Alistipes indistinctus (DSM 22520, JCM 16068, YIT 12060)

Name: Alistipes indistinctus (DSM 22520, JCM 16068, YIT 12060)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14033

Type strain

Culture col. no. DSM 22520 JCM 16068 YIT 12060

NCBI tax ID(s) 742725 626932

Special Collections DSMZ JCM Literature strains

History DSMZ <- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan <- F. Nagai and M. Morotomi JCM <-- Y. Watanabe B131 (=YIT 12060).

Links

Alistipes indistinctus DSM 22520 is an anaerobe, Gram-negative, ovoid-shaped bacterium that was isolated from human faeces of healthy Japanese adult.

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

Name and taxonomic classification

SI-ID 407254

JCM 16068,DSM 22520

@ref 20215

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

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes indistinctus

Full scientific name Alistipes indistinctus Nagai et al. 2010

BacDive ID	Other strains from **Alistipes indistinctus** (2)	Type strain
161696	A. indistinctus JCM 15916
164725	A. indistinctus JCM 34084

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29508	negative	2.4 µm	0.6 µm	ovoid-shaped
125439	negative				99.9
125438	negative				96.292

Pigmentation

29508

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16377	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16377	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16377	anaerobe
29508	anaerobe
125439	facultative anaerobe	90.48

Spore formation

@ref	Spore formation	Confidence
29508
125438		91.875
125439		99.974

Observation

67770

Observationquinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29508	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
29508	17057 ChEBI	cellobiose	+	carbon source
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
29508	17234 ChEBI	glucose	+	carbon source
29508	17754 ChEBI	glycerol	+	carbon source
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
29508	17716 ChEBI	lactose	+	carbon source
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
29508	17306 ChEBI	maltose	+	carbon source
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
29508	29864 ChEBI	mannitol	+	carbon source
29508	37684 ChEBI	mannose	+	carbon source
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29508	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
29508	26546 ChEBI	rhamnose	+	carbon source
29508	17814 ChEBI	salicin	+	carbon source
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
29508	30911 ChEBI	sorbitol	+	carbon source
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
29508	17992 ChEBI	sucrose	+	carbon source
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
29508	27082 ChEBI	trehalose	+	carbon source
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
29508	18222 ChEBI	xylose	+	carbon source

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
29508	acid phosphatase	+	3.1.3.2
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
29508	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
29508	alpha-galactosidase	+	3.2.1.22
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
29508	catalase	+	1.11.1.6
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	acetate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	pentose phosphate pathway	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	purine metabolism	71.28	67 of 94
66794	pyrimidine metabolism	71.11	32 of 45
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	degradation of pentoses	64.29	18 of 28
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	methylglyoxal degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	proline metabolism	54.55	6 of 11
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cysteine metabolism	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	histidine metabolism	48.28	14 of 29
66794	arginine metabolism	45.83	11 of 24
66794	ascorbate metabolism	45.45	10 of 22
66794	lysine metabolism	45.24	19 of 42
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	non-pathway related	42.11	16 of 38
66794	lipid metabolism	41.94	13 of 31
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	ketogluconate metabolism	37.5	3 of 8
66794	oxidative phosphorylation	36.26	33 of 91
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	urea cycle	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	heme metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	glutathione metabolism	21.43	3 of 14

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
16377	-	-	+	-	+	+	+	+	+	+/-	-	+	-	+	+	-	-	-	+	+	not determinedn.d.	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
16377	-	-	+	+	-	+/-	+/-	-	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16377	human faeces of healthy Japanese adult	Homo sapiens	Tokyo	Japan	JPN	Asia
67770	Human feces	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AB600999 (>99% sequence identity) for Alistipes indistinctus subclade from Microbeatlas

Aquatic Samples	502
Soil Samples	131
Animal Samples	32708
Plant Samples	73
Total Samples	33414

