Parabacteroides goldsteinii (DSM 19448, ATCC BAA-1180, CCUG 48944)

Name: Parabacteroides goldsteinii (DSM 19448, ATCC BAA-1180, CCUG 48944)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12500

Type strain

Culture col. no. DSM 19448 ATCC BAA-1180 CCUG 48944 JCM 13446 KCTC 15612 1 more

NCBI tax ID(s) 927665 328812

Special Collections DSMZ CCUG JCM KCTC

History DSMZ <- JCM; JCM 13446 <- CCUG; CCUG 48944 <- Y. Song; WAL 12034 JCM <-- CCUG 48944 <-- Y. Song WAL 12034. KCTC <- DSM <- JCM <- CCUG <- Y Song, WAL 12034

Links

Parabacteroides goldsteinii DSM 19448 is an anaerobe, rod-shaped bacterium that was isolated from human tissue.

rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 290961

KCTC 15612,CCUG 48944,JCM 13446,ATCC BAA-1180,DSM 19448

@ref 20215

Last LPSN update 2026-05-29 08:27:49

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Tannerellaceae

Genus Parabacteroides

Species Parabacteroides goldsteinii

Full scientific name Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006

Synonyms (1)

Bacteroides goldsteinii

BacDive ID	Other strains from **Parabacteroides goldsteinii** (3)	Type strain
131147	P. goldsteinii BS-C3-2, DSM 29187
156627	P. goldsteinii CCUG 63736
169570	P. goldsteinii Cla-AP-3, DSM 111136

Morphology

Cell morphology

@ref	Gram stain	Confidence	Cell shape
67771			rod-shaped
67771	negative
125439	negative	90.529

Colony morphology

58398

Incubation period1 day

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8022	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8022	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)		Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8022	positive	growth	37
58398	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8022	anaerobe
58398	anaerobe
67771	anaerobe
125439	facultative anaerobe	92.25

Spore formation

@ref	Spore formation	Confidence
125439		96.741
125438		91.792

Observation

@ref	Observation
67770	quinones: MK-9, MK-10
67771	quinones: MK-9, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	gelatinase	-		from API 20A
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	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
8022	-	-	+	-	+	+	+	-	+	-	-	+	-	-	+	+/-	+	-	+	+	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
8022	-	-	+	+	-	+/-	+/-	-	-	+	+	+	+	-	-	-	+	+	-	+	+	+	-	+	+	+	+	+	+/-
8022	-	-	+	+	-	+	+	-	-	+	+	+	-	-	-	-	+	+	-	+	+	+	-	+	+	+/-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Other	-
#Infection	#Patient	#Specimen

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
8022	human tissue	Homo sapiens			USA	USA	North America
58398	Human abdominal fluid	Homo sapiens	1984	Los Angeles	USA	USA	North America
67770	Human clinical specimens of intestinal origin	Homo sapiens
67771	From human clinical specimens of intestinal origin(human tissue)	Homo sapiens			USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AY974070 (>99% sequence identity) for Parabacteroides goldsteinii subclade from Microbeatlas

Aquatic Samples	3273
Soil Samples	1445
Animal Samples	136228
Plant Samples	557
Total Samples	141503

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8022	2	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	Para_gold_DSM_19448_V1 assembly for Parabacteroides goldsteinii DSM 19448 = WAL 12034	scaffold	GCA_000969835	927665.4	2619619296	927665	71.15
66792	82E8 assembly for Parabacteroides goldsteinii DSM 19448 = WAL 12034	contig	GCA_900624825	927665.28		927665	59.67
67770	81H9 assembly for Parabacteroides goldsteinii DSM 19448 = WAL 12034	contig	GCA_900624735	927665.27		927665	51.91

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Parabacteroides goldsteinii gene for 16S ribosomal RNA, partial sequence, strain: JCM 13446	AB547650	1476	927665
8022	Parabacteroides goldsteinii strain JCM13446 16S ribosomal RNA gene, partial sequence	EU136697	2002	927665
67770	Parabacteroides goldsteinii strain WAL 12034 16S ribosomal RNA gene, partial sequence	AY974070	1396	328812

