbiome on Immunotherapy Response in Urologic Cancers.	Pfail J, Drobner J, Doppalapudi K, Saraiya B, Packiam V, Ghodoussipour S.	J Cancer Immunol (Wilmington)	10.33696/cancerimmunol.6.078	2024
	Gut microbiota in acute leukemia: Current evidence and future directions.	Zhou Y, Zhou C, Zhang A.	Front Microbiol	10.3389/fmicb.2022.1045497	2022
Genetics	Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.	Zeybel M, Arif M, Li X, Altay O, Yang H, Shi M, Akyildiz M, Saglam B, Gonenli MG, Yigit B, Ulukan B, Ural D, Shoaie S, Turkez H, Nielsen J, Zhang C, Uhlen M, Boren J, Mardinoglu A.	Adv Sci (Weinh)	10.1002/advs.202104373	2022
	Potential interaction between timing of infant complementary feeding and breastfeeding duration in determination of early childhood gut microbiota composition and BMI.	Differding MK, Doyon M, Bouchard L, Perron P, Guerin R, Asselin C, Masse E, Hivert MF, Mueller NT.	Pediatr Obes	10.1111/ijpo.12642	2020
Genetics	Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.	Kim H, Kim ES, Cho JH, Song M, Cho JH, Kim S, Keum GB, Kwak J, Doo H, Pandey S, Park SH, Lee JH, Jung H, Hur TY, Kim JK, Oh KK, Kim HB, Lee JH.	J Microbiol Biotechnol	10.4014/jmb.2209.09013	2023
	Nutritional Interventions Targeting Gut Microbiota during Cancer Therapies.	Rinninella E, Raoul P, Cintoni M, Palombaro M, Pulcini G, Gasbarrini A, Gasbarrini A, Mele MC.	Microorganisms	10.3390/microorganisms9071469	2021
	Immune Checkpoint Inhibitor Therapy for Metastatic Melanoma: What Should We Focus on to Improve the Clinical Outcomes?	Hossain SM, Ly K, Sung YJ, Braithwaite A, Li K.	Int J Mol Sci	10.3390/ijms251810120	2024
	Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.	Govaert M, Rotsaert C, Vannieuwenhuyse C, Duysburgh C, Medlin S, Marzorati M, Jarrett H.	Nutrients	10.3390/nu16162791	2024
	Intestinal microbiota reduces genotoxic endpoints induced by high-energy protons.	Maier I, Berry DM, Schiestl RH.	Radiat Res	10.1667/rr13352.1	2014
	Causal relationship between the gut microbiome and basal cell carcinoma, melanoma skin cancer, ease of skin tanning: evidence from three two-sample mendelian randomisation studies.	Lou J, Cui S, Li J, Jin G, Fan Y, Huang N.	Front Immunol	10.3389/fimmu.2024.1279680	2024
Genetics	miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.	Liu L, Cao S, Lin W, Gao Z, Yang L, Zhu L, Yang B, Zhang G, Zhu R, Wu D.	Gut Microbes	10.1080/19490976.2024.2434029	2024
	Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study.	Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1181328	2023
	Crosstalk between gut microbiota and cancer chemotherapy: current status and trends.	Yang S, Hao S, Ye H, Zhang X.	Discov Oncol	10.1007/s12672-024-01704-8	2024
	Alteration of the gut microbiome and correlated metabolism in a rat model of long-term depression.	Li Y, Li J, Cheng R, Liu H, Zhao Y, Liu Y, Chen Y, Sun Z, Zhai Z, Wu M, Yan Y, Sun Y, Zhang Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1116277	2023
Genetics	Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries.	Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.11.047	2024
	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
	Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.	Islam SMS, Ryu HM, Sohn S.	Cells	10.3390/cells11121903	2022
	Effects of Glucosinolate-Enriched Red Radish (Raphanus sativus) on In Vitro Models of Intestinal Microbiota and Metabolic Syndrome-Related Functionalities.	Roses C, Garcia-Ibanez P, Agudelo A, Viadel B, Tomas-Cobos L, Gallego E, Carvajal M, Milagro FI, Barcelo A.	ACS Omega	10.1021/acsomega.2c08128	2023
Phylogeny	Impact of a Model Used to Simulate Chronic Socio-Environmental Stressors Encountered during Spaceflight on Murine Intestinal Microbiota.	Alauzet C, Cunat L, Wack M, Lanfumey L, Legrand-Frossi C, Lozniewski A, Agrinier N, Cailliez-Grimal C, Frippiat JP.	Int J Mol Sci	10.3390/ijms21217863	2020
	Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.	White MG, Damania A, Alshenaifi J, Sahasrabhojane P, Peacock O, Losh J, Wong MC, Lutter-Berkova Z, Chang GJ, Futreal A, Wargo JA, Ajami NJ, Kopetz S, You YN.	Ann Surg	10.1097/sla.0000000000006015	2023
	Intestinal Permeability Associated with the Loss of Skeletal Muscle Strength in Middle-Aged and Older Adults in Rural Area of Beijing, China.	Li C, Li Y, Wang N, Ge Z, Shi Z, Wang J, Ding B, Bi Y, Wang Y, Hong Z.	Healthcare (Basel)	10.3390/healthcare10061100	2022
	Metabolomic analysis of gut metabolites in patients with colorectal cancer: Association with disease development and outcome.	Xie Z, Zhu R, Huang X, Yao F, Jin S, Huang Q, Wang D, Li H, Wang Q, Long H, Wu Q.	Oncol Lett	10.3892/ol.2023.13944	2023
Genetics	Dynamic changes in gut microbiota during pregnancy among Chinese women and influencing factors: A prospective cohort study.	Li M, Zhang G, Cui L, Zhang L, Zhou Q, Mu C, Chi R, Zhang N, Ma G.	Front Microbiol	10.3389/fmicb.2023.1114228	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