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16377	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2514499v1 assembly for Alistipes indistinctus YIT 12060	complete	GCA_025144995	742725.163	8119061705	742725	98.77
66792	Alis_indi_YIT_V1 assembly for Alistipes indistinctus YIT 12060	scaffold	GCA_000231275	742725.3	2513237277	742725	75.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Alistipes indistinctus gene for 16S ribosomal RNA, partial sequence	AB600999	1490		742725
16377	Alistipes indistinctus YIT 12060 gene for 16S rRNA, partial sequence	AB490804	1482		742725

GC content

@ref	GC-content (mol%)	Method
16377	55.2	high performance liquid chromatography (HPLC)
29508	55.2
67770	54.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2514499v1 assembly for Alistipes indistinctus YIT 12060
BV-BRC: 742725.163

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.48	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	motility	BacteriaNetⓘ	yes	68.00	no
125439	spore_formation	BacteriaNetⓘ	no	99.97	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes indistinctus YIT 12060 YIT 12060
NCBI: GCA_025144995.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.29	yes
125438	anaerobic	anaerobicⓘ	yes	80.49	yes
125438	aerobic	aerobicⓘ	no	89.07	yes
125438	spore-forming	spore-formingⓘ	no	91.88	yes
125438	thermophilic	thermophileⓘ	no	94.68	yes
125438	flagellated	motile2+ⓘ	no	89.77	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma.	Zhang J, Yang J, Luo J, Wu W, Luo H, Wei W, Lyu H, Wang Y, Yi H, Zhang Y, Fan Z, Lyu H, Kanakaveti VP, Qin B, Yuan P, Yang R, Zhang H, Zuo T, Felsher DW, Lee MH, Li K.	Nat Commun	10.1038/s41467-025-58407-z	2025
	Gut Microbiome-Wide Search for Bacterial Azoreductases Reveals Potentially Uncharacterized Azoreductases Encoded in the Human Gut Microbiome.	Braccia DJ, Minabou Ndjite G, Weiss A, Levy S, Abeysinghe S, Jiang X, Pop M, Hall B.	Drug Metab Dispos	10.1124/dmd.122.000898	2023
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
	A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria.	Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS.	Nat Microbiol	10.1038/s41564-022-01176-y	2022
Metabolism	A bacterial bile acid metabolite modulates T_reg activity through the nuclear hormone receptor NR4A1.	Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR.	Cell Host Microbe	10.1016/j.chom.2021.07.013	2021
Enzymology	The gut microbiome influences the bioavailability of olanzapine in rats.	Cussotto S, Walsh J, Golubeva AV, Zhdanov AV, Strain CR, Fouhy F, Stanton C, Dinan TG, Hyland NP, Clarke G, Cryan JF, Griffin BT.	EBioMedicine	10.1016/j.ebiom.2021.103307	2021
	Administration of Alistipes indistinctus prevented the progression from nonalcoholic fatty liver disease to nonalcoholic steatohepatitis by enhancing the gut barrier and increasing Lactobacillus spp.	Xu X, Wang Y, Wu X, Cai T, Dong L, Liang S, Zhu L, Song X, Dong Y, Zheng Y, Li L, Sun W.	Biochem Biophys Res Commun	10.1016/j.bbrc.2024.151033	2024
	Exploring bacterial metabolites in microbe-human host dialogue and their therapeutic potential in Alzheimer's diseases.	Singh SD, Bharali P, Nagamani S.	Mol Divers	10.1007/s11030-024-11028-y	2025
	Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia.	Xu YX, Liu LD, Zhu JY, Zhu SS, Ye BQ, Yang JL, Huang JY, Huang ZH, You Y, Li WK, He JL, Xia M, Liu Y.	Cell Host Microbe	10.1016/j.chom.2024.02.001	2024