GC content

@ref	GC-content (mol%)	Method
8022	43
67770	43	high performance liquid chromatography (HPLC)
67771	43.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Para_gold_DSM_19448_V1 assembly for Parabacteroides goldsteinii DSM 19448 = WAL 12034
BV-BRC: 927665.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.25	no
125439	gram_stain	BacteriaNetⓘ	negative	90.53	no
125439	spore_formation	BacteriaNetⓘ	no	96.74	no
125439	motility	BacteriaNetⓘ	no	73.34	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parabacteroides goldsteinii DSM 19448 = WAL 12034
PATRIC: 927665.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	89.31	no
125438	anaerobic	anaerobicⓘ	yes	86.74	yes
125438	aerobic	aerobicⓘ	no	93.27	yes
125438	spore-forming	spore-formingⓘ	no	91.79	no
125438	thermophilic	thermophileⓘ	no	94.61	yes
125438	flagellated	motile2+ⓘ	no	88.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Investigation of ED4 supplementation on cardiovascular parameters in rats with elevated systemic TMAO.	Qiu YT, Huang PH, Chen YW, Shih MK, Lee BH, Sun PP, Hou CY, Chen SY.	NPJ Sci Food	10.1038/s41538-025-00552-2	2025
	Influence of Symbiotic Fermentation Broth on Regulating Metabolism with Gut Microbiota and Metabolite Profiles Is Estimated Using a Third-Generation Sequencing Platform.	Wu CY, Huang CK, Hong WS, Liu YH, Shih MC, Lin JC.	Metabolites	10.3390/metabo13090999	2023
	Draft Genome Sequence of Parabacteroides goldsteinii with Putative Novel Metallo-beta-Lactamases Isolated from a Blood Culture from a Human Patient.	Krogh TJ, Agergaard CN, Moller-Jensen J, Justesen US.	Genome Announc	10.1128/genomea.00937-15	2015
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
	Hirsutella sinensis polysaccharides and Parabacteroides goldsteinii reduce lupus severity in imiquimod-treated mice.	Chang SH, Ko YF, Liau JC, Wu CY, Hwang TL, Ojcius DM, Young JD, Martel J.	Biomed J	10.1016/j.bj.2024.100754	2025
	Characterization and Safety Evaluation of Autoclaved Gut Commensal Parabacteroides goldsteinii RV-01.	Lin TL, Chen WJ, Hung CM, Wong YL, Lu CC, Lai HC.	Int J Mol Sci	10.3390/ijms252312660	2024
	The Role of Next-Generation Probiotics in Obesity and Obesity-Associated Disorders: Current Knowledge and Future Perspectives.	Vallianou NG, Kounatidis D, Tsilingiris D, Panagopoulos F, Christodoulatos GS, Evangelopoulos A, Karampela I, Dalamaga M.	Int J Mol Sci	10.3390/ijms24076755	2023
	Gut Microbiota Contributes to Spontaneous Colitis in E3 Ligase Itch-Deficient Mice.	Kathania M, Tsakem EL, Theiss AL, Venuprasad K.	J Immunol	10.4049/jimmunol.1701478	2020
	Therapeutic potential of the gut commensal bacterium Parabacteroides goldsteinii in human health and disease treatment.	Li Z, Zhang L, Wan Z, Liu H, Zhang T, Li Y.	Front Microbiol	10.3389/fmicb.2025.1618892	2025
	Interaction Between Microbiota and Immunity: Molecular Mechanisms, Biological Functions, Diseases, and New Therapeutic Opportunities.	Zeng J, He Z, Wang G, Ma Y, Zhang F.	MedComm (2020)	10.1002/mco2.70265	2025
	Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies.	Lopez-Moreno A, Acuna I, Torres-Sanchez A, Ruiz-Moreno A, Cerk K, Rivas A, Suarez A, Monteoliva-Sanchez M, Aguilera M.	Nutrients	10.3390/nu13051617	2021
	Unraveling the Obesity-Combating Potential of Parabacteroides goldsteinii and Bacteroides sartorii: A Dual-Probiotic Approach.	Wu Y, Liu Z, Zhang H, Zhou L, Liang W, Su P, Zeng Z, Zhao F, Qiu J, Chen C.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10537-y	2025
	Multi-omics analysis of outer membrane vesicles from P. goldsteinii in a psoriasis mouse model.	Du A, Chen J, Xie Z, Yang Y, Chen CB, Lu CW, Liu CC, Chen M, Chung WH, Lin C, Ke R, Chang CJ.	Life Sci	10.1016/j.lfs.2025.123776	2025
	Gut Microbiome Interventions: From Dysbiosis to Next-Generation Probiotics (NGPs) for Disease Management.	Gupta MK, Srivastava R.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10582-7	2025
	Gut commensal bacteria Parabacteroides goldsteinii-derived outer membrane vesicles suppress skin inflammation in psoriasis.	Su D, Li M, Xie Y, Xu Z, Lv G, Jiu Y, Lin J, Chang CJ, Chen H, Cheng F.	J Control Release	10.1016/j.jconrel.2024.11.014	2025
Enzymology	Associations between the gut microbiota and the metabolism rate of tacrolimus in kidney transplant recipients during the early posttransplant period.	Dukaew N, Noppakun K, Thongkumkoon P, Na Takuathung M, Inpan R, Kongta N, Suyayai N, Manoree C, Koonrungsesomboon N.	Arch Pharm Res	10.1007/s12272-025-01549-x	2025
	Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.	Wang H, Ma H, Yan H, Pei Z, Zhao J, Zhang H, Zhang Z, Lu W.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10493-7	2025
	Parabacteroides goldsteinii enriched by Pericarpium Citri Reticulatae 'Chachiensis' polysaccharides improves colitis via the inhibition of lipopolysaccharide-involved PI3K-Akt signaling pathway.	Li Z, Li C, Chen B, Li B, Huang G, Huang Y, Hou Y, Zhong P, Jin J, Li D, Tsim KWK, Gan L, Chen WH, Wu R.	Int J Biol Macromol	10.1016/j.ijbiomac.2024.133726	2024
	Correlation between dietary factors and Parkinson's disease revealed by the analysis of Mendelian randomization.	Zeng S, Yusufujiang A, Zhang C, Yang C, Li H.	Front Nutr	10.3389/fnut.2024.1273874	2024
Pathogenicity	Parabacteroides goldsteinii Alleviates Intestinal Inflammation in Dextran Sulfate Sodium-Treated Pigs.	Deng X, Guo T, He Y, Gao S, Su J, Pan H, Li A.	Animals (Basel)	10.3390/ani15091231	2025
	Guizhi Shaoyao Zhimu decoction inhibits neutrophil extracellular traps formation to relieve rheumatoid arthritis via gut microbial outer membrane vesicles.	Ye H, Wang H, Han B, Chen K, Wang X, Ma F, Cheng L, Zheng S, Zhao X, Zhu J, Li J, Hong M.	Phytomedicine	10.1016/j.phymed.2024.156254	2025
	Schizophyllum commune fruiting body polysaccharides inhibit glioma by mediating ARHI regulation of PI3K/AKT signalling pathway.	Zheng SX, Chen JP, Liang RS, Zhuang BB, Wang CH, Zhang GL, Shi SS, Chen J.	Int J Biol Macromol	10.1016/j.ijbiomac.2024.135326	2024
	Maternal puerperal infection caused by Parabacteroides goldsteinii: a case report.	Peng L, Chen X, Wang Z, Yi L, Jin Z.	Front Med (Lausanne)	10.3389/fmed.2024.1450931	2024
	Parabacteroides goldsteinii mitigates the lipopolysaccharide-induced inflammatory response in IPEC-J2 cells.	Zhang J, Li A, He Y, Guo T, Ge Y, Pan H, Dong C.	Front Vet Sci	10.3389/fvets.2025.1577126	2025
Genetics	Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing.	Hosoda T, Suzuki M, Matsuno T, Matsui K, Ohyama K, Doi Y.	Microbiol Spectr	10.1128/spectrum.01014-25	2025
	Bifidobacterium infantis modulates intestinal microecology to inhibit the spread of antimicrobial resistance.	Li Z, Hu J, Pan Y, Xi Y, Zhang L.	mSystems	10.1128/msystems.00728-25	2025
	Ginsenoside F2-Mediated Intestinal Microbiota and Its Metabolite Propionic Acid Positively Impact the Gut-Skin Axis in Atopic Dermatitis Mice.	Li D, Luo ZB, Zhu J, Wang JX, Jin ZY, Qi S, Jin M, Quan LH.	J Agric Food Chem	10.1021/acs.jafc.3c06015	2024
	Efficient production of lacto-N-fucopentaose III in engineered Escherichia coli using alpha1,3-fucosyltransferase from Parabacteroides goldsteinii.	Sugita T, Sampei S, Koketsu K.	J Biotechnol	10.1016/j.jbiotec.2022.12.002	2023
	Non-Invasive Analyses of Altered Schaedler Flora in C57Bl/6J and Balb/c Mice to Monitor Hygiene Status of a Housing Facility.	Nistelberger R, Gibler P, Barones L, Absenger A, Kral-Pointner JB, Salzmann M, Hartmann B, Podesser BK, Hohensinner PJ, Plasenzotti R.	Animals (Basel)	10.3390/ani15121725	2025
	Tauroursodeoxycholic acid protects Schwann cells from high glucose-induced cytotoxicity by targeting NLRP3 to regulate cell migration and pyroptosis.	Wang Q, Li W, Zhang X, Chung SL, Dai J, Jin Z.	Biotechnol Appl Biochem	10.1002/bab.2518	2024
Pathogenicity	The co-regulation of the gut microbiome and host genes might play essential roles in metformin gastrointestinal intolerance.	Zhang H, Lai J, Zhang L, Zhang W, Liu X, Gong Q, Tian H, Yang M, Yang T, Zhao R, Li D, Huang H, Zhao Y, Yan S, Yu M, Xiyang Y, Shi L, Yang L, Wang L, Chen W, Cao X.	Toxicol Appl Pharmacol	10.1016/j.taap.2023.116732	2023
	Circulating microbiome DNA features and its effect on predicting clinicopathological characteristics of patients with colorectal cancer.	Ma L, Shi M, Zhang X, Liu Y, Jin H, Li D, Zhang H, Feng L, Zuo J, Wang Y, Liu J, Han J.	J Transl Med	10.1186/s12967-025-06164-4	2025
	A lysine-restricted diet ameliorates obesity via enrichment of Parabacteroides goldsteinii and 1,4-methylimidazoleacetic acid.	Zhao F, Zou Z, Liu Z, Wang J, Wu Y, Zhang J, Liu Q, Liang W, Yao J, Jiang X, Routledge MN, Khan A, Zhang H, Qiu J, Chen C.	Nat Commun	10.1038/s41467-025-64892-z	2025
	Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.	Ahn JS, Han EJ, Chung HJ.	Front Microbiol	10.3389/fmicb.2025.1533580	2025
	Interactions between gut microbiota and cardiovascular drugs: effects on drug therapeutic effect and side effect.	Wang T, Lan Q, Deng H, Han W, Zhang R, Zhong J.	Front Cardiovasc Med	10.3389/fcvm.2025.1570008	2025
	Perturbation of maternal gut microbiota in mice during a critical perinatal window influences early neurobehavioral outcomes in offspring.	Morel C, Martinez Sanchez I, Cherifi Y, Chartrel N, Diaz Heijtz R.	Neuropharmacology	10.1016/j.neuropharm.2023.109479	2023
	The immune system's mediation of the protective effect of Parabacteroides against obesity: A Mendelian randomization study.	Ouyang Y, Liao Y, Lei B, Liu L, Gao Y, Chen B, Liu H.	Medicine (Baltimore)	10.1097/md.0000000000044671	2025
	Ornithine aspartate effects on bacterial composition and metabolic pathways in a rat model of steatotic liver disease.	Lange EC, Rampelotto PH, Longo L, de Freitas LBR, Uribe-Cruz C, Alvares-da-Silva MR.	World J Hepatol	10.4254/wjh.v16.i5.832	2024
	Urolithin C reveals anti-NAFLD potential via AMPK-ferroptosis axis and modulating gut microbiota.	Xu J, Tian H, Ji Y, Dong L, Liu Y, Wang Y, Gao X, Shi H, Li H, Yang L.	Naunyn Schmiedebergs Arch Pharmacol	10.1007/s00210-023-02492-8	2023
	Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model.	Yuan J, Qin S, Hu S, Liu Z, Song Y, Li L.	Appl Microbiol Biotechnol	10.1007/s00253-022-12044-4	2022
	Analyzing the causal relationship between gut microbiotas, blood metabolites, and COVID-19 susceptibility: A Mendelian randomization study.	Yao XY, Zhang YH, Weng YW, Xie JF, Zheng KC.	Medicine (Baltimore)	10.1097/md.0000000000041445	2025
	Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron.	Sakamoto M, Ikeyama N, Iino T, Ohkuma M.	Anaerobe	10.1016/j.anaerobe.2022.102642	2022
	Roles of intestinal Parabacteroides in human health and diseases.	Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lu X.	FEMS Microbiol Lett	10.1093/femsle/fnac072	2022
	Isoliquiritigenin Attenuates Adipose Tissue Inflammation and Metabolic Syndrome by Modifying Gut Bacteria Composition in Mice.	Ishibashi R, Furusawa Y, Honda H, Watanabe Y, Fujisaka S, Nishikawa M, Ikushiro S, Kurihara S, Tabuchi Y, Tobe K, Takatsu K, Nagai Y.	Mol Nutr Food Res	10.1002/mnfr.202101119	2022
	Commensal bacterial outer membrane protein A induces interleukin-22 production.	Wang Y, Ngo VL, Zou J, Gewirtz AT.	Cell Rep	10.1016/j.celrep.2024.114292	2024
Genetics	Metagenomic and Metabolomic Profiling Reveals the Impact of High-Fat Diet on Malignant Pleural Effusion.	Chen QY, Shao MM, Dong SF, Shi HZ, Yi FS.	Thorac Cancer	10.1111/1759-7714.70126	2025
Pathogenicity	Proinflammatory macrophages transporting gut-derived bacterial DNA drive autoimmune arthritis in spondyloarthropathy.	Cai B, Giri R, Cameron AJ, Rahman MA, Small A, Altmann C, Lim Y, Rehaume LM, Morrison M, Wechalekar MD, Begun J, Bergot AS, Thomas R.	JCI Insight	10.1172/jci.insight.188028	2025
Enzymology	Unraveling the Anti-Obesity Potential of White Kidney Bean alpha-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.	Yan J, Zhao J, Naizemuding P, Zhao W, Sun J, Wang Y, Yang J, Li D, Zhang F, Cao H.	Food Sci Nutr	10.1002/fsn3.71043	2025
	Deciphering the therapeutic effects of Xiyanping injection: insights into pulmonary and gut microbiome modulation, SerpinB2/PAI-2 targeting, and alleviation of influenza a virus-induced lung injury.	Liu T, Li S, Wang X, Liu M, Wang Y, Ying J, Zhang S, Lin Y, Wang N, Bai Y, Xie L, Chen T, Feng Q, Xu X.	Virol J	10.1186/s12985-025-02636-7	2025
	The increased tendency for anemia in traditional Chinese medicine deficient body constitution is associated with the gut microbiome.	Liang Y, Chen Y, Lin Y, Huang W, Qiu Q, Sun C, Yuan J, Xu N, Chen X, Xu F, Shang X, Deng Y, Liu Y, Tan F, He C, Li J, Deng Q, Zhang X, Guan H, Liang Y, Fang X, Jiang X, Han L, Huang L, Yang Z.	Front Nutr	10.3389/fnut.2024.1359644	2024
Phylogeny	Differences in gut microbiota among patients with anastomotic leak following colorectal cancer surgery.	Yan J, Wang Q, Li Q, Lu J, Tong Q.	Front Microbiol	10.3389/fmicb.2025.1578990	2025
	Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands.	Boiten KE, Notermans DW, Rentenaar RJ, van Prehn J, Bode LGM, Maat I, van der Zwet W, Jansz A, Siebers TJH, Rossen JWA, de Greeff SC, Hendrickx APA, Kuijper EJ, Veloo ACM.	J Antimicrob Chemother	10.1093/jac/dkae043	2024