Metabolism	Role of intestinal flora in the development of nonalcoholic fatty liver disease in children.	Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y, Wang L, Wang L.	Microbiol Spectr	10.1128/spectrum.01006-23	2024
Proteome	Insights into the proteomic profile of newly harvested corn and metagenomic analysis of the broiler intestinal microbiota.	Yin D, Wang Y, Wang L, Wu Y, Bian X, Aggrey SE, Yuan J.	J Anim Sci Biotechnol	10.1186/s40104-021-00656-1	2022
Phylogeny	The impact of gut microbiota changes on the intestinal mucus barrier in burned mice: a study using 16S rRNA and metagenomic sequencing.	Zha X, Su S, Wu D, Zhang P, Wei Y, Fan S, Huang Q, Peng X.	Burns Trauma	10.1093/burnst/tkad056	2023
	Bi-Directional Interactions between Glucose-Lowering Medications and Gut Microbiome in Patients with Type 2 Diabetes Mellitus: A Systematic Review.	Li R, Shokri F, Rincon AL, Rivadeneira F, Medina-Gomez C, Ahmadizar F.	Genes (Basel)	10.3390/genes14081572	2023
Genetics	Integration analysis of tumor metagenome and peripheral immunity data of diffuse large-B cell lymphoma.	Zhang Y, Han S, Xiao X, Zheng L, Chen Y, Zhang Z, Gao X, Zhou S, Yu K, Huang L, Fu J, Hong Y, Jiang J, Qian W, Yang H, Shen J.	Front Immunol	10.3389/fimmu.2023.1146861	2023
	Novel therapeutic strategies and recent advances in gut microbiota synergy with nanotechnology for colorectal cancer treatment.	Han Q, Li J, Li Z, Aishajiang R, Yu D.	Mater Today Bio	10.1016/j.mtbio.2025.101601	2025
Phylogeny	Far infrared radiation induces changes in gut microbiota and activates GPCRs in mice.	Khan I, Pathan S, Li XA, Leong WK, Liao WL, Wong V, Hsiao WLW.	J Adv Res	10.1016/j.jare.2019.12.003	2020
	Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients.	Elbere I, Silamikelis I, Dindune II, Kalnina I, Briviba M, Zaharenko L, Silamikele L, Rovite V, Gudra D, Konrade I, Sokolovska J, Pirags V, Klovins J.	PLoS One	10.1371/journal.pone.0241338	2020
	Microbiota as a state-of-the-art approach in precision medicine for pancreatic cancer management: A comprehensive systematic review.	Hesami Z, Sabzehali F, Khorsand B, Alipour S, Sadeghi A, Asri N, Pazienza V, Houri H.	iScience	10.1016/j.isci.2025.112314	2025
	Modulation of Anti-Tumour Immune Responses by Probiotic Bacteria.	Aindelis G, Chlichlia K.	Vaccines (Basel)	10.3390/vaccines8020329	2020
Phylogeny	Composition of the Gut Microbiota Associated with the Response to Immunotherapy in Advanced Cancer Patients: A Chinese Real-World Pilot Study.	Cheng X, Wang J, Gong L, Dong Y, Shou J, Pan H, Yu Z, Fang Y.	J Clin Med	10.3390/jcm11185479	2022
Pathogenicity	Secoisolariciresinol diglucoside attenuates neuroinflammation and cognitive impairment in female Alzheimer's disease mice via modulating gut microbiota metabolism and GPER/CREB/BDNF pathway.	Jia M, Ning F, Wen J, Wang X, Chen J, Hu J, Chen X, Liu Z.	J Neuroinflammation	10.1186/s12974-024-03195-4	2024
	The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins.	Szczesniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D.	mBio	10.1128/mbio.00980-23	2023
Metabolism	Microbiome and pancreatic cancer: time to think about chemotherapy.	de Castilhos J, Tillmanns K, Blessing J, Larano A, Borisov V, Stein-Thoeringer CK.	Gut Microbes	10.1080/19490976.2024.2374596	2024
Phylogeny	Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota.	Bars-Cortina D, Ramon E, Rius-Sansalvador B, Guino E, Garcia-Serrano A, Mach N, Khannous-Lleiffe O, Saus E, Gabaldon T, Ibanez-Sanz G, Rodriguez-Alonso L, Mata A, Garcia-Rodriguez A, Obon-Santacana M, Moreno V.	BMC Genomics	10.1186/s12864-024-10621-7	2024
	Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers.	Liu Z, Hong LL, Ling ZQ.	Cancer Med	10.1002/cam4.6298	2023
Genetics	Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease.	Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, Vlamakis H, Sokol H, Xavier RJ.	Gastroenterology	10.1053/j.gastro.2020.08.045	2020
	Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.	Zakharevich NV, Morozov MD, Kanaeva VA, Filippov MS, Zyubko TI, Ivanov AB, Ulyantsev VI, Klimina KM, Olekhnovich EI.	Life Sci Alliance	10.26508/lsa.202302480	2024
	The Influence of Essential Oils on Gut Microbial Profiles in Pigs.	Ruzauskas M, Bartkiene E, Stankevicius A, Bernatoniene J, Zadeike D, Lele V, Starkute V, Zavistanaviciute P, Grigas J, Zokaityte E, Pautienius A, Juodeikiene G, Jakstas V.	Animals (Basel)	10.3390/ani10101734	2020
Genetics	Characteristics of the gut microbiome in esports players compared with those in physical education students and professional athletes.	Kulecka M, Fraczek B, Balabas A, Czarnowski P, Zeber-Lubecka N, Zapala B, Baginska K, Glowienka M, Szot M, Skorko M, Kluska A, Piatkowska M, Mikula M, Ostrowski J.	Front Nutr	10.3389/fnut.2022.1092846	2022
Phylogeny	Modulation of Gut Microbial Community and Metabolism by Dietary Glycyl-Glutamine Supplementation May Favor Weaning Transition in Piglets.	Yan Y, Xu B, Yin B, Xu X, Niu Y, Tang Y, Wang X, Xie C, Yang T, Zhou S, Yan X, Ma L.	Front Microbiol	10.3389/fmicb.2019.03125	2019
	Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.	West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ, Iwai S.	Sci Rep	10.1038/s41598-022-21327-9	2022
Metabolism	Fecal Metabolic Profiling of Breast Cancer Patients during Neoadjuvant Chemotherapy Reveals Potential Biomarkers.	Zidi O, Souai N, Raies H, Ben Ayed F, Mezlini A, Mezrioui S, Tranchida F, Sabatier JM, Mosbah A, Cherif A, Shintu L, Kouidhi S.	Molecules	10.3390/molecules26082266	2021
	Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model.	Kundra P, Geirnaert A, Pugin B, Morales Martinez P, Lacroix C, Greppi A.	Front Nutr	10.3389/fnut.2022.1070155	2022
	Comprehensive Analysis Reveals Novel Interactions between Circulating MicroRNAs and Gut Microbiota Composition in Human Obesity.	Assmann TS, Cuevas-Sierra A, Riezu-Boj JI, Milagro FI, Martinez JA.	Int J Mol Sci	10.3390/ijms21249509	2020
	Identification of the Crucial Role of CCL22 in F. nucleatum-Related Colorectal Tumorigenesis that Correlates With Tumor Microenvironment and Immune Checkpoint Therapy.	Wang H, Luo K, Guan Z, Li Z, Xiang J, Ou S, Tao Y, Ran S, Ye J, Ma T, Qiao T, Zhang Z, Jin Y, Song Y, Huang R.	Front Genet	10.3389/fgene.2022.811900	2022
	Bio-Fermented Malic Acid Facilitates the Production of High-Quality Chicken via Enhancing Muscle Antioxidant Capacity of Broilers.	Qiu K, He W, Zhang H, Wang J, Wang J, Qi G, Guo N, Zhang X, Wu S.	Antioxidants (Basel)	10.3390/antiox11122309	2022
Pathogenicity	Alcohol pretreatment of stools effect on culturomics.	Afouda P, Hocquart M, Pham TP, Kuete E, Ngom II, Dione N, Valles C, Bellali S, Lagier JC, Dubourg G, Raoult D.	Sci Rep	10.1038/s41598-020-62068-x	2020
	Changes in intestinal microbiota in postmenopausal oestrogen receptor-positive breast cancer patients treated with (neo)adjuvant chemotherapy.	Aarnoutse R, Ziemons J, Hillege LE, de Vos-Geelen J, de Boer M, Bisschop SMP, Vriens BEPJ, Vincent J, van de Wouw AJ, Le GN, Venema K, Rensen SS, Penders J, Smidt ML.	NPJ Breast Cancer	10.1038/s41523-022-00455-5	2022
	Synergistic activity of Enterococcus Faecium-induced ferroptosis via expansion of IFN-gamma⁺CD8⁺ T cell population in advanced hepatocellular carcinoma treated with sorafenib.	Yu H, Lin G, Jiang J, Yao J, Pan Z, Xie H, Bo Z, He Q, Yang J, Chen Z, Li J, Wang Y, Yu Z, Assaraf YG, Chen G.	Gut Microbes	10.1080/19490976.2024.2410474	2024
Genetics	Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy.	Olekhnovich EI, Ivanov AB, Babkina AA, Sokolov AA, Ulyantsev VI, Fedorov DE, Ilina EN.	mSystems	10.1128/msystems.01023-22	2023
	Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children.	Bonham KS, Fahur Bottino G, McCann SH, Beauchemin J, Weisse E, Barry F, Cano Lorente R, RESONANCE Consortium, Huttenhower C, Bruchhage M, D'Sa V, Deoni S, Klepac-Ceraj V.	Sci Adv	10.1126/sciadv.adi0497	2023
	Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis.	Guo M, Wu G, Tan Y, Li Y, Jin X, Qi W, Guo X, Zhang C, Zhu Z, Zhao L.	mBio	10.1128/mbio.03519-22	2023
Pathogenicity	Effects of Lactobacillus plantarum Q180 on Postprandial Lipid Levels and Intestinal Environment: A Double-Blind, Randomized, Placebo-Controlled, Parallel Trial.	Park YE, Kim MS, Shim KW, Kim YI, Chu J, Kim BK, Choi IS, Kim JY.	Nutrients	10.3390/nu12010255	2020
Genetics	Gut Microbiome Alterations in Patients With Thyroid Nodules.	Li A, Li T, Gao X, Yan H, Chen J, Huang M, Wang L, Yin D, Li H, Ma R, Zeng Q, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.643968	2021
	Exploring Gut Microbiota Imbalance in Irritable Bowel Syndrome: Potential Therapeutic Effects of Probiotics and Their Metabolites.	Garcia Mansilla MJ, Rodriguez Sojo MJ, Lista AR, Ayala Mosqueda CV, Ruiz Malagon AJ, Galvez J, Rodriguez Nogales A, Rodriguez Sanchez MJ.	Nutrients	10.3390/nu17010155	2024
	The Obesity-Related Gut Bacterial and Viral Dysbiosis Can Impact the Risk of Colon Cancer Development.	Campisciano G, de Manzini N, Delbue S, Cason C, Cosola D, Basile G, Ferrante P, Comar M, Palmisano S.	Microorganisms	10.3390/microorganisms8030431	2020
Phylogeny	Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers.	Yang Y, Li X, Cao Z, Qiao Y, Lin Q, Liu J, Zhao Z, An Q, Zhang C, Zhang H, Pan H.	Pol J Microbiol	10.33073/pjm-2021-001	2021
	Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.	Chen J, Siliceo SL, Ni Y, Nielsen HB, Xu A, Panagiotou G.	Microbiome	10.1186/s40168-023-01604-z	2023
	Alterations in co-abundant bacteriome in colorectal cancer and its persistence after surgery: a pilot study.	Png CW, Chua YK, Law JH, Zhang Y, Tan KK.	Sci Rep	10.1038/s41598-022-14203-z	2022
	Deep metagenomic characterization of gut microbial community and function in preeclampsia.	Lv LJ, Li SH, Wen JY, Wang GY, Li H, He TW, Lv QB, Xiao MC, Duan HL, Chen MC, Yi ZT, Yan QL, Yin AH.	Front Cell Infect Microbiol	10.3389/fcimb.2022.933523	2022
	Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities.	Pandey H, Tang DWT, Wong SH, Lal D.	Cancers (Basel)	10.3390/cancers15030866	2023
	The Effect of Antibiotics Treatment on the Maternal Immune Response and Gut Microbiome in Pregnant and Non-Pregnant Mice.	Faas MM, Liu Y, Wekema L, Weiss GA, van Loo-Bouwman CA, Silva Lagos L.	Nutrients	10.3390/nu15122723	2023
	Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape.	Grant ET, Parrish A, Boudaud M, Hunewald O, Hirayama A, Ollert M, Fukuda S, Desai MS.	Microbiome	10.1186/s40168-024-01898-7	2024
Metabolism	Bacterial extracellular vesicles affect endocrine therapy in MCF7 cells.	An J, Kim JB, Yang EY, Kim HO, Lee WH, Yang J, Kwon H, Paik NS, Lim W, Kim YK, Moon BI.	Medicine (Baltimore)	10.1097/md.0000000000025835	2021
	Potential links between the microbiota and T cell immunity determine the tumor cell fate.	Mohseni AH, Taghinezhad-S S, Casolaro V, Lv Z, Li D.	Cell Death Dis	10.1038/s41419-023-05560-2	2023
	A Method for Isolation and Proteomic Analysis of Outer Membrane Vesicles from Fecal Samples by LC-MS/MS.	Wu J, An M, Zhu J, Tan Z, Chen GY, Stidham RW, Lubman DM.	J Proteomics Bioinform	10.4172/0974-276x.1000494	2019
	Conversion of unresponsiveness to immune checkpoint inhibition by fecal microbiota transplantation in patients with metastatic melanoma: study protocol for a randomized phase Ib/IIa trial.	Borgers JSW, Burgers FH, Terveer EM, van Leerdam ME, Korse CM, Kessels R, Flohil CC, Blank CU, Schumacher TN, van Dijk M, Henderickx JGE, Keller JJ, Verspaget HW, Kuijper EJ, Haanen JBAG.	BMC Cancer	10.1186/s12885-022-10457-y	2022
	Gut microbiota and their influence in brain cancer milieu.	BharathwajChetty B, Kumar A, Deevi P, Abbas M, Alqahtani A, Liang L, Sethi G, Liu L, Kunnumakkara AB.	J Neuroinflammation	10.1186/s12974-025-03434-2	2025
	Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats.	Utami NW, Sone T, Tanaka M, Nakatsu CH, Saito A, Asano K.	Biosci Microbiota Food Health	10.12938/bmfh.32.167	2013
	Gut Microbiome: A Promising Biomarker for Immunotherapy in Colorectal Cancer.	Temraz S, Nassar F, Nasr R, Charafeddine M, Mukherji D, Shamseddine A.	Int J Mol Sci	10.3390/ijms20174155	2019
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
	Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth.	Testerman T, Li Z, Galuppo B, Graf J, Santoro N.	Hepatol Commun	10.1002/hep4.1944	2022
Pathogenicity	Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation.	Draper LA, Ryan FJ, Dalmasso M, Casey PG, McCann A, Velayudhan V, Ross RP, Hill C.	BMC Biol	10.1186/s12915-020-00906-0	2020
	Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study.	Traversi D, Rabbone I, Scaioli G, Vallini C, Carletto G, Racca I, Ala U, Durazzo M, Collo A, Ferro A, Carrera D, Savastio S, Cadario F, Siliquini R, Cerutti F.	Sci Rep	10.1038/s41598-020-74678-6	2020
	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
	Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.	Ishaq HM, Mohammad IS, Hussain R, Parveen R, Shirazi JH, Fan Y, Shahzad M, Hayat K, Li H, Ihsan A, Muhammad KS, Usman M, Zhang S, Yuan L, Ullah S, Paiva-Santos AC, Xu J.	J Cancer	10.7150/jca.66816	2022
	Host metabolome and faecal microbiome shows potential interactions impacted by age and weaning times in calves.	Amin N, Schwarzkopf S, Troscher-Mussotter J, Camarinha-Silva A, Danicke S, Huber K, Frahm J, Seifert J.	Anim Microbiome	10.1186/s42523-023-00233-z	2023
	Proof of Concept of Culturomics Use of Time of Care.	Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D.	Front Cell Infect Microbiol	10.3389/fcimb.2020.524769	2020
	Microbiota Induced Changes in the Immune Response in Pregnant Mice.	Faas MM, Liu Y, Borghuis T, van Loo-Bouwman CA, Harmsen H, de Vos P.	Front Immunol	10.3389/fimmu.2019.02976	2019
	The gut dysbiosis-cancer axis: illuminating novel insights and implications for clinical practice.	Asseri AH, Bakhsh T, Abuzahrah SS, Ali S, Rather IA.	Front Pharmacol	10.3389/fphar.2023.1208044	2023
Metabolism	Intestinal inflammation alters mucosal carbohydrate foraging and monosaccharide incorporation into microbial glycans.	Weiss GA, Grabinger T, Glaus Garzon J, Hasler T, Greppi A, Lacroix C, Khanzhin N, Hennet T.	Cell Microbiol	10.1111/cmi.13269	2021
	Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial.	Zhang X, Ren H, Zhao C, Shi Z, Qiu L, Yang F, Zhou X, Han X, Wu K, Zhong H, Li Y, Li J, Ji L.	Diabetologia	10.1007/s00125-022-05768-5	2022
	Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients.	Marfil-Sanchez A, Seelbinder B, Ni Y, Varga J, Berta J, Hollosi V, Dome B, Megyesfalvi Z, Dulka E, Galffy G, Weiss GJ, Panagiotou G, Lohinai Z.	PLoS One	10.1371/journal.pone.0259898	2021
	Phage-encoded carbohydrate-interacting proteins in the human gut.	Rothschild-Rodriguez D, Hedges M, Kaplan M, Karav S, Nobrega FL.	Front Microbiol	10.3389/fmicb.2022.1083208	2022
Phylogeny	Bacterial rose garden for metagenomic SNP-based phylogeny visualization.	Alexeev D, Bibikova T, Kovarsky B, Melnikov D, Tyakht A, Govorun V.	BioData Min	10.1186/s13040-015-0045-5	2015