	Mendelian randomization study revealed a gut microbiota-immune system-kidney junction axis in chronic kidney disease.	Tan J, Xiong Z, Yu S, Lu W, Yu L.	Sci Rep	10.1038/s41598-025-05941-x	2025
Genetics	A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.	Yuan J, Sun Z, Sun R, Wang J, Wu C, Liu B, Zhao X, Li Q, Zhao J, Cai K.	Biology (Basel)	10.3390/biology14080980	2025
	A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis.	Lee SB, Gupta H, Min BH, Ganesan R, Sharma SP, Won SM, Jeong JJ, Cha MG, Kwon GH, Jeong MK, Hyun JY, Eom JA, Park HJ, Yoon SJ, Lee SY, Choi MR, Kim DJ, Oh KK, Suk KT.	Artif Cells Nanomed Biotechnol	10.1080/21691401.2024.2347380	2024
Genetics	PuRenDan alleviates type 2 diabetes mellitus symptoms by modulating the gut microbiota and its metabolites.	Ma X, Qiu Y, Mao M, Lu B, Zhao H, Pang Z, Li S.	J Ethnopharmacol	10.1016/j.jep.2023.117627	2024
Genetics	Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.	Cai X, Dai J, Xie Y, Xu S, Liu M.	Sci Rep	10.1038/s41598-024-71740-5	2024
	Microbial stars: shedding light on gut microbes' role in insulin resistance and innovative diabetes therapies.	Zhang J.	Gut Microbes	10.1080/19490976.2024.2307581	2024
	Roles of traditional Chinese medicine extracts in hyperuricemia and gout treatment: Mechanisms and clinical applications.	Wang YB, Jin CZ.	World J Gastroenterol	10.3748/wjg.v30.i47.5076	2024
Genetics	Evidence from mendelian randomization identifies several causal relationships between primary membranous nephropathy and gut microbiota.	Wu J, Zhang J, Huang G, Zhong Y, Yang Y, Deng P.	Ren Fail	10.1080/0886022x.2024.2349136	2024
	Akkermansia muciniphila is associated with normal muscle mass and Eggerthella is related with sarcopenia in cirrhosis.	Efremova I, Alieva A, Maslennikov R, Poluektova E, Zharkova M, Kudryavtseva A, Krasnov G, Zharikov Y, Nerestyuk Y, Karchevskaya A, Ivashkin V.	Front Nutr	10.3389/fnut.2024.1438897	2024
	Targeting keystone species helps restore the dysbiosis of butyrate-producing bacteria in nonalcoholic fatty liver disease.	Wu D, Liu L, Jiao N, Zhang Y, Yang L, Tian C, Lan P, Zhu L, Loomba R, Zhu R.	Imeta	10.1002/imt2.61	2022
	Alterations of gut microbiome in chronic rhinosinusitis: insights from a mendelian randomization study.	Wang KS, Tu JH, Wang QX, Zhou SZ, Wu JR, Qiu QH.	Braz J Otorhinolaryngol	10.1016/j.bjorl.2025.101698	2025
Metabolism	Lipid alterations in acute myocardial infarction are associated with gut microbiota.	Zuo J, Wang P, Xue K, Tan Y, Zhang T, Li Y, He F, Wu W, Yan Z, Cong L, Li G.	Microbiol Spectr	10.1128/spectrum.02370-24	2025
	Gut microbiota-directed intervention with high-amylose maize ameliorates metabolic dysfunction in diet-induced obese mice.	Chiou WC, Lai WH, Cai YL, Du ML, Lai HM, Chen JC, Huang HC, Liu HK, Huang C.	Food Funct	10.1039/d2fo01211a	2022
Genetics	Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.	Kazen AB, Umfleet LG, Aboulalazm FA, Cohen AD, Terhune S, Mason L, Obarski S, Franczak M, Kindel TL, Wang Y, Kirby JR.	Brain Sci	10.3390/brainsci15060538	2025
Genetics	Gut microbiome composition and metabolic activity in metabolic-associated fatty liver disease.	Zhang D, Wang Q, Li D, Chen S, Chen J, Zhu X, Bai F.	Virulence	10.1080/21505594.2025.2482158	2025