	Black Raspberry Modulates Cecal and Oral Microbiomes at the Early Stage of a Dibenzo[def,p]chrysene-Induced Murine Oral Cancer Model.	Zhao J, Sun YW, Chen KM, Aliaga C, Bisanz JE, El-Bayoumy K.	Cancer Prev Res (Phila)	10.1158/1940-6207.capr-24-0347	2025
	Protective effect of gut microbiota restored by fecal microbiota transplantation in a sepsis model in juvenile mice.	Han YJ, Kim S, Shin H, Kim HW, Park JD.	Front Immunol	10.3389/fimmu.2024.1451356	2024
	Effect of Oral Administration of Polyethylene Glycol 400 on Gut Microbiota Composition and Diet-Induced Obesity in Mice.	Ishibashi R, Matsuhisa R, Nomoto M, Chudan S, Nishikawa M, Tabuchi Y, Ikushiro S, Nagai Y, Furusawa Y.	Microorganisms	10.3390/microorganisms11081882	2023
	Gut microbiota influence anastomotic healing in colorectal cancer surgery through modulation of mucosal proinflammatory cytokines.	Hajjar R, Gonzalez E, Fragoso G, Oliero M, Alaoui AA, Calve A, Vennin Rendos H, Djediai S, Cuisiniere T, Laplante P, Gerkins C, Ajayi AS, Diop K, Taleb N, Therien S, Schampaert F, Alratrout H, Dagbert F, Loungnarath R, Sebajang H, Schwenter F, Wassef R, Ratelle R, Debroux E, Cailhier JF, Routy B, Annabi B, Brereton NJB, Richard C, Santos MM.	Gut	10.1136/gutjnl-2022-328389	2023
	Changes in bile acid profiles and short-term weight loss in response to a low-calorie diet: a pilot study.	Jiang MX, Ling CJ, Qian SC, Zhai JN, Huang JY, Su KK, Wu XW, Han QZ, Wang L.	Front Nutr	10.3389/fnut.2025.1598933	2025
Enzymology	Gut microbiota modulates COPD pathogenesis: role of anti-inflammatory Parabacteroides goldsteinii lipopolysaccharide.	Lai HC, Lin TL, Chen TW, Kuo YL, Chang CJ, Wu TR, Shu CC, Tsai YH, Swift S, Lu CC.	Gut	10.1136/gutjnl-2020-322599	2022
	Advances in the Drug Delivery Systems for Psoriasis Topical Therapy.	Liu Y, Chang R, Deng H, Liang F, Xu X, Luo Y.	Int J Nanomedicine	10.2147/ijn.s529899	2025
	The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet.	Li Y, Liu M, Kong B, Zhang G, Zhang Q.	Front Microbiol	10.3389/fmicb.2024.1439652	2024
	Apple polysaccharide improves age-matched cognitive impairment and intestinal aging through microbiota-gut-brain axis.	Zhang W, Zhong Y, Wang Z, Tang F, Zheng C.	Sci Rep	10.1038/s41598-024-67132-4	2024
Genetics	Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.	Luo Y, Sheikh TMM, Li X, Yuan Y, Yao F, Wang M, Guo X, Wu J, Shafiq M, Xie Q, Jiao X.	Virulence	10.1080/21505594.2024.2428843	2024
	Comparison of effects on colitis-associated tumorigenesis and gut microbiota in mice between Ophiocordyceps sinensis and Cordyceps militaris.	Ji Y, Tao T, Zhang J, Su A, Zhao L, Chen H, Hu Q.	Phytomedicine	10.1016/j.phymed.2021.153653	2021
	Bacterial targets of fecal host miRNAs in high-fat diet-fed mice.	Silamikele L, Silamikelis I, Kotovica PP, Klovins J.	PLoS One	10.1371/journal.pone.0315871	2025
Genetics	RFW captures species-level metagenomic functions by integrating genome annotation information.	Mi K, Xu R, Liu X.	Cell Rep Methods	10.1016/j.crmeth.2024.100932	2024
	Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.	Kaspersen HP, Estensmo EL, Slettemeas JS, Haverkamp THA, Sjurseth SK, Granstad S, Sekse C, Frederiksen RF, Urdahl AM.	Microb Genom	10.1099/mgen.0.001466	2025
Phylogeny	Microbial Signatures of Obesity-Aggravated Psoriasis: Insights from an Imiquimod-Based Mouse Model	Constantin C, Dobre E, Istvan P, Munteanu A, Surcel M, Isvoranu G, Neagu M.	Int J Mol Sci		2025
	Inflammatory Proteins Mediate the Effect of Gut Microbiota on Graves' Ophthalmopathy: A Mendelian Randomization Study.	Li Y, Chen L, Lin S, An W, Miao L, Wan M, Zhang B.	Transl Vis Sci Technol	10.1167/tvst.14.6.34	2025
	Amelioration of Maternal Immune Activation-Induced Autism Relevant Behaviors by Gut Commensal Parabacteroides goldsteinii.	Lin TL, Lu CC, Chen TW, Huang CW, Lu JJ, Lai WF, Wu TS, Lai CH, Lai HC, Chen YL.	Int J Mol Sci	10.3390/ijms232113070	2022
	Gut microbial metabolism is linked to variations in circulating non-high density lipoprotein cholesterol.	Zhou S, Liu L, Ye B, Xu Y, You Y, Zhu S, Ju J, Yang J, Li W, Xia M, Liu Y.	EBioMedicine	10.1016/j.ebiom.2024.105150	2024
	Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research.	Guo J, Shi W, Li X, Yang B, Qin C, Su L.	Microorganisms	10.3390/microorganisms12040646	2024
Genetics	Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.	Liwinski T, Auer MK, Schroder J, Pieknik I, Casar C, Schwinge D, Henze L, Stalla GK, Lang UE, von Klitzing A, Briken P, Hildebrandt T, Desbuleux JC, Biedermann SV, Holterhus PM, Bang C, Schramm C, Fuss J.	BMC Med	10.1186/s12916-024-03548-z	2024
	Intestinal Permeability, Gut Inflammation, and Gut Immune System Response Are Linked to Aging-Related Changes in Gut Microbiota Composition: A Study in Female Mice.	Gamez-Macias PE, Felix-Soriano E, Samblas M, Sainz N, Moreno-Aliaga MJ, Gonzalez-Muniesa P.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glae045	2024
Genetics	Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.	Chen J, Luo Y, Hao Y, Wang Q, Wang Q.	Front Nutr	10.3389/fnut.2025.1676238	2025
Pathogenicity	Gut microbiome and metabolites mediate the benefits of caloric restriction in mice after acute kidney injury.	Zhu XX, Fu X, Meng XY, Su JB, Zheng GL, Xu AJ, Chen G, Zhang Y, Liu Y, Hou XH, Qiu HB, Sun QY, Hu JY, Lv ZL, Wang Y, Jiang HB, Bao N, Han ZJ, Lu QB, Sun HJ.	Redox Biol	10.1016/j.redox.2024.103373	2024
	Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.	Wang IC, Swanson JL, Waters JL, Kochukov MY, Buffington SA, Dooling SW, Arenkiel BR, Costa-Mattioli M.	iScience	10.1016/j.isci.2025.113709	2025
	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
Genetics	Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.	Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N.	Nat Commun	10.1038/s41467-024-52097-9	2024
Genetics	Causal relationships between gut microbiota and depression/anxiety disorders: A 2-sample Mendelian randomization study.	Fan T, Li L, Chen Y.	Medicine (Baltimore)	10.1097/md.0000000000039543	2024
	Free lipoproteins from Bifidobacterium longum alleviate osteoarthritis through modulation of the gut microbiome.	Sane F, Piva F, Romond MB.	Microbiome Res Rep	10.20517/mrr.2023.12	2023
	Hydrogels Modulating the Microbiome: Therapies for Tissue Regeneration with Infection Control	Jimenez-Gastelum G, Villegas-Mercado C, Cota-Quintero J, Arzola-Rodriguez S, Ramos-Payan R, Bermudez M.	Gels		2025
	Aging-induced Alternation in the Gut Microbiota Impairs Host Antibacterial Defense.	Gu P, Wei R, Liu R, Yang Q, He Y, Guan J, He W, Li J, Zhao Y, Xie L, He J, Guo Q, Hu J, Bao J, Wang W, Guo J, Zeng Z, Chen Z, Jiang Y, Liu Z, Chen P.	Adv Sci (Weinh)	10.1002/advs.202411008	2025
	Coptis chinensis shows distinct effects on hyperlipidemia and gut microbiota in high-fat diet induced mice with cold or hot syndrome.	Yang Y, Zhan J, Cheng J, Cao Y, Wu C.	Chin Herb Med	10.1016/j.chmed.2025.04.009	2025
	Gut microbiome is associated with asthma and race in children with food allergy.	Mahdavinia M, Fyolek JP, Jiang J, Thivalapill N, Bilaver LA, Warren C, Fox S, Nimmagadda SR, Newmark PJ, Sharma H, Assa'ad A, Seed PC, Gupta RS.	J Allergy Clin Immunol	10.1016/j.jaci.2023.07.024	2023
	The Role of Gut Microbiota Modification in Nonalcoholic Fatty Liver Disease Treatment Strategies.	Yaghmaei H, Bahanesteh A, Soltanipur M, Takaloo S, Rezaei M, Siadat SD.	Int J Hepatol	10.1155/2024/4183880	2024
	Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.	Leve M, Manghi P, Bredon M, Lefevre A, Manara S, Armanini F, Emond P, Planchais J, Rolhion N, Segata N, Sokol H.	iScience	10.1016/j.isci.2025.113751	2025
	Gut Commensal Parabacteroides goldsteinii MTS01 Alters Gut Microbiota Composition and Reduces Cholesterol to Mitigate Helicobacter pylori-Induced Pathogenesis.	Lai CH, Lin TL, Huang MZ, Li SW, Wu HY, Chiu YF, Yang CY, Chiu CH, Lai HC.	Front Immunol	10.3389/fimmu.2022.916848	2022
	Proinflammatory and GABA eating bacteria in Parkinson's disease gut microbiome from a meta-analysis prospective.	Marzouk NH, Rashwan HH, El-Hadidi M, Ramadan R, Mysara M.	NPJ Parkinsons Dis	10.1038/s41531-025-00950-z	2025
	Anti-PD-L1 Antibody and/or 17beta-Estradiol Treatment Induces Changes in the Gut Microbiome in MC38 Colon Tumor Model.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Choi J, Lee HN.	Cancer Res Treat	10.4143/crt.2022.1427	2023
	Sodium butyrate alleviates R97-116 peptide-induced myasthenia gravis in mice by improving the gut microbiota and modulating immune response.	Sun J, Chen J, Xie Q, Sun M, Zhang W, Wang H, Liu N, Wang Q, Wang M.	J Inflamm (Lond)	10.1186/s12950-023-00363-w	2023
Pathogenicity	Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.	Soni S, Mittal P, Lo JH, Yang Y, Smbatyan G, Lee K, Wan J, Kumagai H, Yen K, Mehta HH, Miller B, Torres-Gonzalez L, Battaglin F, Shah UH, Bartolini M, Zhang W, Craig DW, Millstein J, Cohen P, Lenz HJ.	Neoplasia	10.1016/j.neo.2025.101245	2025
	Bifidobacterium animalis Supplementation Improves Intestinal Barrier Function and Alleviates Antibiotic-Associated Diarrhea in Mice.	Du X, Liu M, Li J, Liu Y, Ge S, Gao H, Zhang M.	Foods	10.3390/foods14101704	2025
	Microbiota-derived proteins synergize with IL-23 to drive IL22 production in model type 3 innate lymphoid cells.	Wang Y, Allan DSJ, Gewirtz AT.	PLoS One	10.1371/journal.pone.0317248	2025
	Chitosan Oligosaccharide Ameliorates Metabolic Syndrome Induced by Overnutrition via Altering Intestinal Microbiota.	Wang Y, Liu S, Tang D, Dong R, Feng Q.	Front Nutr	10.3389/fnut.2021.743492	2021
	Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development.	Wang L, Tu YX, Chen L, Zhang Y, Pan XL, Yang SQ, Zhang SJ, Li SH, Yu KC, Song S, Xu HL, Yin ZC, Yue JQ, Ni QL, Tang T, Zhang JL, Guo M, Zhang S, Yao F, Liang XJ, Chen ZX.	Adv Sci (Weinh)	10.1002/advs.202206238	2023
Pathogenicity	Ethanol extract of propolis prevents high-fat diet-induced insulin resistance and obesity in association with modulation of gut microbiota in mice.	Cai W, Cai W, Xu J, Li G, Liu T, Guo X, Wang H, Luo L.	Food Res Int	10.1016/j.foodres.2019.108939	2020
	Effects of alcohol on gut microbiome in adolescent and adult MMTV-Wnt1 mice.	Li H, Meza LA, Shahi SK, Zhang Z, Wen W, Hu D, Lin H, Mangalam AK, Luo J.	Front Oncol	10.3389/fonc.2025.1557040	2025
	Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model.	Du B, Xiao X, Wang H, Li W, Xia Z, Yang P, Huang SK, Yuan R, Liu J, Han M, Zou Y, Zhu J, He D, Lyu J, Jin X, Xu X, Wang J, Yang H, Xiao L, Liu X, Kristiansen K.	Environ Health Perspect	10.1289/ehp11874	2023
Transcriptome	Gut metatranscriptomics based de novo assembly reveals microbial signatures predicting immunotherapy outcomes in non-small cell lung cancer.	Dora D, Kiraly P, Somodi C, Ligeti B, Dulka E, Galffy G, Lohinai Z.	J Transl Med	10.1186/s12967-024-05835-y	2024
	Formononetin derived from Parabacteroides merdae alleviates MPTP-induced Parkinson's disease in mice by inhibiting ferroptosis via the PI3K-AKT-ferritinophagy axis.	Dong X, Yang T, Jin Z.	Commun Biol	10.1038/s42003-025-09067-8	2025
Genetics	Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.	Yang J, Wang H, Lin X, Liu J, Feng Y, Bai Y, Liang H, Hu T, Wu Z, Lai J, Liu J, Zou Y, Wei S, Yan P.	mSystems	10.1128/msystems.01366-24	2024
	Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity.	Hieta J, Benchraka C, Parnanen K, Houttu N, Mokkala K, Lotankar M, Kataja EL, Lahti L, Laitinen K.	Brain Behav Immun Health	10.1016/j.bbih.2025.101042	2025
	Potential of gut microbiota metabolites in treating COPD: network pharmacology and Mendelian randomization approaches.	Cao Z, Zhao S, Wu T, Sun F, Hu S, Shi L.	Front Microbiol	10.3389/fmicb.2024.1416651	2024
Pathogenicity	Gut commensal Parabacteroides goldsteinii plays a predominant role in the anti-obesity effects of polysaccharides isolated from Hirsutella sinensis.	Wu TR, Lin CS, Chang CJ, Lin TL, Martel J, Ko YF, Ojcius DM, Lu CC, Young JD, Lai HC.	Gut	10.1136/gutjnl-2017-315458	2019
Transcriptome	Lactiplantibacillus plantarum Attenuates Diet-Induced Obesity and Insulin Resistance Through Gut Microbiota-Driven PPAR/PI3K-Axis Modulation.	Gao Y, Zhu A, Li J, Liu H, Li X, Zhang H.	Microb Biotechnol	10.1111/1751-7915.70227	2025
Pathogenicity	Unraveling the gut microbiota's role in obesity: key metabolites, microbial species, and therapeutic insights.	Iqbal M, Yu Q, Tang J, Xiang J.	J Bacteriol	10.1128/jb.00479-24	2025
	Multi-omics analysis reveals the mechanism of Lactobacillus plantarum in alleviating metabolic disorders in type 2 diabetic mice through the gut-liver axis.	Zhang C, Gao Y, Huang Y, Qin Y, Li Y, Chen Q, Wu T, Zhang Y, Zhang Y, Deng D, Huang B, Chen M, Han M.	mSystems	10.1128/msystems.00965-25	2025
	Sunlight Exposure and Phototherapy: Perspectives for Healthy Aging in an Era of COVID-19.	Nakano T, Chiang KC, Chen CC, Chen PJ, Lai CY, Hsu LW, Ohmori N, Goto T, Chen CL, Goto S.	Int J Environ Res Public Health	10.3390/ijerph182010950	2021
Phylogeny	Gut Microbiota Profile Changes in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease: A Metagenomic Study.	De Caro C, Spagnuolo R, Quirino A, Mazza E, Carrabetta F, Maurotti S, Cosco C, Bennardo F, Roberti R, Russo E, Giudice A, Giudice A, Pujia A, Doldo P, Matera G, Marascio N.	Int J Mol Sci	10.3390/ijms25105453	2024