Metabolism	Neutrophil Extracellular Traps Promote the Development and Growth of Human Salivary Stones.	Schapher M, Koch M, Weidner D, Scholz M, Wirtz S, Mahajan A, Herrmann I, Singh J, Knopf J, Leppkes M, Schauer C, Gruneboom A, Alexiou C, Schett G, Iro H, Munoz LE, Herrmann M.	Cells	10.3390/cells9092139	2020
Genetics	Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.	Pudlo NA, Urs K, Crawford R, Pirani A, Atherly T, Jimenez R, Terrapon N, Henrissat B, Peterson D, Ziemer C, Snitkin E, Martens EC.	mSystems	10.1128/msystems.00947-21	2022
Genetics	Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model.	Ghimire S, Wongkuna S, Sankaranarayanan R, Ryan EP, Bhat GJ, Scaria J.	Front Microbiol	10.3389/fmicb.2021.751225	2021
	Oral and gut dysbiosis leads to functional alterations in Parkinson's disease.	Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW, Chung SJ.	NPJ Parkinsons Dis	10.1038/s41531-022-00351-6	2022
Metabolism	Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma.	Ianiro G, Rossi E, Thomas AM, Schinzari G, Masucci L, Quaranta G, Settanni CR, Lopetuso LR, Armanini F, Blanco-Miguez A, Asnicar F, Consolandi C, Iacovelli R, Sanguinetti M, Tortora G, Gasbarrini A, Gasbarrini A, Segata N, Cammarota G.	Nat Commun	10.1038/s41467-020-18127-y	2020
Pathogenicity	Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV.	Zhang Y, Andreu-Sanchez S, Vadaq N, Wang D, Matzaraki V, van der Heijden WA, Gacesa R, Weersma RK, Zhernakova A, Vandekerckhove L, de Mast Q, Joosten LAB, Netea MG, van der Ven AJAM, Fu J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1202035	2023
	Cell-Free Supernatant of Odoribacter splanchnicus Isolated From Human Feces Exhibits Anti-colorectal Cancer Activity.	Oh BS, Choi WJ, Kim JS, Ryu SW, Yu SY, Lee JS, Park SH, Kang SW, Lee J, Jung WY, Kim YM, Jeong JH, Lee JH.	Front Microbiol	10.3389/fmicb.2021.736343	2021
	mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.	Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G.	Nat Methods	10.1038/s41592-023-02125-1	2024
	Gut Microbiota Dysbiosis and Altered Bile Acid Catabolism Lead to Metabolic Disorder in Psoriasis Mice.	Hao Y, Zhou P, Zhu YJ, Zou S, Zhao Q, Yu J, Hu Y, Li J.	Front Microbiol	10.3389/fmicb.2022.853566	2022
Pathogenicity	N-(1-carbamoyl-2-phenylethyl) butyramide reduces antibiotic-induced intestinal injury, innate immune activation and modulates microbiota composition.	Lama A, Annunziata C, Coretti L, Pirozzi C, Di Guida F, Nitrato Izzo A, Cristiano C, Mollica MP, Chiariotti L, Pelagalli A, Lembo F, Meli R, Mattace Raso G.	Sci Rep	10.1038/s41598-019-41295-x	2019
	Crosstalk between the gut microbiota and innate lymphoid cells in intestinal mucosal immunity.	Guo Y, Liu Y, Rui B, Lei Z, Ning X, Liu Y, Li M.	Front Immunol	10.3389/fimmu.2023.1171680	2023
Pathogenicity	Gut Dysbiosis in Ocular Mucous Membrane Pemphigoid.	Low L, Suleiman K, Shamdas M, Bassilious K, Poonit N, Rossiter AE, Acharjee A, Loman N, Murray PI, Wallace GR, Rauz S.	Front Cell Infect Microbiol	10.3389/fcimb.2022.780354	2022
	Rumen Microbiome and Metabolome of Tibetan Sheep (Ovis aries) Reflect Animal Age and Nutritional Requirement.	Li H, Yu Q, Li T, Shao L, Su M, Zhou H, Qu J.	Front Vet Sci	10.3389/fvets.2020.00609	2020
Metabolism	IMPARO: inferring microbial interactions through parameter optimisation.	Vidanaarachchi R, Shaw M, Tang SL, Halgamuge S.	BMC Mol Cell Biol	10.1186/s12860-020-00269-y	2020
Enzymology	Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.	Kwak S, Choi J, Hink T, Reske KA, Blount K, Jones C, Bost MH, Sun X, Burnham CD, Dubberke ER, Dantas G, CDC Prevention Epicenter Program.	Microbiome	10.1186/s40168-020-00907-9	2020
	Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis.	Gomez-Perez AM, Ruiz-Limon P, Salas-Salvado J, Vioque J, Corella D, Fito M, Vidal J, Atzeni A, Torres-Collado L, Alvarez-Sala A, Martinez MA, Goday A, Benaiges D, Garcia-Gavilan J, Bernal Lopez MR, Moreno-Indias I, Tinahones FJ.	Gut Microbes	10.1080/19490976.2023.2223339	2023
Proteome	Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS.	Wu J, Zhu J, Yin H, Liu X, An M, Pudlo NA, Martens EC, Chen GY, Lubman DM.	J Proteome Res	10.1021/acs.jproteome.6b00450	2016
Metabolism	Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome.	Steimle A, Neumann M, Grant ET, Turner JD, Desai MS.	Int J Mol Sci	10.3390/ijms22136855	2021
	Investigation of Immunomodulatory and Gut Microbiota-Altering Properties of Multicomponent Nutraceutical Prepared from Lactic Acid Bacteria, Bovine Colostrum, Apple Production By-Products and Essential Oils.	Grigas J, Ruzauskas M, Pautienius A, Bartkiene E, Lele V, Starkute V, Zavistanaviciute P, Zokaityte E, Bernatoniene J, Ivanauskas L, Jakstas V, Stankevicius A.	Foods	10.3390/foods10061313	2021
Pathogenicity	Oral Supplements of Combined Bacillus licheniformis Zhengchangsheng® and Xylooligosaccharides Improve High-Fat Diet-Induced Obesity and Modulate the Gut Microbiota in Rats.	Li Y, Liu M, Liu H, Wei X, Su X, Li M, Yuan J.	Biomed Res Int	10.1155/2020/9067821	2020
	Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy.	Li W, Deng X, Chen T.	Front Oncol	10.3389/fonc.2021.644454	2021
Pathogenicity	The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals.	Singh P, Rawat A, Alwakeel M, Sharif E, Al Khodor S.	Sci Rep	10.1038/s41598-020-77806-4	2020
	Monitoring and Modulating Diet and Gut Microbes to Enhance Response and Reduce Toxicity to Cancer Treatment.	Knisely A, Seo YD, Wargo JA, Chelvanambi M.	Cancers (Basel)	10.3390/cancers15030777	2023
	Biomarkers of response to PD-1 pathway blockade.	Li H, van der Merwe PA, Sivakumar S.	Br J Cancer	10.1038/s41416-022-01743-4	2022
	Microbiome in Cancer Development and Treatment.	Ciernikova S, Sevcikova A, Mladosievicova B, Mego M.	Microorganisms	10.3390/microorganisms12010024	2023
	Intestinal microbiota: a novel perspective in colorectal cancer biotherapeutics.	Ding C, Tang W, Fan X, Wu G.	Onco Targets Ther	10.2147/ott.s170626	2018
Metabolism	Metabolic Fate and Distribution of 2´-Fucosyllactose: Direct Influence on Gut Microbial Activity but not on Brain.	Kuntz S, Kunz C, Borsch C, Vazquez E, Buck R, Reutzel M, Eckert GP, Rudloff S.	Mol Nutr Food Res	10.1002/mnfr.201900035	2019
	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
	Discovery of bioactive microbial gene products in inflammatory bowel disease.	Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA.	Nature	10.1038/s41586-022-04648-7	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
Genetics	Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men.	Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT.	Genome Med	10.1186/s13073-021-00921-y	2021
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
	The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer.	Parida S, Sharma D.	Biochim Biophys Acta Rev Cancer	10.1016/j.bbcan.2019.04.001	2019
	An online atlas of human plasma metabolite signatures of gut microbiome composition.	Dekkers KF, Sayols-Baixeras S, Baldanzi G, Nowak C, Hammar U, Nguyen D, Varotsis G, Brunkwall L, Nielsen N, Eklund AC, Bak Holm J, Nielsen HB, Ottosson F, Lin YT, Ahmad S, Lind L, Sundstrom J, Engstrom G, Smith JG, Arnlov J, Orho-Melander M, Fall T.	Nat Commun	10.1038/s41467-022-33050-0	2022
	The Oral-Gut Axis: Periodontal Diseases and Gastrointestinal Disorders.	Lam GA, Albarrak H, McColl CJ, Pizarro A, Sanaka H, Gomez-Nguyen A, Cominelli F, Paes Batista da Silva A.	Inflamm Bowel Dis	10.1093/ibd/izac241	2023
	Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice.	Parrish A, Boudaud M, Grant ET, Willieme S, Neumann M, Wolter M, Craig SZ, De Sciscio A, Cosma A, Hunewald O, Ollert M, Desai MS.	Nat Microbiol	10.1038/s41564-023-01464-1	2023
	The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease.	Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, Voskuil MD, Fu J, Wijmenga C, Zhernakova A, Weersma RK, Vich Vila A.	J Crohns Colitis	10.1093/ecco-jcc/jjab020	2021
	The intestinal and biliary microbiome in autoimmune liver disease-current evidence and concepts.	Liwinski T, Heinemann M, Schramm C.	Semin Immunopathol	10.1007/s00281-022-00936-6	2022
	Short-chain fatty acids promote the effect of environmental signals on the gut microbiome and metabolome in mice.	Marrocco F, Delli Carpini M, Garofalo S, Giampaoli O, De Felice E, Di Castro MA, Maggi L, Scavizzi F, Raspa M, Marini F, Tomassini A, Nicolosi R, Cason C, Trettel F, Miccheli A, Iebba V, D'Alessandro G, Limatola C.	Commun Biol	10.1038/s42003-022-03468-9	2022
	Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.	Mirhakkak MH, Schauble S, Klassert TE, Brunke S, Brandt P, Loos D, Uribe RV, Senne de Oliveira Lino F, Ni Y, Vylkova S, Slevogt H, Hube B, Weiss GJ, Sommer MOA, Panagiotou G.	ISME J	10.1038/s41396-020-00848-z	2021
Genetics	An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community.	Koo H, McFarland BC, Hakim JA, Crossman DK, Crowley MR, Rodriguez JM, Benveniste EN, Morrow CD.	R Soc Open Sci	10.1098/rsos.192200	2020
Transcriptome	Mechanism of the Immunomodulatory Effect of the Combination of Live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus on Immunocompromised Rats.	Lv L, Mu D, Du Y, Yan R, Jiang H.	Front Immunol	10.3389/fimmu.2021.694344	2021
	A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors.	Dohlman AB, Klug J, Mesko M, Gao IH, Lipkin SM, Shen X, Iliev ID.	Cell	10.1016/j.cell.2022.09.015	2022
	The Cross-Talk Between Gut Microbiota and Lungs in Common Lung Diseases.	Zhang D, Li S, Wang N, Tan HY, Zhang Z, Feng Y.	Front Microbiol	10.3389/fmicb.2020.00301	2020
	Dietary multi-enzyme complex improves In Vitro nutrient digestibility and hind gut microbial fermentation of pigs.	Recharla N, Kim D, Ramani S, Song M, Park J, Balasubramanian B, Puligundla P, Park S.	PLoS One	10.1371/journal.pone.0217459	2019
Pathogenicity	Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.	Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC.	BMC Genomics	10.1186/s12864-016-2777-0	2016
	Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity.	Wilson BC, Vatanen T, Jayasinghe TN, Leong KSW, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Holland DJ, Cutfield WS, O'Sullivan JM.	Microbiome	10.1186/s40168-021-01060-7	2021
Phylogeny	16S rDNA Full-Length Assembly Sequencing Technology Analysis of Intestinal Microbiome in Polycystic Ovary Syndrome.	Dong S, Jiao J, Jia S, Li G, Zhang W, Yang K, Wang Z, Liu C, Li D, Wang X.	Front Cell Infect Microbiol	10.3389/fcimb.2021.634981	2021
	Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction.	Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N.	Cell Rep	10.1016/j.celrep.2022.111093	2022
	Intestinal Microbiota in Colorectal Cancer Surgery.	Koliarakis I, Athanasakis E, Sgantzos M, Mariolis-Sapsakos T, Xynos E, Chrysos E, Souglakos J, Tsiaoussis J.	Cancers (Basel)	10.3390/cancers12103011	2020
	The Gut Microbiota: A Potential Gateway to Improved Health Outcomes in Breast Cancer Treatment and Survivorship.	Sampsell K, Hao D, Reimer RA.	Int J Mol Sci	10.3390/ijms21239239	2020
Phylogeny	Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy.	Shiao SL, Kershaw KM, Limon JJ, You S, Yoon J, Ko EY, Guarnerio J, Potdar AA, McGovern DPB, Bose S, Dar TB, Noe P, Lee J, Kubota Y, Maymi VI, Davis MJ, Henson RM, Choi RY, Yang W, Tang J, Gargus M, Prince AD, Zumsteg ZS, Underhill DM.	Cancer Cell	10.1016/j.ccell.2021.07.002	2021
Pathogenicity	Role of the Microbiota in Lung Cancer: Insights on Prevention and Treatment.	Pizzo F, Maroccia Z, Hammarberg Ferri I, Fiorentini C.	Int J Mol Sci	10.3390/ijms23116138	2022
	Bioinorganic hybrid bacteriophage for modulation of intestinal microbiota to remodel tumor-immune microenvironment against colorectal cancer.	Dong X, Pan P, Zheng DW, Bao P, Zeng X, Zhang XZ.	Sci Adv	10.1126/sciadv.aba1590	2020
	Beyond the Gut: The intratumoral microbiome's influence on tumorigenesis and treatment response.	Zhang H, Fu L, Leiliang X, Qu C, Wu W, Wen R, Huang N, He Q, Cheng Q, Liu G, Cheng Y.	Cancer Commun (Lond)	10.1002/cac2.12597	2024
	Microbes as Medicines: Harnessing the Power of Bacteria in Advancing Cancer Treatment.	Sawant SS, Patil SM, Gupta V, Kunda NK.	Int J Mol Sci	10.3390/ijms21207575	2020
	Responses of Intestinal Mucosal Barrier Functions of Rats to Simulated Weightlessness.	Jin M, Zhang H, Zhao K, Xu C, Shao D, Huang Q, Shi J, Yang H.	Front Physiol	10.3389/fphys.2018.00729	2018
Pathogenicity	Whole Blueberry and Isolated Polyphenol-Rich Fractions Modulate Specific Gut Microbes in an In Vitro Colon Model and in a Pilot Study in Human Consumers.	Ntemiri A, Ghosh TS, Gheller ME, Tran TTT, Blum JE, Pellanda P, Vlckova K, Neto MC, Howell A, Thalacker-Mercer A, O'Toole PW.	Nutrients	10.3390/nu12092800	2020
	The gut microbiota and colorectal surgery outcomes: facts or hype? A narrative review.	Agnes A, Puccioni C, D'Ugo D, Gasbarrini A, Gasbarrini A, Biondi A, Persiani R.	BMC Surg	10.1186/s12893-021-01087-5	2021
	Gut microbiota modulation: a novel strategy for prevention and treatment of colorectal cancer.	Fong W, Li Q, Yu J.	Oncogene	10.1038/s41388-020-1341-1	2020
Metabolism	Using Tn-seq To Identify Pigmentation-Related Genes of Porphyromonas gingivalis: Characterization of the Role of a Putative Glycosyltransferase.	Klein BA, Cornacchione LP, Collins M, Malamy MH, Duncan MJ, Hu LT.	J Bacteriol	10.1128/jb.00832-16	2017
	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
	Gastrointestinal cancers: the role of microbiota in carcinogenesis and the role of probiotics and microbiota in anti-cancer therapy efficacy.	Kazmierczak-Siedlecka K, Ruszkowski J, Skonieczna-Zydecka K, Jedrzejczak J, Folwarski M, Makarewicz W.	Cent Eur J Immunol	10.5114/ceji.2020.103353	2020
Genetics	Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.	Barone M, Garelli S, Rampelli S, Agostini A, Matysik S, D'Amico F, Krautbauer S, Mazza R, Salituro N, Fanelli F, Iozzo P, Sanz Y, Candela M, Brigidi P, Pagotto U, Turroni S.	BMC Med	10.1186/s12916-022-02689-3	2022
	Toward an improved definition of a healthy microbiome for healthy aging.	Ghosh TS, Shanahan F, O'Toole PW.	Nat Aging	10.1038/s43587-022-00306-9	2022
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	Prebiotic-Induced Anti-tumor Immunity Attenuates Tumor Growth.	Li Y, Elmen L, Segota I, Xian Y, Tinoco R, Feng Y, Fujita Y, Segura Munoz RR, Schmaltz R, Bradley LM, Ramer-Tait A, Zarecki R, Long T, Peterson SN, Ronai ZA.	Cell Rep	10.1016/j.celrep.2020.01.035	2020
	Gut dysbiosis contributes to amyloid pathology, associated with C/EBPbeta/AEP signaling activation in Alzheimer's disease mouse model.	Chen C, Ahn EH, Kang SS, Liu X, Alam A, Ye K.	Sci Adv	10.1126/sciadv.aba0466	2020
	Interactions between gut microbiota and skeletal muscle.	Gizard F, Fernandez A, De Vadder F.	Nutr Metab Insights	10.1177/1178638820980490	2020