	Alistipes senegalensis is Critically Involved in Gut Barrier Repair Mediated by Panax Ginseng Neutral Polysaccharides in Aged Mice.	Wang D, Wang H, Li Y, Lu J, Tang X, Yang D, Wang M, Zhao D, Liu F, Zhang S, Sun L.	Adv Sci (Weinh)	10.1002/advs.202416427	2025
	Major heavy metals and human gut microbiota composition: a systematic review with nutritional approach.	Rezazadegan M, Forootani B, Hoveyda Y, Rezazadegan N, Amani R.	J Health Popul Nutr	10.1186/s41043-025-00750-4	2025
	Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.	Zhu M, Wang Q, Yang Y, Liu X, Zhang J, Li G, Liu W, Xiang X, Chen J.	Nutr J	10.1186/s12937-025-01116-6	2025
Genetics	Gut microbiota, circulating inflammatory proteins and sepsis: a bi-directional Mendelian randomization study.	Li Z, Lin L, Kong Y, Feng J, Ren X, Wang Y, Chen X, Wu S, Yang R, Li J, Liu Y, Lu Y, Chen J.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1398756	2024
	Exploring the mediating role of the plasma lipidome in the pathway from the gut microbiota to dementia: a Mendelian randomization study.	Li B, Sun X, Luo X, Kan Y, Wang W, Wang T, Wu C, Hu Y, Bi X.	Arch Med Sci	10.5114/aoms/201447	2025
	Complete Genome Sequence of Alistipes indistinctus Strain 2BBH45, Isolated from the Feces of a Healthy Japanese Male.	Ogata Y, Sakamoto M, Ohkuma M, Hattori M, Suda W.	Microbiol Resour Announc	10.1128/mra.01284-20	2021
	Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.	Lim MY, Hong S, Nam YD.	Front Immunol	10.3389/fimmu.2024.1512683	2024
	Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?	Garcia-Martinez Y, Alexandrova E, Iebba V, Ferravante C, Spinelli M, Franci G, Amoresano A, Weisz A, Trepiccione F, Borriello M, Ingrosso D, Perna AF.	BMC Microbiol	10.1186/s12866-024-03590-0	2024
Phylogeny	Identification of colorectal cancer progression-associated intestinal microbiome and predictive signature construction.	Liu J, Huang X, Chen C, Wang Z, Huang Z, Qin M, He F, Tang B, Long C, Hu H, Pan S, Wu J, Tang W.	J Transl Med	10.1186/s12967-023-04119-1	2023
Pathogenicity	Nutraceutical Capsules LL1 and Silymarin Supplementation Act on Mood and Sleep Quality Perception by Microbiota-Gut-Brain Axis: A Pilot Clinical Study.	Santamarina AB, Nehmi Filho V, Freitas JA, Franco LAM, Fonseca JV, Martins RC, Turri JAO, Silva BFRBD, Gusmao AF, Olivieri EHR, Otoch JP, Pessoa AFM.	Nutrients	10.3390/nu16183049	2024
	Network pharmacology-based insights into the role of gut microbiota metabolites in insulin resistance.	Xiao B, Chen X, Zong R, Guan Y, Zhu Z, Bi S.	Front Microbiol	10.3389/fmicb.2025.1617496	2025
	Fecal Microbiome and Urine Metabolome Profiling of Type 2 Diabetes.	Yi HM, Won S, Pak J, Park SE, Kim MR, Kim JH, Park EY, Hwang SY, Lee MH, Son HS, Kwak S.	J Microbiol Biotechnol	10.4014/jmb.2411.11071	2025
Pathogenicity	Gut microbial dysbiosis correlates with stroke severity markers in aged rats.	Hammond TC, Messmer S, Frank JA, Lukins D, Colwell R, Lin AL, Pennypacker KR.	Front Stroke	10.3389/fstro.2022.1026066	2022
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
	Comprehensive analysis of vaginal microbiota, metabolites, and inflammatory factors in preterm and term pregnancies.	Shen LP, Cai BJ, Guan JX, Peng T, Jin L.	Front Microbiol	10.3389/fmicb.2025.1689494	2025
	Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.	Li N, Gao G, Zhang T, Zhao C, Zhao Y, Zhang Y, Sun Z.	Curr Microbiol	10.1007/s00284-025-04246-6	2025
	Cetobacterium somerae-derived argininosuccinic acid promotes intestinal and liver ureagenesis to alleviate ammonia intoxication.	Wang S, Li X, Zhang M, Li M.	Microbiome	10.1186/s40168-025-02152-4	2025
Phylogeny	Gut microbiota is associated with the disease characteristics of patients with newly diagnosed diffuse large B-cell lymphoma.	Li Z, Shi J, Wu X, Yan S, Gao Z, Liu Y.	Am J Cancer Res	10.62347/dimg6893	2025
	Prenatal lead exposure is negatively associated with the gut microbiome in childhood.	Eggers S, Midya V, Bixby M, Gennings C, Torres-Olascoaga LA, Walker RW, Wright RO, Arora M, Tellez-Rojo MM.	Front Microbiol	10.3389/fmicb.2023.1193919	2023
	Alteration of the gut microbiome and correlated metabolism in a rat model of long-term depression.	Li Y, Li J, Cheng R, Liu H, Zhao Y, Liu Y, Chen Y, Sun Z, Zhai Z, Wu M, Yan Y, Sun Y, Zhang Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1116277	2023
	Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment.	Shen X, Leng B, Zhang S, Kwok LY, Zhao F, Zhao J, Sun Z, Zhang J.	Microbiome Res Rep	10.20517/mrr.2024.35	2024
Genetics	Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.	Lotankar M, Houttu N, Mokkala K, Laitinen K.	Nutr Rev	10.1093/nutrit/nuae192	2025
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
Pathogenicity	Heat-Killed Bifidobacterium bifidum B1628 May Alleviate Dextran Sulfate Sodium-Induced Colitis in Mice, and the Anti-Inflammatory Effect Is Associated with Gut Microbiota Modulation.	Feng C, Zhang W, Zhang T, He Q, Kwok LY, Tan Y, Zhang H.	Nutrients	10.3390/nu14245233	2022
	Ameliorative Effects of Anthocyanin Metabolites on Western Diet-Induced NAFLD by Modulating Co-Occurrence Networks of Gut Microbiome.	Nakano H, Sakao K, Wada K, Hou DX.	Microorganisms	10.3390/microorganisms11102408	2023
	Linking Nutrients to Multiple Sclerosis Pathogenesis: Biological Evidence and Clinical Implications.	Rosso R, Maglione A, Bronzini M, Virgilio E, Clerico M, Rolla S.	Nutrients	10.3390/nu17213414	2025
	Baseline intestinal microbiota composition influences response to a real-world dietary fiber intervention.	Hoffmann Sarda FA, Giuntini EB, Oliveira A, Souza GS, Prado SBR, Taddei CR, Tadini CC, Bittinger K, Bushman FD, Menezes EW, Hoffmann C.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00817-4	2025
	The gut microbiome and regional fat distribution: Findings from the Baltimore Longitudinal Study of Aging.	Tilves C, Tanaka T, Differding MK, Spira AP, Chia CW, Ferrucci L, Mueller NT.	Obesity (Silver Spring)	10.1002/oby.23717	2023
	Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift.	Chanda D, De D.	Gut Microbes	10.1080/19490976.2024.2304900	2024
	Associations between gut microbiota and sarcopenia or its defining parameters in older adults: A systematic review.	Lapauw L, Rutten A, Dupont J, Amini N, Vercauteren L, Derrien M, Raes J, Raes J, Gielen E.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13569	2024
	Correlation Between Gastroesophageal Reflux Disease and Small Intestinal Bacterial Overgrowth: Analysis of Intestinal Microbiome and Metabolic Characteristics.	Wang ZT, Tan WT, Huang JL, Zhang PF, Li Q, Wang MM, Meng MM, Su H, Guo CM, Liu H.	J Inflamm Res	10.2147/jir.s487185	2025
	Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.	Qie J, Cao M, Xu M, Zhang Y, Luo L, Sun C, Ke D, Yuan S, Jia W, Qiu T, Li T, Du X, Xiao C, Hong Z, Zhang B.	mSystems	10.1128/msystems.01091-25	2025
	Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.	Liu J, Sun J, Yu J, Chen H, Zhang D, Zhang T, Ma Y, Zou C, Zhang Z, Ma L, Yu X.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00399-z	2023
Metabolism	Comparative analysis of hyperuricemia induction methods and probiotic interventions in mice.	Wang Y, Zhang H, Liu S, Sun S, Ren W, Wang T, Zhang S, Yao H, Jin C, Wu N.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100422	2025
	Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.	Zhang Z, Yang Z, Lin S, Jiang S, Zhou X, Li J, Lu W, Zhang J.	Gut Microbes	10.1080/19490976.2025.2520407	2025
	[Associations of Socioeconomic Factors,Nutrients Intake,and Gut Microbiota of Healthy Pregnant Women in the Third Trimester with Gestational Weight Gain].	Ma LK, Xue Y, He TC, Zhang YM.	Zhongguo Yi Xue Ke Xue Yuan Xue Bao	10.3881/j.issn.1000-503x.10505	2018
	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
	Immunomodulatory Role of Vitamin D on Gut Microbiome in Children.	Tabassum A, Ali A, Zahedi FD, Ismail NAS.	Biomedicines	10.3390/biomedicines11051441	2023
	Gut Microbiota Feature of Senile Osteoporosis by Shallow Shotgun Sequencing Using Aged Rats Model.	Wang N, Ma S, Fu L.	Genes (Basel)	10.3390/genes13040619	2022
	The Prebiotic Effect of Kaempferol in Regulating Bile Acid Metabolism.	Li X, Huang G, Khan I, Ding Z, Hsiao WLW, Liu Z.	Food Sci Nutr	10.1002/fsn3.70023	2025
	Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation.	Chatthanathon P, Leelahavanichkul A, Cheibchalard T, Wilantho A, Hirankarn N, Somboonna N.	Sci Rep	10.1038/s41598-024-77672-4	2024
	Pterostilbene Protects against Osteoarthritis through NLRP3 Inflammasome Inactivation and Improves Gut Microbiota as Evidenced by In Vivo and In Vitro Studies.	Lee YC, Chang YT, Cheng YH, Pranata R, Hsu HH, Chen YL, Chen RJ.	J Agric Food Chem	10.1021/acs.jafc.3c09749	2024
	Olsenella scatoligenes-derived skatole promotes smooth muscle cell proliferation and migration to aggravate atherosclerosis.	Zhao Y, Chen J, Zhu S, Xu Y, Zhu J, Yang J, Zhou W, Yang Y, Lin M, Chen Q, Xia M, Chen Y, Liu Y.	ISME J	10.1093/ismejo/wraf238	2025
Metabolism	Exploring the functional diversity and metabolic activities of the human gut microbiome in Thai adults in response to a prebiotic diet.	Kingkaw A, Patumcharoenpol P, Suratannon N, Nakphaichit M, Roytrakul S, Vongsangnak W.	Microbiol Spectr	10.1128/spectrum.01599-24	2025
	High-risk genotypes for type 1 diabetes are associated with the imbalance of gut microbiome and serum metabolites.	Yue T, Tan H, Wang C, Liu Z, Yang D, Ding Y, Xu W, Yan J, Zheng X, Weng J, Luo S.	Front Immunol	10.3389/fimmu.2022.1033393	2022
	Influence of Nonenzymatic Browning Reactions on the Digestibility and Gut Microbiota Fermentation of Starch and Protein.	Ding W, Bai Y, Rose DJ.	Compr Rev Food Sci Food Saf	10.1111/1541-4337.70299	2025
	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
	Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.	Liu Y, Qiu Q, Chen Y, Deng Y, Huang W, Sun C, Shang X, Chen X, Wang C, Han L, Chen S, Yuan J, Xu F, Yang Z, Fang X, Huang L.	Microbiol Spectr	10.1128/spectrum.01459-24	2025