	Composition of gut microbiota in obese and normal-weight Uygur adults and its association with adipocyte-related factors.	Muheyati D, Han J, Lv M, Jielili M, Jing Z, Zaibibuli K, Aisike G, Aihemaiti A, Yu Y, Kaliszewski CR.	Sci Rep	10.1038/s41598-024-76351-8	2024
	Impact of Edible Insect Polysaccharides on Mouse Gut Microbiota: A Study on White-Spotted Flower Chafer Larva (Protaetia brevitarsis seulensis) and Silkworm Pupa (Bombyx mori).	Lee JH, Son H, Subramaniyam S, Lim HJ, Park S, Choi RY, Kim IW, Seo M, Kweon HY, Kim Y, Kim SW, Choi JS, Shin Y.	Foods	10.3390/foods14010006	2024
	Innovative treatments for obesity and NAFLD: A bibliometric study on antioxidants, herbs, phytochemicals, and natural compounds.	Pezzino S, Sofia M, Mazzone C, Litrico G, Greco LP, Gallo L, La Greca G, Latteri S.	Heliyon	10.1016/j.heliyon.2024.e35498	2024
Phylogeny	Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.	Filippi Xavier L, Gacesa R, da Rocha GHO, Broering MF, Scharf P, Lima FDS, Faber KN, Harmsen H, Hoffmann C, Farsky SHP.	Front Immunol	10.3389/fimmu.2025.1679071	2025
	Exploring global research status and trends in anti-obesity effects of traditional Chinese medicine through intestinal microbiota: a bibliometric study.	Huang W, Wang J, Kuang M, Xiao Z, Fan B, Sun G, Tan Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1271473	2023
	Exploring the mechanisms of chronic obstructive pulmonary disease and Crohn's disease: a bioinformatics-based study.	Zhang X, Liu C, Cao L, Tang H, Jiang H, Hu C, Dong X, Zhou F, Qin K, Liu Q, Shen J, Zhou Y.	Sci Rep	10.1038/s41598-024-78697-5	2024
	Gut Microbiota Is Associated with Onset and Severity of Type 1 Diabetes in Nonobese Diabetic Mice Treated with Anti-PD-1.	Patel S, Becker E, Ploix C, Steiner G, Scepanovic P, Fueth M, de Vera Mudry MC, Eichinger-Chapelon A, Marrer-Berger E, Claesson MJ.	Immunohorizons	10.4049/immunohorizons.2300103	2023
Metabolism	Low-dose valine attenuates diet-induced metabolic dysfunction-associated steatotic liver disease (MASLD) in mice by enhancing leptin sensitivity and modulating the gut microbiome.	Felicianna, Lo EKK, Chen C, Ismaiah MJ, Zhang F, Leung HKM, El-Nezami H.	Mol Metab	10.1016/j.molmet.2024.102059	2024
Pathogenicity	The effect of penicillin administration in early life on murine gut microbiota and blood lymphocyte subsets.	Daniluk J, Daniluk U, Rusak M, Dabrowska M, Reszec J, Garbowicz M, Huminska K, Dabrowski A.	Anaerobe	10.1016/j.anaerobe.2017.03.015	2017
	Decorating probiotics with a triggerable and catalytic shell for synergistically enhanced colitis biotherapy	Li Z, Wei X, Chen W, Qiu X, Shi J, Li Y, Wang Z, Chen X, Wang Y, Cheng L, Teng B, Corke H, Zhang B, Yang Q.	Mater Today Bio		2025
	Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.	Guo Z, Wang X, Li Y, Zhang Y, Guo P, Zhang J, Zhang Z, Ma X.	Front Immunol	10.3389/fimmu.2025.1563225	2025
Phylogeny	Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study	Issilbayeva A, Sergazy S, Zhashkeyev A, Gulyayev A, Kozhakhmetov S, Shulgau Z, Nurgaziyev M, Nurgaziyeva A, Zhetkenev S, Mukhanbetzhanov N, Jarmukhanov Z, Mukhanbetzhanova Z, Vinogradova E, Zhumadilov Z, Kushugulova A, Aljofan M.	Front Med (Lausanne)		2025
	Roxadustat alleviates the inflammatory status in patients receiving maintenance hemodialysis with erythropoiesis-stimulating agent resistance by increasing the short-chain fatty acids producing gut bacteria.	Zhao XN, Liu SX, Wang ZZ, Zhang S, You LL.	Eur J Med Res	10.1186/s40001-023-01179-3	2023
	Roseburia hominis improves host metabolism in diet-induced obesity.	Huang W, Zhu W, Lin Y, Chan FKL, Xu Z, Ng SC.	Gut Microbes	10.1080/19490976.2025.2467193	2025
	Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention.	Takahashi H, Fujii T, Yamakawa S, Yamada C, Fujiki K, Kondo N, Funasaka K, Hirooka Y, Tochio T.	BMC Microbiol	10.1186/s12866-023-03021-6	2023
Pathogenicity	Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota.	Kang Y, Li Y, Du Y, Guo L, Chen M, Huang X, Yang F, Hong J, Kong X.	Int J Obes (Lond)	10.1038/s41366-018-0187-x	2019
	Histone Deacetylase Inhibition by Gut Microbe-Generated Short-Chain Fatty Acids Entrains Intestinal Epithelial Circadian Rhythms.	Fawad JA, Luzader DH, Hanson GF, Moutinho TJ, McKinney CA, Mitchell PG, Brown-Steinke K, Kumar A, Park M, Lee S, Bolick DT, Medlock GL, Zhao JY, Rosselot AE, Chou CJ, Eshleman EM, Alenghat T, Hong CI, Papin JA, Moore SR.	Gastroenterology	10.1053/j.gastro.2022.07.051	2022
	A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage.	Li T, Ding N, Guo H, Hua R, Lin Z, Tian H, Yu Y, Fan D, Yuan Z, Gonzalez FJ, Wu Y.	Cell Host Microbe	10.1016/j.chom.2023.12.015	2024
	Research status and development trends of probiotics in clinical applications.	Li Y, Yao Y, Zhang Z, Gan Y.	Front Nutr	10.3389/fnut.2025.1650883	2025
	Genetic Insights into the Gut-Lung Axis: Mendelian Randomization Analysis on Gut Microbiota, Lung Function, and COPD.	Cheng ZX, Hua JL, Jie ZJ, Li XJ, Zhang J.	Int J Chron Obstruct Pulmon Dis	10.2147/copd.s441242	2024
	The Potential of Alternative Therapies and Vaccine Candidates against Helicobacter pylori.	Sukri A, Hanafiah A, Patil S, Lopes BS.	Pharmaceuticals (Basel)	10.3390/ph16040552	2023
	Respiratory diseases and the gut microbiota: an updated review.	Yu X, Yu X, Wang Y, Guo X, Wang C, Wang F.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1629005	2025
Genetics	Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.	Zhang Q, Hutchison ER, Pan C, Warren MF, Keller MP, Attie AD, Lusis AJ, Rey FE.	Microbiome	10.1186/s40168-025-02093-y	2025
Pathogenicity	Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy.	Ishizaka A, Koga M, Mizutani T, Suzuki Y, Matano T, Yotsuyanagi H.	BMC Microbiol	10.1186/s12866-024-03431-0	2024
	The role of gut-lung axis in COPD: Pathogenesis, immune response, and prospective treatment.	Song Z, Meng Y, Fricker M, Li X, Tian H, Tan Y, Qin L.	Heliyon	10.1016/j.heliyon.2024.e30612	2024
	Effects of GLP-1 Analogues and Agonists on the Gut Microbiota: A Systematic Review.	Gofron KK, Wasilewski A, Malgorzewicz S.	Nutrients	10.3390/nu17081303	2025
Metabolism	Comparison of gnotobiotic communities reveals milk-adapted metabolic functions and unexpected amino acid metabolism by the pre-weaning microbiome.	Lubin JB, Silverman MA, Planet PJ.	Gut Microbes	10.1080/19490976.2024.2387875	2024
Phylogeny	Identifying fecal microbiota signatures of colorectal cancer in a Vietnamese cohort.	Nhung PTT, Le HTT, Nguyen QH, Huyen DT, Quyen DV, Song LH, Van Thuan T, Tran TTT.	Front Microbiol	10.3389/fmicb.2024.1388740	2024
	Causal relationship between gut microbiota and diabetic complications: a two-sample Mendelian randomization study.	Liu J, Chen Y, Peng C.	Diabetol Metab Syndr	10.1186/s13098-024-01424-7	2024
	The Effect of Formula-based Nutritional Treatment on Colitis in a Murine Model.	Jang S, Kim Y, Lee C, Kwon B, Noh J, Jee JJ, Yoon SS, Koh H, Park S.	J Korean Med Sci	10.3346/jkms.2021.36.e342	2021
Transcriptome	Longitudinal multi-omics analysis of the gut-liver axis: Unraveling the molecular mechanisms of metabolic homeostasis regulation by Pd@Pt nanozymes.	Wang Y, Cheng N, Zhang Q, Chang F, Wang T, Kan M, Han Y, Zhai B, Huang K, He X.	Mater Today Bio	10.1016/j.mtbio.2025.101685	2025
Pathogenicity	An ultrasonic degraded polysaccharide extracted from Pueraria lobata ameliorate ischemic brain injury in mice by regulating the gut microbiota and LPS-TLR4 pathway.	Zhang Y, Dou Z, Li S, Zhang H, Zeng S, Zuo X, Xiao Y, Zhang L, Li Z, Zhu Q, Zhang W, Niu H, Duan Q, Chen X, Li Z, Zhou H, Wang Q.	Ultrason Sonochem	10.1016/j.ultsonch.2024.107200	2025
Pathogenicity	Rhubarb extract prevents hepatic inflammation induced by acute alcohol intake, an effect related to the modulation of the gut microbiota.	Neyrinck AM, Etxeberria U, Taminiau B, Daube G, Van Hul M, Everard A, Cani PD, Bindels LB, Delzenne NM.	Mol Nutr Food Res	10.1002/mnfr.201500899	2017
	The Effects of Tocotrienol on Gut Microbiota: A Scoping Review.	Kumareswaran A, Ekeuku SO, Mohamed N, Muhammad N, Hanafiah A, Pang KL, Wong SK, Chew DCH, Chin KY.	Life (Basel)	10.3390/life13091882	2023
Metabolism	In-depth multiomic characterization of the effects of obesity in high-fat diet-fed mice.	Li B, Chen J, Ou X, Liu X, Xu Z, Xiang X, Yang Y, Wang Q.	FEBS Open Bio	10.1002/2211-5463.13788	2024
	Structural characterization, antioxidant activity, and fermentation characteristics of Flammulina velutipes residue polysaccharide degraded by ultrasonic assisted H₂O₂-Vc technique.	Que Y, Zhang Y, Liang F, Wang L, Yang Y, Zhang J, Wang W, Sun Y, Zhong C, Zhang H, He C, Guan L, Ma H.	Ultrason Sonochem	10.1016/j.ultsonch.2024.107085	2024
	Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice.	Serrano M, Srivastava A, Buck G, Zhu B, Edupuganti L, Adegbulugbe E, Shankaranarayanan D, Kopp JB, Raj DS.	Am J Nephrol	10.1159/000526957	2022
	Enteric-Coated Aspirin Induces Small Intestinal Injury via the Nrf2/Gpx4 Pathway: A Promising Model for Chronic Enteropathy.	Zhang M, Xia S, Feng L, Han X, Zhang Y, Huang Y, Liu Y, Zhao K, Guan J, Tian D, Liao J, Yu Y.	Drug Des Devel Ther	10.2147/dddt.s493049	2025
Phylogeny	A pilot study exploring the association of bronchial bacterial microbiota and recurrent wheezing in infants with atopy.	Tang W, Zhang L, Ai T, Xia W, Xie C, Fan Y, Chen S, Chen Z, Yao J, Peng Y.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1013809	2023
	Offspring metabolic programming via the maternal diet increases susceptibility to metabolic dysregulation.	Li X, Shiraki N, Watanabe T, Fukui R, Furukawa K, Kato Y, Nakahara Y, Kume S, Taguchi A, Wada Y, Warman DJ, Saito K, Nakajima-Adachi H, Hachimura S, Kato H, Jia H.	EBioMedicine	10.1016/j.ebiom.2025.105817	2025
Metabolism	Eggshell membrane powder lowers plasma triglyceride and liver total cholesterol by modulating gut microbiota and accelerating lipid metabolism in high-fat diet-fed mice.	Ramli NS, Jia H, Sekine A, Lyu W, Furukawa K, Saito K, Hasebe Y, Kato H.	Food Sci Nutr	10.1002/fsn3.1545	2020
	Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain.	Tejada JN, Walters WA, Wang Y, Kordahi M, Chassaing B, Pickard J, Nunez G, Ley R, Gewirtz AT.	Gut Microbes	10.1080/19490976.2024.2392872	2024
	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
Metabolism	Altered Gut Microbiota Composition and Immune Response in Experimental Steatohepatitis Mouse Models.	Ishioka M, Miura K, Minami S, Shimura Y, Ohnishi H.	Dig Dis Sci	10.1007/s10620-016-4393-x	2017
	Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.	Nomura K, Ishikawa D, Okahara K, Ito S, Haga K, Takahashi M, Arakawa A, Shibuya T, Osada T, Kuwahara-Arai K, Kirikae T, Nagahara A.	J Clin Med	10.3390/jcm10081749	2021
	Association between post-stroke cognitive impairment and gut microbiota: A PRISMA-compliant systematic review and meta-analysis.	Hu X, Mao Y, Luo F, Wang X.	Medicine (Baltimore)	10.1097/md.0000000000034764	2023
	Regulation of intestinal flora by Suaeda salsa extract ameliorates hyperglycemia in a mouse model of type 2 diabetes mellitus.	Yin X, Sui Y, Chu Z, Han S, Ge X, Liu T, Zeng F, Chen L, Shao R, Xu W.	Front Nutr	10.3389/fnut.2024.1499196	2024
	Akkermansia muciniphila-derived hypoacylated rough-type lipopolysaccharides alleviate diet-induced obesity via activation of TLR4-IL-23-IL-22 immune axis.	Sun L, Zhang Y, Dong W, Sun J, Wang T, Shao F, Dai H, Han J, Wang W, Wang S, Zhao T, Wang L, Liu C, Liu S, Liu H.	Imeta	10.1002/imt2.70066	2025
	The Dose-Response Effect of Fluoride Exposure on the Gut Microbiome and Its Functional Pathways in Rats.	Mo Z, Wang J, Meng X, Li A, Li Z, Que W, Wang T, Tarnue KF, Ma X, Liu Y, Yan S, Wu L, Zhang R, Pei J, Wang X.	Metabolites	10.3390/metabo13111159	2023
	Select Gut Microbiota Impede Rotavirus Vaccine Efficacy.	Ngo VL, Wang Y, Wang Y, Shi Z, Britton R, Zou J, Ramani S, Jiang B, Gewirtz AT.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2024.101393	2024
	Parabacteroides distasonis promotes liver regeneration by increasing beta-hydroxybutyric acid (BHB) production and BHB-driven STAT3 signals.	Guo M, Jiang X, Ouyang H, Zhang X, Zhang S, Wang P, Bi G, Wu T, Zhou W, Liang F, Yang X, Fan S, Fang JH, Chen P, Bi H.	Acta Pharm Sin B	10.1016/j.apsb.2025.01.024	2025
	First Exploration of the Altered Microbial Gut-Lung Axis in the Pathogenesis of Human Refractory Chronic Cough.	Baldi S, Fabbrizzi A, Di Gloria L, Pallecchi M, Nannini G, D'Ambrosio M, Luceri C, Bartolucci G, Ramazzotti M, Fontana G, Mannini C, Lavorini F, Amedei A.	Lung	10.1007/s00408-024-00681-7	2024
	Gut microbiota and metabolism in systemic lupus erythematosus: from dysbiosis to targeted interventions.	Zhu JH, Wu LP, Deng L, Zang SG, Li XB, Chen X, Yu JX.	Eur J Med Res	10.1186/s40001-025-03264-1	2025
	Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction.	Lu L, Li Y, Su H, Ren S, Liu Y, Shao G, Liu W, Ji G, Xu H.	J Pharm Anal	10.1016/j.jpha.2024.101138	2025