	Multifaceted modes of action of the anticancer probiotic Enterococcus hirae.	Goubet AG, Wheeler R, Fluckiger A, Qu B, Lemaitre F, Iribarren K, Mondragon L, Tidjani Alou M, Pizzato E, Durand S, Derosa L, Aprahamian F, Bossut N, Moya-Nilges M, Derrien D, Chen G, Leduc M, Joseph A, Pons N, Le Chatelier E, Segata N, Yonekura S, Iebba V, Kepp O, Raoult D, Andre F, Kroemer G, Boneca IG, Zitvogel L, Daillere R.	Cell Death Differ	10.1038/s41418-021-00753-8	2021
	A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis.	Fouhy F, Ronan NJ, O'Sullivan O, McCarthy Y, Walsh AM, Murphy DM, Daly M, Flanagan ET, Fleming C, McCarthy M, Shortt C, Eustace JA, Shanahan F, Rea MC, Ross RP, Stanton C, Plant BJ.	Sci Rep	10.1038/s41598-017-06880-y	2017
	Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD.	Gut Pathog	10.1186/1757-4749-5-8	2013
Enzymology	Succinivibrionaceae is dominant family in fecal microbiota of Behçet's Syndrome patients with uveitis.	Tecer D, Gogus F, Kalkanci A, Erdogan M, Hasanreisoglu M, Ergin C, Karakan T, Kozan R, Coban S, Diker KS.	PLoS One	10.1371/journal.pone.0241691	2020
	Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark.	Pinna NK, Anjana RM, Saxena S, Dutta A, Gnanaprakash V, Rameshkumar G, Aswath S, Raghavan S, Rani CSS, Radha V, Balasubramanyam M, Pant A, Nielsen T, Jorgensen T, Faerch K, Kashani A, Silva MCA, Vestergaard H, Hansen TH, Hansen T, Arumugam M, Nair GB, Das B, Pedersen O, Mohan V, Mande SS.	Genome Med	10.1186/s13073-021-00851-9	2021
Phylogeny	Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.	Lagkouvardos I, Lesker TR, Hitch TCA, Galvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T.	Microbiome	10.1186/s40168-019-0637-2	2019
	Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.	Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T.	ISME Commun	10.1038/s43705-021-00017-z	2021
Genetics	Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible 0401 mice but not arthritis-resistant 0402 mice.	Gomez A, Luckey D, Yeoman CJ, Marietta EV, Berg Miller ME, Murray JA, White BA, Taneja V.	PLoS One	10.1371/journal.pone.0036095	2012
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
	Big Data Approaches for Modeling Response and Resistance to Cancer Drugs.	Jiang P, Sellers WR, Liu XS.	Annu Rev Biomed Data Sci	10.1146/annurev-biodatasci-080917-013350	2018
Metabolism	Microbiome-Microbial Metabolome-Cancer Cell Interactions in Breast Cancer-Familiar, but Unexplored.	Miko E, Kovacs T, Sebo E, Toth J, Csonka T, Ujlaki G, Sipos A, Szabo J, Mehes G, Bai P.	Cells	10.3390/cells8040293	2019
Pathogenicity	Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome.	Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G.	Nat Microbiol	10.1038/s41564-019-0550-2	2019
	Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified.	De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R.	PLoS One	10.1371/journal.pone.0076993	2013
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
Metabolism	NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth.	Chen L, Wilson JE, Koenigsknecht MJ, Chou WC, Montgomery SA, Truax AD, Brickey WJ, Packey CD, Maharshak N, Matsushima GK, Plevy SE, Young VB, Sartor RB, Ting JP.	Nat Immunol	10.1038/ni.3690	2017
	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
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
	Microbial markers in colorectal cancer detection and/or prognosis.	Villeger R, Lopes A, Veziant J, Gagniere J, Barnich N, Billard E, Boucher D, Bonnet M.	World J Gastroenterol	10.3748/wjg.v24.i22.2327	2018
Genetics	Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides.	Ravcheev DA, Thiele I.	Front Genet	10.3389/fgene.2017.00111	2017
Metabolism	Gut microbiota functions: metabolism of nutrients and other food components.	Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K.	Eur J Nutr	10.1007/s00394-017-1445-8	2018
Pathogenicity	Adjusting for age improves identification of gut microbiome alterations in multiple diseases.	Ghosh TS, Das M, Jeffery IB, O'Toole PW.	Elife	10.7554/elife.50240	2020
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
Phylogeny	Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces.	Shkoporov AN, Khokhlova EV, Chaplin AV, Kafarskaia LI, Nikolin AA, Polyakov VY, Shcherbakova VA, Chernaia ZA, Efimov BA.	Int J Syst Evol Microbiol	10.1099/ijs.0.052126-0	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
Phylogeny	Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces.	Morotomi M, Nagai F, Sakon H, Tanaka R	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000810-0	2008

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#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#31196	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 #27523 (see below)
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Barnesiella intestinihominis (DSM 21032, JCM 15079, YIT 11860)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000296465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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