Pathogenicity	The Influence of Dietary Factors on Melanoma Development and Progression: A Comprehensive Review.	Watson AE, Yusuf N.	Nutrients	10.3390/nu17111891	2025
Metabolism	Treatment-Related Mechanisms of Tibetan Medicine Terminalia chebula (TC) Aqueous Extract Against Mouse Gastroenteritis Caused by Yak-Origin Salmonella Determined Using Intestinal Microbiome Analysis and Metabolomics.	Li D, Zhang K, Xue X, Bai Z, Yang, Qi J, Suolang S.	Animals (Basel)	10.3390/ani15050755	2025
	Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.	Li D, Li M, Gao H, Hu K, Xie R, Fan J, Huang M, Liao C, Han C, Guo Z, Chen X, Li M.	Front Microbiol	10.3389/fmicb.2024.1475984	2024
	Fecal Microbiota Restoration Modulates the Microbiome in Inflammation-Driven Colorectal Cancer.	Gates TJ, Yuan C, Shetty M, Kaiser T, Nelson AC, Chauhan A, Starr TK, Staley C, Subramanian S.	Cancers (Basel)	10.3390/cancers15082260	2023
	Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut.	Jiang S, Zhang C, Han Z, Ma W, Wang S, Huo D, Cui W, Zhai Q, Huang S, Zhang J.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00447-8	2023
	The Gut Microbiome, Microsatellite Status and the Response to Immunotherapy in Colorectal Cancer.	Sillo TO, Beggs AD, Middleton G, Akingboye A.	Int J Mol Sci	10.3390/ijms24065767	2023
Genetics	Screening potential biomarkers associated with insulin resistance in high-fat diet-fed mice by integrating metagenomics and untargeted metabolomics.	Zhou Y, Tang J, Du W, Zhang Y, Ye B-C.	Microbiol Spectr	10.1128/spectrum.04094-23	2024
	Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit.	Haberman Y, Kamer I, Amir A, Goldenberg S, Efroni G, Daniel-Meshulam I, Lobachov A, Daher S, Hadar R, Gantz-Sorotsky H, Urban D, Braun T, Bar J.	Sci Rep	10.1038/s41598-023-29136-4	2023
Pathogenicity	The Influence of Probiotic Supplementation on the Obesity Indexes, Neuroinflammatory and Oxidative Stress Markers, Gut Microbial Diversity, and Working Memory in Obese Thai Children.	Khongtan S, Sivamaruthi BS, Thangaleela S, Kesika P, Bharathi M, Sirilun S, Choeisoongnern T, Peerajan S, Sittiprapaporn P, Chaiyasut C.	Foods	10.3390/foods12213890	2023
	The Interaction between Human Microbes and Advanced Glycation End Products: The Role of Klebsiella X15 on Advanced Glycation End Products' Degradation.	Shi A, Ji X, Li W, Dong L, Wu Y, Zhang Y, Liu X, Zhang Y, Wang S.	Nutrients	10.3390/nu16050754	2024
	Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.	Yan P, Sun Y, Luo J, Liu X, Wu J, Miao Y.	Clin Proteomics	10.1186/s12014-023-09396-y	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
Metabolism	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
Metabolism	The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine.	Mousa S, Sarfraz M, Mousa WK.	Metabolites	10.3390/metabo13050674	2023
	Interconnection of the Gut-Skin Axis in NC/Nga Mouse with Atopic Dermatitis: Effects of the Three Types of Bifidobacterium bifidum CBT-BF3 (Probiotics, Postbiotics, and Cytosine-Phosphate-Guanine Oligodeoxynucleotide) on T Cell Differentiation and Gut Microbiota.	Kim GI, Jeong HY, Kim IS, Lee SH, Kim SH, Moon YS, Cho KK.	Food Sci Anim Resour	10.5851/kosfa.2024.e100	2024