	Gastrodia elata Blume extract improves high-fat diet-induced type 2 diabetes by regulating gut microbiota and bile acid profile.	Wang D, Wang JX, Yan C, Liu Y, Liu H, Li D, Zhu J, Luo ZB, Han SZ, Jin ZY, Chang SY, Yang LH, Kang JD, Quan LH.	Front Microbiol	10.3389/fmicb.2022.1091712	2022
	17beta-estradiol in colorectal cancer: friend or foe?	Wu Z, Xiao C, Wang J, Zhou M, You F, Li X.	Cell Commun Signal	10.1186/s12964-024-01745-0	2024
	Gut Microbiota Alteration Influences Colorectal Cancer Metastasis to the Liver by Remodeling the Liver Immune Microenvironment.	Yuan N, Li X, Wang M, Zhang Z, Qiao L, Gao Y, Xu X, Zhi J, Li Y, Li Z, Jia Y.	Gut Liver	10.5009/gnl210177	2022
	Long-Term Tracking of the Effects of Colostrum-Derived Lacticaseibacillus rhamnosus Probio-M9 on Gut Microbiota in Mice with Colitis-Associated Tumorigenesis.	Zhao F, Hiraishi K, Li X, Hu Y, Kojima D, Sun Z, Zhang H, Kurahara LH.	Biomedicines	10.3390/biomedicines12030531	2024
	Lactobacillus plantarum-Derived Postbiotics Ameliorate Acute Alcohol-Induced Liver Injury by Protecting Cells from Oxidative Damage, Improving Lipid Metabolism, and Regulating Intestinal Microbiota.	Ye W, Chen Z, He Z, Gong H, Zhang J, Sun J, Yuan S, Deng J, Liu Y, Zeng A.	Nutrients	10.3390/nu15040845	2023
Genetics	Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.	Huang C, Liu D, Yang S, Huang Y, Wei X, Zhang P, Lin J, Xu B, Liu Y, Guo D, Li Y, Li J, Zhang H.	iScience	10.1016/j.isci.2024.110202	2024
	Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.	Goldman DA, Xue KS, Parrott AB, Lopez JA, Vila JCC, Jeeda RR, Franzese LR, Porter RL, Gray IJ, DeFelice BC, Petrov DA, Good BH, Relman DA, Huang KC.	Proc Natl Acad Sci U S A	10.1073/pnas.2322440122	2025
	Anti-obesity effects exerted by Dioscorea opposita Thunb. polysaccharides in diet-induced obese mice.	Li SN, Zhang DL, Wang ZH, Song WT, Chen WB, Hu GL, Han LY, Zhou JC.	Food Sci Nutr	10.1002/fsn3.3588	2023
	Lung and Gut Microbiome in COPD.	Karakasidis E, Kotsiou OS, Gourgoulianis KI.	J Pers Med	10.3390/jpm13050804	2023
	Lactobacillus casei Zhang exerts probiotic effects to antibiotic-treated rats.	Yao G, Cao C, Zhang M, Kwok LY, Zhang H, Zhang W.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.10.026	2021
	Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4⁺CD8alphaalpha⁺ intraepithelial T cells.	Rodriguez-Marino N, Royer CJ, Rivera-Rodriguez DE, Seto E, Gracien I, Jones RM, Scharer CD, Gracz AD, Cervantes-Barragan L.	Mucosal Immunol	10.1016/j.mucimm.2024.08.010	2024
Genetics	Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.	Zhang C, Liu Z, Yu H, Shen Y, Lu L, Kong F, Sun W, Wei X, Jin L, Ge L, Zeng B.	Front Microbiol	10.3389/fmicb.2025.1537286	2025
	Genetic association and bidirectional Mendelian randomization for causality between gut microbiota and six lung diseases.	Su Y, Zhang Y, Xu J.	Front Med (Lausanne)	10.3389/fmed.2023.1279239	2023
	Dietary switch and intermittent fasting ameliorate the disrupted postprandial short-chain fatty acid response in diet-induced obese mice.	Ceperuelo-Mallafre V, Rodriguez-Pena MM, Badia J, Villanueva-Carmona T, Cedo L, Marsal-Beltran A, Benaiges E, Nunez-Roa C, Salmeron-Pelado L, Osuna-Prieto FJ, Bosch R, Pellitero S, Fernandez-Veledo S, Vendrell J.	EBioMedicine	10.1016/j.ebiom.2025.105827	2025
	Microbiota modulate immune cell populations and drive dynamic structural changes in gut-associated lymphoid tissue	Jan P, Nikola M, Liliana T, Karolina K, Valeria G, Zdenek Z, Tomas H, Anna M, Dagmar S, Martin S, Marianne B, Jan C.	Gut microbes		2025
	Gut microbiome for predicting immune checkpoint blockade-associated adverse events.	Hu M, Lin X, Sun T, Shao X, Huang X, Du W, Guo M, Zhu X, Zhou Y, Tong T, Guo F, Han T, Wu X, Shi Y, Xiao X, Zhang Y, Hong J, Chen H.	Genome Med	10.1186/s13073-024-01285-9	2024
	Lacticaseibacillus rhamnosus LRJ-1 alleviates constipation through promoting gut Bacteroides-derived gamma-aminobutyric acid production.	Xia T, Huang F, Yun F, Liu Y, Wang T, Wang S, Jin S, Ma X, Wang W, He J, Teng K, Zhong J.	Curr Res Food Sci	10.1016/j.crfs.2024.100924	2024
	Gut Microbiota, the Potential Biological Medicine for Prevention, Intervention and Drug Sensitization to Fight Diseases.	Wu H, Chen X, Zhang S, Li J.	Nutrients	10.3390/nu14204220	2022
Proteome	Significance of integrated clinical and proteomic characteristics analysis for pathogenesis and management of Crohn's disease with concomitant psoriasis.	Zhang H, He C, Fan X, Song Q, Lin C, Zhou P, Song Y, Li N, Shi Y, Lin Z, Chen Q, Zheng Y, Wang S, Li Z, Zhang W, Liu Q, Qing Q, Sun Y, Huang B, Li M.	EBioMedicine	10.1016/j.ebiom.2025.105981	2025
	Bile acid is a responsible host factor for high-fat diet-induced gut microbiota alterations in rats: proof of the "bile acid hypothesis".	Watanabe M, Fujita Y, Hagio M, Ishizuka S, Ogura Y, Hayashi T, Fukiya S, Yokota A.	Biosci Microbiota Food Health	10.12938/bmfh.2024-042	2025
	Effects of red ginseng on gut, microbiota, and brain in a mouse model of post-infectious irritable bowel syndrome.	Yu S, Chun E, Ji Y, Lee YJ, Jin M.	J Ginseng Res	10.1016/j.jgr.2021.03.008	2021
	The interactions between traditional Chinese medicine and gut microbiota: Global research status and trends.	Yang S, Hao S, Wang Q, Lou Y, Jia L, Chen D.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1005730	2022
Pathogenicity	Caulerpa lentillifera improves ethanol-induced liver injury and modulates the gut microbiota in rats.	Lin KY, Yang HY, Yang SC, Chen YL, Watanabe Y, Chen JR.	Curr Res Food Sci	10.1016/j.crfs.2023.100546	2023
Metabolism	Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota-Bile Acid Axis.	Jiang J, Zhang H, Hussain M, Abdullah, Feng F, Guan R, Zhong H.	Biology (Basel)	10.3390/biology14070802	2025
Transcriptome	MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities.	Taj B, Adeolu M, Xiong X, Ang J, Nursimulu N, Parkinson J.	Microbiome	10.1186/s40168-023-01562-6	2023
Pathogenicity	Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm.	Pust MM, Rocha Castellanos DM, Rzasa K, Dame A, Pishchany G, Assawasirisin C, Liss A, Fernandez-Del Castillo C, Xavier RJ.	Gut	10.1136/gutjnl-2023-331012	2024
	Gut microbiota-derived tryptophan metabolites improve total parenteral nutrition-associated infections by regulating Group 3 innate lymphoid cells.	Huang L, Wang P, Liu S, Deng G, Qi X, Sun G, Gao X, Zhang L, Zhang Y, Xiao Y, Gao T, Maitiabula G, Wang X.	Imeta	10.1002/imt2.70007	2025
	Gut microbiome influences efficacy of Endostatin combined with PD-1 blockade against colorectal cancer.	Xu J, Tian Y, Zhao B, Hu D, Wu S, Ma J, Yang L.	Mol Biomed	10.1186/s43556-024-00200-3	2024
Pathogenicity	High salt diet alleviates disease severity in native experimental autoimmune uveitis.	Derluyn N, Foucart V, Verce M, Abdo R, Vaudoisey L, Lipski D, Flamand V, Everard A, Bruyns C, Willermain F.	Front Ophthalmol (Lausanne)	10.3389/fopht.2024.1370374	2024
	Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.	Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E.	Microbiol Spectr	10.1128/spectrum.00336-23	2023
	Gut Microbiota Predicts Healthy Late-Life Aging in Male Mice.	Ke S, Mitchell SJ, MacArthur MR, Kane AE, Sinclair DA, Venable EM, Chadaideh KS, Carmody RN, Grodstein F, Mitchell JR, Liu Y.	Nutrients	10.3390/nu13093290	2021
Phylogeny	Gut microbiota changes associated with low-carbohydrate diet intervention for obesity.	Li L, Zhao X, Abdugheni R, Yu F, Zhao Y, Ma BF, Yang Z, Li R, Li Y, Maimaitiyiming Y, Maimaiti M.	Open Life Sci	10.1515/biol-2022-0803	2024
Genetics	Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.	Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M.	Microorganisms	10.3390/microorganisms12020255	2024
Genetics	Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.	Dora D, Revisnyei P, Mihucz A, Kiraly P, Szklenarik G, Dulka E, Galffy G, Lohinai Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1381170	2024
Genetics	Effect of a Probiotic Beverage Enriched with Cricket Proteins on the Gut Microbiota: Composition of Gut and Correlation with Nutritional Parameters.	Dridi C, Millette M, Salmieri S, Aguilar Uscanga BR, Lacroix S, Venneri T, Sarmast E, Allahdad Z, Di Marzo V, Silvestri C, Lacroix M.	Foods	10.3390/foods13020204	2024
Metabolism	Postbiotic heat-killed lactobacilli modulates on body weight associated with gut microbiota in a pig model.	Ryu S, Kyoung H, Park KI, Oh S, Song M, Kim Y.	AMB Express	10.1186/s13568-022-01424-8	2022
	Colonization with Altered Schaedler Flora Impacts Leukocyte Adhesion in Mesenteric Ischemia-Reperfusion Injury.	Bayer F, Ascher S, Kiouptsi K, Kittner JM, Stauber RH, Reinhardt C.	Microorganisms	10.3390/microorganisms9081601	2021
Pathogenicity	Pomegranate flower polysaccharide improves mastitis in mice by regulating intestinal flora and restoring the blood-milk barrier.	Li J, Yin W, Liang Y, Yang Z, Li L, Mai Z, Yu X, Lu Y, Zhang Z, Abula S, Wu Y, Wusiman A, Guo Q.	Front Pharmacol	10.3389/fphar.2024.1427355	2024
Transcriptome	The altered TBI fecal microbiome is stable and functionally distinct.	Pyles RB, Miller AL, Urban RJ, Sheffield-Moore M, Wright TJ, Maxwell CA, Randolph KM, Danesi CP, McGovern KA, Vargas J, Armstrong P, Kreber L, Cumpa G, Randall K, Morrison M, Masel BE.	Front Mol Neurosci	10.3389/fnmol.2024.1341808	2024
	Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.	Jiang L, Hao Y, Han D, Dong W, Yang A, Sun Z, Ge Y, Duan S, Zhang X, Dai Z.	ISME J	10.1093/ismejo/wrae166	2024
	Understanding the ADHD-Gut Axis by Metabolic Network Analysis.	Tas E, Ulgen KO.	Metabolites	10.3390/metabo13050592	2023
Genetics	The gut microbiome as a potential source of non-invasive biomarkers of chronic obstructive pulmonary disease.	Li N, Yi X, Chen C, Dai Z, Deng Z, Pu J, Zhou Y, Li B, Wang Z, Ran P.	Front Microbiol	10.3389/fmicb.2023.1173614	2023
	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
	The effects of probiotics plus dietary fiber on antipsychotic-induced weight gain: a randomized clinical trial.	Huang J, Liu C, Yang Y, Kang D, Xiao J, Long Y, Lang B, Peng X, Wang W, Wang X, Liu F, Zhao J, Shi Z, Yuan TF, Wu R.	Transl Psychiatry	10.1038/s41398-022-01958-2	2022
	Fecal microbiota transplantation from female donors restores gut permeability and reduces liver injury and inflammation in middle-aged male mice exposed to alcohol.	Lamas-Paz A, Mesquita M, Garcia-Lacarte M, Estevez-Vazquez O, Benede-Ubieto R, Gutierrez AH, Wu H, Leal Lasalle H, Vaquero J, Banares R, Martinez-Naves E, Roa S, Nevzorova YA, Jorquera G, Cubero FJ.	Front Nutr	10.3389/fnut.2024.1393014	2024
	The Genus Parabacteroides Is a Potential Contributor to the Beneficial Effects of Truncal Vagotomy-Related Bariatric Surgery.	Liang D, Zhang X, Liu Z, Zheng R, Zhang L, Yu D, Shen X.	Obes Surg	10.1007/s11695-022-06017-9	2022
	Klebsiella oxytoca facilitates microbiome recovery via antibiotic degradation and restores colonization resistance in a diet-dependent manner.	Almasi EDH, Eisenhard L, Osbelt L, Lesker TR, Vetter AC, Knischewski N, Bielecka AA, Gronow A, Muthukumarasamy U, Wende M, Tawk C, Neumann-Schaal M, Bronstrup M, Strowig T.	Nat Commun	10.1038/s41467-024-55800-y	2025
	Oral Supplementation with Algal Sulphated Polysaccharide in Subjects with Inflammatory Skin Conditions: A Randomised Double-Blind Placebo-Controlled Trial and Baseline Dietary Differences.	Roach LA, Meyer BJ, Fitton JH, Winberg P.	Mar Drugs	10.3390/md21070379	2023
Metabolism	Interrelationship of Stress, Environment, and Herpes Simplex Virus Type-1 on Behçet's Disease: Using a Mouse Model.	Islam SMS, Ryu HM, Sayeed HM, Sohn S.	Front Immunol	10.3389/fimmu.2021.607768	2021
	Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.	Feng C, Li N, Gao G, He Q, Kwok LY, Zhang H.	Int J Mol Sci	10.3390/ijms25073768	2024
	Carbon dioxide enhances Akkermansia muciniphila fitness and anti-obesity efficacy in high-fat diet mice.	Wang X, Yang Q, Shi C, Wang Y, Guo D, Wan X, Dong P, Zhang Q, Hu Y, Zhang R, Yang H, Chen W, Liu Z.	ISME J	10.1093/ismejo/wraf034	2025
	Auricularia auricula polysaccharides attenuate obesity in mice through gut commensal Papillibacter cinnamivorans.	Zong X, Zhang H, Zhu L, Deehan EC, Fu J, Wang Y, Jin M.	J Adv Res	10.1016/j.jare.2023.08.003	2023
	Oat Beta-Glucans Modulate the Gut Microbiome, Barrier Function, and Immune Responses in an In Vivo Model of Early-Stage Colorectal Cancer.	Guzowska M, Dziendzikowska K, Kopiasz L, Gajewska M, Wilczak J, Harasym J, Czerwinska M, Gromadzka-Ostrowska J.	Int J Mol Sci	10.3390/ijms252413586	2024
	The Neuroprotective Effects of Spray-Dried Porcine Plasma Supplementation Involve the Microbiota-Gut-Brain Axis.	Rosell-Cardona C, Amat C, Grinan-Ferre C, Polo J, Pallas M, Perez-Bosque A, Moreto M, Miro L.	Nutrients	10.3390/nu14112211	2022
Pathogenicity	Microbial-Based Bioactive Compounds to Alleviate Inflammation in Obesity.	Apalowo OE, Adegoye GA, Obuotor TM.	Curr Issues Mol Biol	10.3390/cimb46030119	2024
	Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.	Hua R, Ding N, Hua Y, Wang X, Xu Y, Qiao X, Shi X, Bai T, Xiong Y, Zhuo X, Fan C, Zhou J, Wu Y, Liu J, Yuan Z, Li T.	Adv Sci (Weinh)	10.1002/advs.202501707	2025
	Exploring the Differences in the Gut Microbiome in Atopic Dermatitis According to the Presence of Gastrointestinal Symptoms.	Han CY, Kwon SK, Yeom M, Hahm DH, Park JW, Park HJ, Kim K.	J Clin Med	10.3390/jcm11133690	2022
Metabolism	The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.	Lyu L, Fan Y, Vogt JK, Clos-Garcia M, Bonnefond A, Pedersen HK, Dutta A, Koivula R, Sharma S, Allin KH, Brorsson C, Cederberg H, Chabanova E, De Masi F, Dermitzakis E, Elders PJ, Blom MT, Hollander M, Eriksen R, Forgie I, Frost G, Giordano GN, Grallert H, Haid M, Hansen TH, Jablonka B, Kokkola T, Mahajan A, Mari A, McDonald TJ, Musholt PB, Pavo I, Prehn C, Ridderstrale M, Ruetten H, Hart LM', Schwenk JM, Stankevic E, Thomsen HS, Vangipurapu J, Vestergaard H, Vinuela A, Walker M, Hansen T, Linneberg A, Nielsen HB, Brunak S, McCarthy MI, Froguel P, Adamski J, Franks PW, Laakso M, Beulens JWJ, Pearson E, Pedersen O.	Genome Med	10.1186/s13073-025-01508-7	2025
Enzymology	First report of Parabacteroides goldsteinii bacteraemia in a patient with complicated intra-abdominal infection.	Awadel-Kariem FM, Patel P, Kapoor J, Brazier JS, Goldstein EJ.	Anaerobe	10.1016/j.anaerobe.2010.01.001	2010
	Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions.	Gnanasekaran T, Sarathi A, Fang Q, Azarm A, Assis Geraldo J, Nigro E, Arumugam M.	mSystems	10.1128/msystems.01249-22	2023
Phylogeny	Functional proteins in breast milk and their correlation with the development of the infant gut microbiota: a study of mother-infant pairs.	Xi M, Liang D, Yan Y, Duan S, Leng H, Yang H, Shi X, Na X, Yang Y, Yang C, Szeto IM, Zhao A.	Front Microbiol	10.3389/fmicb.2023.1239501	2023
Metabolism	Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults.	Hammond TC, Green SJ, Jacobs Y, Chlipala GE, Xing X, Heil S, Chen A, Aware C, Flemister A, Stromberg A, Balchandani P, Lin AL.	Front Aging Neurosci	10.3389/fnagi.2023.1227203	2023
	Next-generation probiotics - do they open new therapeutic strategies for cancer patients?	Kazmierczak-Siedlecka K, Skonieczna-Zydecka K, Hupp T, Duchnowska R, Marek-Trzonkowska N, Polom K.	Gut Microbes	10.1080/19490976.2022.2035659	2022
	The interplay between herbal medicines and gut microbiota in metabolic diseases.	Wang L, Gou X, Ding Y, Liu J, Wang Y, Wang Y, Zhang J, Du L, Peng W, Fan G.	Front Pharmacol	10.3389/fphar.2023.1105405	2023
	Cocaine hydrochloride, cocaine methiodide and methylenedioxypyrovalerone (MDPV) cause distinct alterations in the structure and composition of the gut microbiota.	Angoa-Perez M, Zagorac B, Francescutti DM, Shaffer ZD, Theis KR, Kuhn DM.	Sci Rep	10.1038/s41598-023-40892-1	2023
	Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders.	Becerra CY, Wells RK, Kunihiro BP, Lee RH, Umeda L, Allan NP, Rubas NC, McCracken TA, Nunokawa CKL, Lee MH, Pidlaoan FGS, Phankitnirondorn K, Dye CK, Yamamoto BY, Peres R, Juarez R, Maunakea AK.	Front Genet	10.3389/fgene.2023.1125217	2023
	Poly-omic risk scores predict inflammatory bowel disease diagnosis.	Arehart CH, Sterrett JD, Garris RL, Quispe-Pilco RE, Gignoux CR, Evans LM, Stanislawski MA.	mSystems	10.1128/msystems.00677-23	2024
Genetics	Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions.	Bank NC, Singh V, McCourt B, Burberry A, Roberts KD, Grubb B, Rodriguez-Palacios A.	Gut Microbes	10.1080/19490976.2024.2350150	2024
Metabolism	Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency.	Chassaing B, Gewirtz AT.	PLoS One	10.1371/journal.pone.0195310	2018
	Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice.	Logan IE, Shulzhenko N, Sharpton TJ, Bobe G, Liu K, Nuss S, Jones ML, Miranda CL, Vasquez-Perez S, Pennington JM, Leonard SW, Choi J, Wu W, Gurung M, Kim JP, Lowry MB, Morgun A, Maier CS, Stevens JF, Gombart AF.	Mol Nutr Food Res	10.1002/mnfr.202100389	2021
	Campylobacter jejuni persistently colonizes gnotobiotic altered Schaedler flora C3H/HeN mice and induces mild colitis.	Wymore Brand M, Sahin O, Hostetter JM, Trachsel J, Zhang Q, Wannemuehler MJ.	FEMS Microbiol Lett	10.1093/femsle/fnaa163	2020
	Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator.	Salazar J, Duran P, Diaz MP, Chacin M, Santeliz R, Mengual E, Gutierrez E, Leon X, Diaz A, Bernal M, Escalona D, Hernandez LAP, Bermudez V.	Int J Environ Res Public Health	10.3390/ijerph20105845	2023
Metabolism	Human-derived fecal microbiota transplantation alleviates social deficits of the BTBR mouse model of autism through a potential mechanism involving vitamin B₆ metabolism.	Zheng L, Jiao Y, Zhong H, Tan Y, Yin Y, Liu Y, Liu D, Wu M, Wang G, Huang J, Wang P, Qin M, Wang M, Xiao Y, Lv T, Luo Y, Hu H, Hou S-T, Kui L.	mSystems	10.1128/msystems.00257-24	2024
Pathogenicity	Protective Effects of Dietary Resveratrol against Chronic Low-Grade Inflammation Mediated through the Gut Microbiota in High-Fat Diet Mice.	Wang P, Ma Y, Wang D, Zhao W, Hu X, Chen F, Zhao X.	Nutrients	10.3390/nu14101994	2022
Phylogeny	The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People.	Burakova I, Smirnova Y, Gryaznova M, Syromyatnikov M, Chizhkov P, Popov E, Popov V.	Nutrients	10.3390/nu14163384	2022
	Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species.	Qu Z, Liu H, Yang J, Zheng L, Huang J, Wang Z, Xie C, Zuo W, Xia X, Sun L, Zhou Y, Xie Y, Lu J, Zhu Y, Yu L, Liu L, Zhou H, Dai L, Leung EL.	Nat Commun	10.1038/s41467-025-55845-7	2025
	Non-absorbable antibiotic treatment inhibits colorectal cancer liver metastasis by modulating deoxycholic acid metabolism by intestinal microbes.	Deng J, Yuan W, Tan Q, Wei X, Ma J.	J Cancer	10.7150/jca.63490	2022
Genetics	Weight Loss Promotion in Individuals with Obesity through Gut Microbiota Alterations with a Multiphase Modified Ketogenic Diet.	Wang H, Lv X, Zhao S, Yuan W, Zhou Q, Sadiq FA, Zhao J, Lu W, Wu W.	Nutrients	10.3390/nu15194163	2023
	Combination of Lactobacillus plantarum HAC03 and Garcinia cambogia Has a Significant Anti-Obesity Effect in Diet-Induced Obesity Mice.	Kang YG, Lee T, Ro J, Oh S, Kwak JH, Kim AR.	Nutrients	10.3390/nu15081859	2023
	Changes in Gut Microbiome upon Orchiectomy and Testosterone Administration in AOM/DSS-Induced Colon Cancer Mouse Model.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Lee HN.	Cancer Res Treat	10.4143/crt.2022.080	2023
Pathogenicity	Polydextrose Alleviates Adipose Tissue Inflammation and Modulates the Gut Microbiota in High-Fat Diet-Fed Mice.	Hu Q, Niu Y, Yang Y, Mao Q, Lu Y, Ran H, Zhang H, Li X, Gu H, Su Q.	Front Pharmacol	10.3389/fphar.2021.795483	2021
	Burn injury alters the intestinal microbiome's taxonomic composition and functional gene expression.	Beckmann N, Pugh AM, Caldwell CC.	PLoS One	10.1371/journal.pone.0205307	2018
Phylogeny	16S rRNA Gene Sequencing Reveals Specific Gut Microbes Common to Medicinal Insects.	Geng J, Sui Z, Dou W, Miao Y, Wang T, Wei X, Chen S, Zhang Z, Xiao J, Huang D.	Front Microbiol	10.3389/fmicb.2022.892767	2022
	Spaceflight alters host-gut microbiota interactions.	Gonzalez E, Lee MD, Tierney BT, Lipieta N, Flores P, Mishra M, Beckett L, Finkelstein A, Mo A, Walton P, Karouia F, Barker R, Jansen RJ, Green SJ, Weging S, Kelliher J, Singh NK, Bezdan D, Galazska J, Brereton NJB.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00545-1	2024
	Next generation probiotics in disease amelioration.	Chang CJ, Lin TL, Tsai YL, Wu TR, Lai WF, Lu CC, Lai HC.	J Food Drug Anal	10.1016/j.jfda.2018.12.011	2019
	Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus.	Spring J, Khan AA, Lara S, O'Grady K, Wilks J, Gurbuxani S, Erickson S, Fischbach M, Jacobson A, Chervonsky A, Golovkina T.	Cell Rep	10.1016/j.celrep.2022.111341	2022
	Extraction optimization and characterization of persimmon peel pectin extracted by subcritical water.	Cui Y, Wang S, Wang S, Cao S, Wang X, Lu X.	Food Chem X	10.1016/j.fochx.2022.100486	2022
Metabolism	Daily full spectrum light exposure prevents food allergy-like allergic diarrhea by modulating vitamin D₃ and microbiota composition.	Chen PJ, Nakano T, Lai CY, Chang KC, Chen CL, Goto S.	NPJ Biofilms Microbiomes	10.1038/s41522-021-00213-8	2021
Pathogenicity	Electroacupuncture and human iPSC-derived small extracellular vesicles regulate the gut microbiota in ischemic stroke via the brain-gut axis.	Zhang Q, Deng P, Chen S, Xu H, Zhang Y, Chen H, Zhang J, Sun H.	Front Immunol	10.3389/fimmu.2023.1107559	2023
	Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.	Leung H, Xiong L, Ni Y, Busch A, Bauer M, Press AT, Panagiotou G.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00398-0	2023
	Treatment with Distinct Antibiotic Classes Causes Different Pulmonary Outcomes on Allergic Airway Inflammation Associated with Modulation of Symbiotic Microbiota.	Cavalcante GG, Guimaraes AG, Queiroz-Glauss CP, Goncalves Pereira MH, Dias ASL, Horta LS, de Oliveira JS, Cangussu SD, Magalhaes PP, Russo RC, Santiago HC.	J Immunol Res	10.1155/2022/1466011	2022
	Equipment and Methods for Concurrently Housing Germfree and Gnotobiotic Mice in the Same Room.	Muino AF, Compo NR, Everett BM, Abrahams DF, Baldwin MK, James TN, Wanner SE, Perkins MJ, Parr CE, Wiltshire ND, Miedel EL, Engelman RW.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-23-000019	2023
	Lactobacillus reuteri normalizes altered fear memory in male Cntnap4 knockout mice.	Zhang W, Huang J, Gao F, You Q, Ding L, Gong J, Zhang M, Ma R, Zheng S, Sun X, Zhang Y.	EBioMedicine	10.1016/j.ebiom.2022.104323	2022
	A key role of the subdiaphragmatic vagus nerve in the depression-like phenotype and abnormal composition of gut microbiota in mice after lipopolysaccharide administration.	Zhang J, Ma L, Chang L, Pu Y, Qu Y, Hashimoto K.	Transl Psychiatry	10.1038/s41398-020-00878-3	2020
	Plasminogen Activator Inhibitor-1 Potentiates Neutrophil Infiltration and Tissue Injury in Colitis.	Wang X, Guo L, Huang J, Jiang S, Li N, Mu HH, Xu C.	Int J Biol Sci	10.7150/ijbs.75890	2023
	Susceptibility to epilepsy after traumatic brain injury is associated with preexistent gut microbiome profile.	Medel-Matus JS, Lagishetty V, Santana-Gomez C, Shin D, Mowrey W, Staba RJ, Galanopoulou AS, Sankar R, Jacobs JP, Mazarati AM.	Epilepsia	10.1111/epi.17248	2022
	Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach.	Torres-Sanchez A, Ruiz-Rodriguez A, Ortiz P, Moreno MA, Ampatzoglou A, Gruszecka-Kosowska A, Monteoliva-Sanchez M, Aguilera M.	Int J Mol Sci	10.3390/ijms232112917	2022
	Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT.	Li L, Li R, Tian Q, Luo Y, Li R, Lin X, Ou Y, Guo T, Chen X, Pan A, Manson JE, Liu G.	Cell Rep Med	10.1016/j.xcrm.2024.101801	2024
	Effects of Short-Term Dietary Fiber Intervention on Gut Microbiota in Young Healthy People.	Tian T, Zhang X, Luo T, Wang D, Sun Y, Dai J.	Diabetes Metab Syndr Obes	10.2147/dmso.s313385	2021
	Next generation probiotics for human health: An emerging perspective.	Jan T, Negi R, Sharma B, Kumar S, Singh S, Rai AK, Shreaz S, Rustagi S, Chaudhary N, Kaur T, Kour D, Sheikh MA, Kumar K, Yadav AN, Ahmed N.	Heliyon	10.1016/j.heliyon.2024.e35980	2024
	Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.	Zhu H, Li M, Bi D, Yang H, Gao Y, Song F, Zheng J, Xie R, Zhang Y, Liu H, Yan X, Kong C, Zhu Y, Xu Q, Wei Q, Qin H.	Nat Commun	10.1038/s41467-024-45572-w	2024
	Associations between self-reported psychological symptom severity and gut microbiota: further support for the microgenderome.	Ganci M, Suleyman E, Butt H, Ball M.	BMC Psychiatry	10.1186/s12888-022-03947-7	2022
	Low-dose IL-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation.	Tchitchek N, Nguekap Tchoumba O, Pires G, Dandou S, Campagne J, Churlaud G, Fourcade G, Hoffmann TW, Strozzi F, Gaal C, Bonny C, Le Chatelier E, Erlich SD, Sokol H, Klatzmann D.	JCI Insight	10.1172/jci.insight.159406	2022
	Immunomodulatory Effects of Probiotics on COVID-19 Infection by Targeting the Gut-Lung Axis Microbial Cross-Talk.	Synodinou KD, Nikolaki MD, Triantafyllou K, Kasti AN.	Microorganisms	10.3390/microorganisms10091764	2022
	High fat diets induce early changes in gut microbiota that may serve as markers of ulterior altered physiological and biochemical parameters related to metabolic syndrome. Effect of virgin olive oil in comparison to butter.	Andujar-Tenorio N, Prieto I, Cobo A, Martinez-Rodriguez AM, Hidalgo M, Segarra AB, Ramirez M, Galvez A, Martinez-Canamero M.	PLoS One	10.1371/journal.pone.0271634	2022
	Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota.	Li S, Yang S, Zhou Y, Disoma C, Dong Z, Du A, Zhang Y, Chen Y, Huang W, Chen J, Song D, Chen Z, Liu P, Li S, Zheng R, Liu S, Razzaq A, Chen X, Tao S, Yu C, Feng T, Liao W, Peng Y, Jiang T, Huang J, Wu W, Hu L, Wang L, Li S, Xia Z.	Front Microbiol	10.3389/fmicb.2021.712081	2021
	Pancreatic Cancer Resistance to Treatment: The Role of Microbiota.	Nista EC, Del Gaudio A, Del Vecchio LE, Mezza T, Pignataro G, Piccioni A, Gasbarrini A, Franceschi F, Candelli M.	Biomedicines	10.3390/biomedicines11010157	2023
	Long-Term Exposure to Polystyrene Microspheres and High-Fat Diet-Induced Obesity in Mice: Evaluating a Role for Microbiota Dysbiosis.	Zhai Z, Yang Y, Chen S, Wu Z.	Environ Health Perspect	10.1289/ehp13913	2024
	Fish Oil, Cannabidiol and the Gut Microbiota: An Investigation in a Murine Model of Colitis.	Silvestri C, Pagano E, Lacroix S, Venneri T, Cristiano C, Calignano A, Parisi OA, Izzo AA, Di Marzo V, Borrelli F.	Front Pharmacol	10.3389/fphar.2020.585096	2020
	Chlorella pyrenoidosa Polysaccharides as a Prebiotic to Modulate Gut Microbiota: Physicochemical Properties and Fermentation Characteristics In Vitro.	Lv K, Yuan Q, Li H, Li T, Ma H, Gao C, Zhang S, Liu Y, Zhao L.	Foods	10.3390/foods11050725	2022
	Gut Microbiota Modulation in the Management of Chronic Obstructive Pulmonary Disease: A Literature Review.	Patibandla S, Bhatt N, Lief S, Beauti SM, Ansari AZ.	Cureus	10.7759/cureus.66875	2024
Pathogenicity	Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn's disease.	Metwaly A, Jovic J, Waldschmitt N, Khaloian S, Heimes H, Hacker D, Ahmed M, Hammoudi N, Le Bourhis L, Mayorgas A, Siebert K, Basic M, Schwerd T, Allez M, Panes J, Salas A, Bleich A, Zeissig S, Schnupf P, Cominelli F, Haller D.	Microbiome	10.1186/s40168-023-01508-y	2023
	Beneficial Bacteria Isolated from Food in Relation to the Next Generation of Probiotics.	Sionek B, Szydlowska A, Zielinska D, Neffe-Skocinska K, Kolozyn-Krajewska D.	Microorganisms	10.3390/microorganisms11071714	2023
	Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs.	Morelli G, Patuzzi I, Losasso C, Ricci A, Contiero B, Andrighetto I, Ricci R.	Sci Rep	10.1038/s41598-022-13270-6	2022
Pathogenicity	N-acetylglucosamine-6-O sulfation on intestinal mucins prevents obesity and intestinal inflammation by regulating gut microbiota.	Abo H, Muraki A, Harusato A, Imura T, Suzuki M, Takahashi K, Denning TL, Kawashima H.	JCI Insight	10.1172/jci.insight.165944	2023
Genetics	Human Gut Metagenomes Encode Diverse GH156 Sialidases.	Mann E, Shekarriz S, Surette MG.	Appl Environ Microbiol	10.1128/aem.01755-22	2022
	Effects of the probiotic Lactiplantibacillus plantarum IMC 510® on body composition, biochemical parameters, gut microbiota composition and function, and clinical symptoms of overweight/obese subjects.	Pagliai G, Coman MM, Baldi S, Dinu M, Nannini G, Russo E, Curini L, Colombini B, Lotti S, Pallecchi M, Di Gloria L, Bartolucci G, Ramazzotti M, Verdenelli MC, Sofi F, Amedei A.	Front Nutr	10.3389/fnut.2023.1142527	2023
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
	Goat Milk Consumption Enhances Innate and Adaptive Immunities and Alleviates Allergen-Induced Airway Inflammation in Offspring Mice.	Kao HF, Wang YC, Tseng HY, Wu LS, Tsai HJ, Hsieh MH, Chen PC, Kuo WS, Liu LF, Liu ZG, Wang JY.	Front Immunol	10.3389/fimmu.2020.00184	2020
Phylogeny	Sex-specific association between the gut microbiome and high-fat diet-induced metabolic disorders in mice.	Peng C, Xu X, Li Y, Li X, Yang X, Chen H, Zhu Y, Lu N, He C.	Biol Sex Differ	10.1186/s13293-020-0281-3	2020
	New insights on strain-specific impacts of probiotics on insulin resistance: evidence from animal study.	Kobyliak N, Falalyeyeva T, Tsyryuk O, Eslami M, Kyriienko D, Beregova T, Ostapchenko L.	J Diabetes Metab Disord	10.1007/s40200-020-00506-3	2020
	Commensal gut microbiota-derived acetate and propionate enhance heart adaptation in response to cardiac pressure overload in mice.	Lin CJ, Cheng YC, Chen HC, Chao YK, Nicholson MW, Yen ECL, Kamp TJ, Hsieh PCH.	Theranostics	10.7150/thno.76002	2022
Pathogenicity	2'-fucosyllactose Supplementation Improves Gut-Brain Signaling and Diet-Induced Obese Phenotype and Changes the Gut Microbiota in High Fat-Fed Mice.	Lee S, Goodson M, Vang W, Kalanetra K, Barile D, Raybould H.	Nutrients	10.3390/nu12041003	2020
	Lactobacillaceae differentially impact butyrate-producing gut microbiota to drive CNS autoimmunity.	Montgomery TL, Toppen LC, Eckstrom K, Heney ER, Kennedy JJ, Scarborough MJ, Krementsov DN.	Gut Microbes	10.1080/19490976.2024.2418415	2024
Enzymology	The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.	Almuhayawi M, Altun O, Abdulmajeed AD, Ullberg M, Ozenci V.	PLoS One	10.1371/journal.pone.0142398	2015
	Dysbiotic Gut Bacteria in Obesity: An Overview of the Metabolic Mechanisms and Therapeutic Perspectives of Next-Generation Probiotics.	Breton J, Galmiche M, Dechelotte P.	Microorganisms	10.3390/microorganisms10020452	2022
	Feeding dietary fermentable fiber improved fecal microbial composition and increased acetic acid production in a nursery pig model.	Zhang G, Zhao J, Song X, Yang M, Wang H, Wu Y.	J Anim Sci	10.1093/jas/skad260	2023
	Fecal Microbial Transplant in Individuals With Immune-Mediated Dry Eye.	Watane A, Cavuoto KM, Rojas M, Dermer H, Day JO, Banerjee S, Galor A.	Am J Ophthalmol	10.1016/j.ajo.2021.06.022	2022
	MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.	Li Y, Gu B, Liu G, Xia W, Fan K, Mei Y, Huang P, Pan S.	J Thorac Dis	10.3978/j.issn.2072-1439.2014.02.15	2014
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
	Cranberry polyphenols and agave agavins impact gut immune response and microbiota composition while improving gut barrier function, inflammation, and glucose metabolism in mice fed an obesogenic diet.	Medina-Larque AS, Rodriguez-Daza MC, Roquim M, Dudonne S, Pilon G, Levy E, Marette A, Roy D, Jacques H, Desjardins Y.	Front Immunol	10.3389/fimmu.2022.871080	2022
	GlcNac produced by the gut microbiome enhances host influenza resistance by modulating NK cells.	Hu X, Sun X, Zhao Y, Iv C, Sun X, Jin M, Zhang Q.	Gut Microbes	10.1080/19490976.2023.2271620	2023
Pathogenicity	Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation.	Tsou AM, Goettel JA, Bao B, Biswas A, Kang YH, Redhu NS, Peng K, Putzel GG, Saltzman J, Kelly R, Gringauz J, Barends J, Hatazaki M, Frei SM, Emani R, Huang Y, Shen Z, Fox JG, Glickman JN, Horwitz BH, Snapper SB.	Microbiome	10.1186/s40168-021-01161-3	2021
Metabolism	Xenometabolite signatures in the UC Davis type 2 diabetes mellitus rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.	Mercer KE, Yeruva L, Pack L, Graham JL, Stanhope KL, Chintapalli SV, Wankhade UD, Shankar K, Havel PJ, Adams SH, Piccolo BD.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00105.2020	2020
Pathogenicity	Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression.	Zhao SS, Chen L, Yang J, Wu ZH, Wang XY, Zhang Q, Liu WJ, Liu HX.	Microbiol Spectr	10.1128/spectrum.02612-22	2022
Genetics	The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research	Huang K, Xu Y, Feng T, Lan H, Ling F, Xiang H, Liu Q.	Biology (Basel)		2024
	Probiotic Effects of Lactobacillus fermentum ZJUIDS06 and Lactobacillus plantarum ZY08 on Hypercholesteremic Golden Hamsters.	Yang D, Lyu W, Hu Z, Gao J, Zheng Z, Wang W, Firrman J, Ren D.	Front Nutr	10.3389/fnut.2021.705763	2021
Genetics	The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice.	Xu L, Surathu A, Raplee I, Chockalingam A, Stewart S, Walker L, Sacks L, Patel V, Li Z, Rouse R.	BMC Genomics	10.1186/s12864-020-6665-2	2020
	The gut-lung axis: Gut microbiota changes associated with pulmonary fibrosis in mouse models induced by bleomycin.	Quan Y, Yin Z, Chen S, Lang J, Han L, Yi J, Zhang L, Yue Q, Tian W, Chen P, Du S, Wang J, Dai Y, Hua H, Zeng J, Li L, Zhao J.	Front Pharmacol	10.3389/fphar.2022.985223	2022
	Chlorogenic Acid Ameliorates Post-Infectious Irritable Bowel Syndrome by Regulating Extracellular Vesicles of Gut Microbes.	Zheng C, Zhong Y, Zhang W, Wang Z, Xiao H, Zhang W, Xie J, Peng X, Luo J, Xu W.	Adv Sci (Weinh)	10.1002/advs.202302798	2023
Metabolism	Persistent changes in liver methylation and microbiome composition following reversal of diet-induced non-alcoholic-fatty liver disease.	Kim H, Worsley O, Yang E, Purbojati RW, Liang AL, Tan W, Moses DID, Hartono S, Fan V, Lim TKH, Schuster SC, Foo RS, Chow PKH, Pettersson S.	Cell Mol Life Sci	10.1007/s00018-019-03114-4	2019
	Robust cross-cohort gut microbiome associations with COVID-19 severity.	Li J, Li J, Ghosh TS, McCann R, Mallon P, Hill C, Draper L, Schult D, Fanning LJ, Shannon R, Sadlier C, Horgan M, O'Mahony L, O'Toole PW.	Gut Microbes	10.1080/19490976.2023.2242615	2023
	Human Fecal Microbiota Transplantation Reduces the Susceptibility to Dextran Sulfate Sodium-Induced Germ-Free Mouse Colitis.	Yang Y, Zheng X, Wang Y, Tan X, Zou H, Feng S, Zhang H, Zhang Z, He J, Cui B, Zhang X, Wu Z, Dong M, Cheng W, Tao S, Wei H.	Front Immunol	10.3389/fimmu.2022.836542	2022
	The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss.	Aoun A, Darwish F, Hamod N.	Prev Nutr Food Sci	10.3746/pnf.2020.25.2.113	2020
	Synbiotic approach restores intestinal homeostasis and prolongs survival in leukaemic mice with cachexia.	Bindels LB, Neyrinck AM, Claus SP, Le Roy CI, Grangette C, Pot B, Martinez I, Walter J, Cani PD, Delzenne NM.	ISME J	10.1038/ismej.2015.209	2016
	Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study.	Zeng Q, Zhao M, Wang F, Li Y, Li H, Zheng J, Chen X, Zhao X, Ji L, Gao X, Liu C, Wang Y, Cheng S, Xu J, Pan B, Sun J, Li Y, Li D, He Y, Zheng L.	Front Endocrinol (Lausanne)	10.3389/fendo.2022.906310	2022
	Unlocking the wasting enigma: Highlights from the 8th Cachexia Conference.	Ebner N, von Haehling S.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.12106	2016
	Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects.	Benitez-Paez A, Hartstra AV, Nieuwdorp M, Sanz Y.	Gut Microbes	10.1080/19490976.2022.2078621	2022
	Next-Generation Probiotics as Novel Therapeutics for Improving Human Health: Current Trends and Future Perspectives.	Abouelela ME, Helmy YA.	Microorganisms	10.3390/microorganisms12030430	2024
	Multi-omics reveal microbial determinants impacting the treatment outcome of antidepressants in major depressive disorder.	Wang Y, Zhou J, Ye J, Sun Z, He Y, Zhao Y, Ren S, Zhang G, Liu M, Zheng P, Wang G, Yang J.	Microbiome	10.1186/s40168-023-01635-6	2023
	FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes.	Colnet B, Sieber CMK, Perraudeau F, Leclerc M.	Front Microbiol	10.3389/fmicb.2021.632567	2021
Phylogeny	A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community.	Joseph S, Aduse-Opoku J, Hashim A, Hanski E, Streich R, Knowles SCL, Pedersen AB, Wade WG, Curtis MA.	mSystems	10.1128/msystems.01222-20	2021
	Short-term high-fat feeding exacerbates degeneration in retinitis pigmentosa by promoting retinal oxidative stress and inflammation.	Kutsyr O, Noailles A, Martinez-Gil N, Maestre-Carballa L, Martinez-Garcia M, Maneu V, Cuenca N, Lax P.	Proc Natl Acad Sci U S A	10.1073/pnas.2100566118	2021
Pathogenicity	Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.	Islam SMS, Ryu HM, Sayeed HM, Byun HO, Jung JY, Kim HA, Suh CH, Sohn S.	Front Immunol	10.3389/fimmu.2021.712312	2021
Pathogenicity	Eukaryotic and Prokaryotic Microbiota Interactions.	Kodio A, Menu E, Ranque S.	Microorganisms	10.3390/microorganisms8122018	2020
	Response of germ-free mice to colonization with O. formigenes and altered Schaedler flora.	Li X, Ellis ML, Dowell AE, Kumar R, Morrow CD, Schoeb TR, Knight J.	Appl Environ Microbiol	10.1128/aem.02381-16	2016
	The interplay between PCOS pathology and diet on gut microbiota in a mouse model.	Rodriguez Paris V, Wong XYD, Solon-Biet SM, Edwards MC, Aflatounian A, Gilchrist RB, Simpson SJ, Handelsman DJ, Kaakoush NO, Walters KA.	Gut Microbes	10.1080/19490976.2022.2085961	2022
Transcriptome	The Oral Mouse Microbiome Promotes Tumorigenesis in Oral Squamous Cell Carcinoma.	Stashenko P, Yost S, Choi Y, Danciu T, Chen T, Yoganathan S, Kressirer C, Ruiz-Tourrella M, Das B, Kokaras A, Frias-Lopez J.	mSystems	10.1128/msystems.00323-19	2019
Pathogenicity	Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease.	Li N, Dai Z, Wang Z, Deng Z, Zhang J, Pu J, Cao W, Pan T, Zhou Y, Yang Z, Li J, Li B, Ran P.	Respir Res	10.1186/s12931-021-01872-z	2021
Metabolism	Dietary supplementation with spray-dried porcine plasma has prebiotic effects on gut microbiota in mice.	Moreto M, Miro L, Amat C, Polo J, Manichanh C, Perez-Bosque A.	Sci Rep	10.1038/s41598-020-59756-z	2020
Enzymology	A Novel Selective Medium for Isolation of Bacteroides fragilis from Clinical Specimens.	Ho PL, Ho LY, Yau CY, Tong MK, Chow KH.	J Clin Microbiol	10.1128/jcm.01988-16	2017
Genetics	Gut Metabolites Are More Predictive of Disease and Cohoused States than Gut Bacterial Features in a Polycystic Ovary Syndrome-Like Mouse Model.	Ho B, Ryback D, Benson B, Mason CN, Torres PJ, Quinn RA, Thackray VG, Kelley ST.	mSystems	10.1128/msystems.01149-20	2021
	Helicobacter bilis Infection Alters Mucosal Bacteria and Modulates Colitis Development in Defined Microbiota Mice.	Atherly T, Mosher C, Wang C, Hostetter J, Proctor A, Brand MW, Phillips GJ, Wannemuehler M, Jergens AE.	Inflamm Bowel Dis	10.1097/mib.0000000000000944	2016
	Impact of Gut Microbiota and Microbiota-Related Metabolites on Hyperlipidemia.	Jia X, Xu W, Zhang L, Li X, Wang R, Wu S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.634780	2021
	Role of gut microbiota in identification of novel TCM-derived active metabolites.	Lin TL, Lu CC, Lai WF, Wu TS, Lu JJ, Chen YM, Tzeng CM, Liu HT, Wei H, Lai HC.	Protein Cell	10.1007/s13238-020-00784-w	2021
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
	Dietary ellagic acid ameliorated Clostridium perfringens-induced subclinical necrotic enteritis in broilers via regulating inflammation and cecal microbiota.	Tang Y, Zhang X, Wang Y, Guo Y, Zhu P, Li G, Zhang J, Ma Q, Zhao L.	J Anim Sci Biotechnol	10.1186/s40104-022-00694-3	2022
	Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract.	Ott LC, Stromberg ZR, Redweik GAJ, Wannemuehler MJ, Mellata M.	mSphere	10.1128/msphere.00847-19	2020
	A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes.	Liu Z, Coales I, Penney N, McDonald JAK, Phetcharaburanin J, Seyfried F, Li JV, Li JV.	mSystems	10.1128/msystems.01047-20	2020
Metabolism	Tongxinluo May Alleviate Inflammation and Improve the Stability of Atherosclerotic Plaques by Changing the Intestinal Flora.	Qi Y, Liu W, Yan X, Zhang C, Zhang C, Liu L, Zheng X, Suo M, Ti Y, Ni M, Zhang M, Bu P.	Front Pharmacol	10.3389/fphar.2022.805266	2022
	A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response.	Evans JC, McEneany VL, Coyne MJ, Caldwell EP, Sheahan ML, Von SS, Coyne EM, Tweten RK, Comstock LE.	Nat Commun	10.1038/s41467-022-31925-w	2022
Pathogenicity	Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice.	Liu Z, Wang N, Ma Y, Wen D.	Front Microbiol	10.3389/fmicb.2019.00390	2019
Pathogenicity	Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse.	van de Wouw M, Walsh AM, Crispie F, van Leuven L, Lyte JM, Boehme M, Clarke G, Dinan TG, Cotter PD, Cryan JF.	Microbiome	10.1186/s40168-020-00846-5	2020
Metabolism	Gut Microbiota Serves a Predictable Outcome of Short-Term Low-Carbohydrate Diet (LCD) Intervention for Patients with Obesity.	Zhang S, Wu P, Tian Y, Liu B, Huang L, Liu Z, Lin N, Xu N, Ruan Y, Zhang Z, Wang M, Cui Z, Zhou H, Xie L, Chen H, Sun J.	Microbiol Spectr	10.1128/spectrum.00223-21	2021
	Crosstalk between gut microbiota and antidiabetic drug action.	Kyriachenko Y, Falalyeyeva T, Korotkyi O, Molochek N, Kobyliak N.	World J Diabetes	10.4239/wjd.v10.i3.154	2019
Metabolism	Desulfovibrio vulgaris, a potent acetic acid-producing bacterium, attenuates nonalcoholic fatty liver disease in mice.	Hong Y, Sheng L, Zhong J, Tao X, Zhu W, Ma J, Yan J, Zhao A, Zheng X, Wu G, Li B, Han B, Ding K, Zheng N, Jia W, Li H.	Gut Microbes	10.1080/19490976.2021.1930874	2021
	Polyphenols as Drivers of a Homeostatic Gut Microecology and Immuno-Metabolic Traits of Akkermansia muciniphila: From Mouse to Man.	Rodriguez-Daza MC, de Vos WM.	Int J Mol Sci	10.3390/ijms24010045	2022
Pathogenicity	Different Roles of Tocopherols and Tocotrienols in Chemoprevention and Treatment of Prostate Cancer.	Jiang Q.	Adv Nutr	10.1016/j.advnut.2024.100240	2024
	Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation.	Iljazovic A, Roy U, Galvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, Schmidt-Hohagen K, Neumann-Schaal M, Strowig T.	Mucosal Immunol	10.1038/s41385-020-0296-4	2021
Pathogenicity	Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium.	Li J, Mandal G, Mandal G, Rosen BP.	Anaerobe	10.1016/j.anaerobe.2016.03.012	2016
	Calorie restriction slows age-related microbiota changes in an Alzheimer's disease model in female mice.	Cox LM, Schafer MJ, Sohn J, Vincentini J, Weiner HL, Ginsberg SD, Blaser MJ.	Sci Rep	10.1038/s41598-019-54187-x	2019
Phylogeny	Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics.	Zaborin A, Penalver Bernabe B, Keskey R, Keskey R, Sangwan N, Hyoju S, Gottel N, Gilbert JA, Zaborina O, Alverdy JC.	mSystems	10.1128/msystems.00377-20	2020
Metabolism	Microbiome and ischemic stroke: A systematic review.	Lee YT, Mohd Ismail NI, Wei LK.	PLoS One	10.1371/journal.pone.0245038	2021
	Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life.	Wymore Brand M, Proctor AL, Hostetter JM, Zhou N, Friedberg I, Jergens AE, Phillips GJ, Wannemuehler MJ.	PLoS One	10.1371/journal.pone.0266005	2022
	A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.	Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotna T, Ouattara DA, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A.	Nat Commun	10.1038/s41467-021-26963-9	2021
Pathogenicity	In vitro activity of Biapenem plus RPX7009, a carbapenem combined with a serine beta-lactamase inhibitor, against anaerobic bacteria.	Goldstein EJ, Citron DM, Tyrrell KL, Merriam CV.	Antimicrob Agents Chemother	10.1128/aac.02418-12	2013
	The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community.	Wymore Brand M, Wannemuehler MJ, Phillips GJ, Proctor A, Overstreet AM, Jergens AE, Orcutt RP, Fox JG.	ILAR J	10.1093/ilar/ilv012	2015
	MALDI-TOF identification of the human Gut microbiome in people with and without diarrhea in Senegal.	Samb-Ba B, Mazenot C, Gassama-Sow A, Dubourg G, Richet H, Hugon P, Lagier JC, Raoult D, Fenollar F.	PLoS One	10.1371/journal.pone.0087419	2014
Enzymology	A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice.	Gomes-Neto JC, Mantz S, Held K, Sinha R, Segura Munoz RR, Schmaltz R, Benson AK, Walter J, Ramer-Tait AE.	J Microbiol Methods	10.1016/j.mimet.2017.02.003	2017
Pathogenicity	The DPP-4 inhibitor vildagliptin impacts the gut microbiota and prevents disruption of intestinal homeostasis induced by a Western diet in mice.	Olivares M, Neyrinck AM, Potgens SA, Beaumont M, Salazar N, Cani PD, Bindels LB, Delzenne NM.	Diabetologia	10.1007/s00125-018-4647-6	2018
Metabolism	Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.	Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA.	Cell Syst	10.1016/j.cels.2018.08.003	2018
	Vibrio vulnificus induces the death of a major bacterial species in the mouse gut via cyclo-Phe-Pro.	Kim JA, Jang BR, Kim YR, Jung YC, Kim KS, Lee KH.	Microbiome	10.1186/s40168-021-01095-w	2021
Metabolism	Commensal Escherichia coli Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production.	Kittana H, Gomes-Neto JC, Heck K, Geis AL, Segura Munoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE.	Front Immunol	10.3389/fimmu.2018.02318	2018
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
Pathogenicity	Commensal-derived metabolites govern Vibrio cholerae pathogenesis in host intestine.	You JS, Yong JH, Kim GH, Moon S, Nam KT, Ryu JH, Yoon MY, Yoon SS.	Microbiome	10.1186/s40168-019-0746-y	2019
	Changes in Microbial Community Composition Related to Sex and Colon Cancer by Nrf2 Knockout.	Song CH, Kim N, Nam RH, Choi SI, Yu JE, Nho H, Surh YJ.	Front Cell Infect Microbiol	10.3389/fcimb.2021.636808	2021
Metabolism	Gut-brain axis metabolic pathway regulates antidepressant efficacy of albiflorin.	Zhao ZX, Fu J, Ma SR, Peng R, Yu JB, Cong L, Pan LB, Zhang ZG, Tian H, Che CT, Wang Y, Jiang JD.	Theranostics	10.7150/thno.28068	2018
	Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia.	Naidenov B, Lim A, Willyerd K, Torres NJ, Johnson WL, Hwang HJ, Hoyt P, Gustafson JE, Chen C.	Front Microbiol	10.3389/fmicb.2019.01446	2019
	Surgical Menopause and Estrogen Therapy Modulate the Gut Microbiota, Obesity Markers, and Spatial Memory in Rats.	Zeibich L, Koebele SV, Bernaud VE, Ilhan ZE, Dirks B, Northup-Smith SN, Neeley R, Maldonado J, Nirmalkar K, Files JA, Mayer AP, Bimonte-Nelson HA, Krajmalnik-Brown R.	Front Cell Infect Microbiol	10.3389/fcimb.2021.702628	2021
Phylogeny	A fast and robust protocol for metataxonomic analysis using RNAseq data.	Cox JW, Ballweg RA, Taft DH, Velayutham P, Haslam DB, Porollo A.	Microbiome	10.1186/s40168-016-0219-5	2017
Genetics	Kelpie: generating full-length 'amplicons' from whole-metagenome datasets.	Greenfield P, Tran-Dinh N, Midgley D.	PeerJ	10.7717/peerj.6174	2019
Metabolism	Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.	Biggs MB, Medlock GL, Moutinho TJ, Lees HJ, Swann JR, Kolling GL, Papin JA.	ISME J	10.1038/ismej.2016.130	2017
Pathogenicity	Attenuation of Colitis by Serum-Derived Bovine Immunoglobulin/Protein Isolate in a Defined Microbiota Mouse Model.	Henderson AL, Brand MW, Darling RJ, Maas KJ, Detzel CJ, Hostetter J, Wannemuehler MJ, Weaver EM.	Dig Dis Sci	10.1007/s10620-015-3726-5	2015
Phylogeny	Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.	Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C.	Microbiome	10.1186/s40168-017-0384-1	2018
	Identification of PGN_1123 as the Gene Encoding Lipid A Deacylase, an Enzyme Required for Toll-Like Receptor 4 Evasion, in Porphyromonas gingivalis.	Jain S, Chang AM, Singh M, McLean JS, Coats SR, Kramer RW, Darveau RP.	J Bacteriol	10.1128/jb.00683-18	2019
	Gut dysbiosis breaks immunological tolerance toward the central nervous system during young adulthood.	Yadav SK, Boppana S, Ito N, Mindur JE, Mathay MT, Patel A, Dhib-Jalbut S, Ito K.	Proc Natl Acad Sci U S A	10.1073/pnas.1615715114	2017
Metabolism	Upregulation of colonic luminal polyamines produced by intestinal microbiota delays senescence in mice.	Kibe R, Kurihara S, Sakai Y, Suzuki H, Ooga T, Sawaki E, Muramatsu K, Nakamura A, Yamashita A, Kitada Y, Kakeyama M, Benno Y, Matsumoto M.	Sci Rep	10.1038/srep04548	2014
	Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5^-/- mice.	Li Y, Tinoco R, Elmen L, Segota I, Xian Y, Fujita Y, Sahu A, Zarecki R, Marie K, Feng Y, Khateb A, Frederick DT, Ashkenazi SK, Kim H, Perez EG, Day CP, Segura Munoz RS, Schmaltz R, Yooseph S, Tam MA, Zhang T, Avitan-Hersh E, Tzur L, Roizman S, Boyango I, Bar-Sela G, Orian A, Kaufman RJ, Bosenberg M, Goding CR, Baaten B, Levesque MP, Dummer R, Brown K, Merlino G, Ruppin E, Flaherty K, Ramer-Tait A, Long T, Peterson SN, Bradley LM, Ronai ZA.	Nat Commun	10.1038/s41467-019-09525-y	2019
	Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome.	Ussar S, Griffin NW, Bezy O, Fujisaka S, Vienberg S, Softic S, Deng L, Bry L, Gordon JI, Kahn CR.	Cell Metab	10.1016/j.cmet.2015.07.007	2015
Pathogenicity	Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota.	Chang CJ, Lin CS, Lu CC, Martel J, Ko YF, Ojcius DM, Tseng SF, Wu TR, Chen YY, Young JD, Lai HC.	Nat Commun	10.1038/ncomms8489	2015
	Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut.	Zitomersky NL, Coyne MJ, Comstock LE.	Infect Immun	10.1128/iai.01348-10	2011
	Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease.	Bloom SM, Bijanki VN, Nava GM, Sun L, Malvin NP, Donermeyer DL, Dunne WM, Allen PM, Stappenbeck TS.	Cell Host Microbe	10.1016/j.chom.2011.04.009	2011
	Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD.	Gut Pathog	10.1186/1757-4749-5-8	2013
Phylogeny	Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.	Sakamoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64192-0	2006
	Coprococcus intestinalis sp. nov., Parabacteroides caecihominis sp. nov., and "Akkermansia massiliensis" B2-R-115 with High Probiotic Potential from the Human Gut Microbiome.	Shamsuzzaman M, Dahal RH, Choi YJ, Kim S, Kim J.	Curr Microbiol	10.1007/s00284-025-04491-9	2025
	Segatella intestinalis sp. nov., and Parabacteroides caeci sp. nov., novel potential probiotics from the human gut microbiome.	Shamsuzzaman M, Dahal RH, Choi YJ, Kim S, Kim J.	Antonie Van Leeuwenhoek	10.1007/s10482-025-02150-4	2025
Genetics	Parabacteroides pekinense sp. nov.: a new bacterium isolated from the stool of a healthy man living in China.	Li Z, Zhou X, Xu W, Chen R, Zhao B, Wu C.	New Microbes New Infect	10.1016/j.nmni.2022.100973	2022
Phylogeny	Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus).	Sakamoto M, Ohkuma M.	Int J Syst Evol Microbiol	10.1099/ijs.0.040931-0	2013
Phylogeny	Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters.	Jabari L, Gannoun H, Cayol JL, Hedi A, Sakamoto M, Falsen E, Ohkuma M, Hamdi M, Fauque G, Ollivier B, Fardeau ML.	Int J Syst Evol Microbiol	10.1099/ijs.0.032508-0	2012
Phylogeny	Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov.	Clavel T, Saalfrank A, Charrier C, Haller D.	Arch Microbiol	10.1007/s00203-010-0568-6	2010
Genetics	Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen.	Bellali S, Lo CI, Naud S, Fonkou MDM, Armstrong N, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2019.100602	2019
Genetics	Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics.	Andrieu C, Mailhe M, Ricaboni D, Fonkou MDM, Bilen M, Cadoret F, Tomei E, Armstrong N, Vitton V, Benezech A, Davoust B, Levasseur A, Lagier JC, Fournier PE, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2018.06.006	2018
Phylogeny	Parabacteroides chongii sp. nov., isolated from blood of a patient with peritonitis.	Kim H, Im WT, Kim M, Kim D, Seo YH, Yong D, Jeong SH, Lee K	J Microbiol	10.1007/s12275-018-8122-3	2018
Phylogeny	Parabacteroides gordonii sp. nov., isolated from human blood cultures.	Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M, Komiya H, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.010611-0	2009
Phylogeny	"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.	Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SM	J Clin Microbiol	10.1128/JCM.43.9.4522-4527.2005	2005

References

#8022	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19448
#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 )
#58398	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48944
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68367	Automatically annotated from API 20A .
#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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Parabacteroides goldsteinii (DSM 19448, ATCC BAA-1180, CCUG 48944)

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