Pathogenicity	Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial.	Santamarina AB, Filho VN, de Freitas JA, Franco LAM, Martins RC, Fonseca JV, Orellana Turri JA, Hufnagel MT, Demarque DP, da Silva BFRB, Gusmao AF, Olivieri EHR, de Souza E, de Souza EA, Otoch JP, Pessoa AFM.	Mol Nutr Food Res	10.1002/mnfr.202400806	2025
	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
	Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure.	Kang Y, Chen S, Chen Y, Tian L, Wu Q, Zheng M, Li Z.	Int J Hyg Environ Health	10.1016/j.ijheh.2021.113882	2022
	Gut Microbiota Modulates the Protective Role of Ginsenoside Compound K Against Sodium Valproate-Induced Hepatotoxicity in Rat.	Zhou L, Zeng X, Liao J, Chen L, Ouyang D.	Front Microbiol	10.3389/fmicb.2022.936585	2022
Enzymology	Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.	Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2022.11.015	2023
	Analyzing the overall effects of the microbiome abundance data with a Bayesian predictive value approach.	Zhang X, Yi N.	Stat Methods Med Res	10.1177/09622802221107106	2022
	Complement C1q is a key player in tumor-associated macrophage-mediated CD8⁺ T cell and NK cell dysfunction in malignant pleural effusion.	Yi FS, Qiao X, Dong SF, Chen QY, Wei RQ, Shao MM, Shi HZ.	Int J Biol Sci	10.7150/ijbs.100607	2024
	Research trends on the gut microbiota in endocrine metabolism: a thematic and bibliometric analysis.	Dogan D, Celik T.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1371727	2024
	Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China.	Yang Y, Chen J, Gao H, Cui M, Zhu M, Xiang X, Wang Q.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1374544	2024
Genetics	Effect of minocycline, methyl prednisolone, or combination treatment on the colonic bacterial population in a state of colonic inflammation using the murine dextran sulfate sodium model.	Khajah MA, Hawai S.	Microb Cell Fact	10.1186/s12934-023-02242-8	2023
	Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review.	Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.804644	2022
	A microbial causal mediation analytic tool for health disparity and applications in body mass index.	Wang C, Ahn J, Tarpey T, Yi SS, Hayes RB, Li H.	Microbiome	10.1186/s40168-023-01608-9	2023
	Prenatal metal exposures and childhood gut microbial signatures are associated with depression score in late childhood.	Midya V, Nagdeo K, Lane JM, Torres-Olascoaga LA, Torres-Calapiz M, Gennings C, Horton MK, Tellez-Rojo MM, Wright RO, Arora M, Eggers S.	Sci Total Environ	10.1016/j.scitotenv.2024.170361	2024
	The Combination of Lead and Bacillus coagulans R11 Increased the Concentration of Alpha-Solanine in the Cecum of Laying Hens and the Pathogens Abundance Decreased.	Xing SC, Chen JY, Chen YX, Wu RT, Huang CB, Zhang Y, Mi JD, Liao XD.	Front Microbiol	10.3389/fmicb.2020.585197	2020
	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
	Serum metabolomic profiling uncovered metabolic shifts in individuals upon moderate-altitude exposure and identified the potentiality of beta-alanine to ameliorate hyperuricemia.	Chen X, Zou G, Yang Z, Qi X, Song F, Peng L, Wang D, Zhou J, Ma J, He H, Hong Y, Wang YE, Fan Y, Liu Z, Li X.	Redox Biol	10.1016/j.redox.2025.103546	2025
	Effects of Long-Term Fasting on Gut Microbiota, Serum Metabolome, and Their Association in Male Adults.	Wu F, Guo Y, Wang Y, Sui X, Wang H, Zhang H, Xin B, Yang C, Zhang C, Jiang S, Qu L, Feng Q, Dai Z, Shi C, Li Y.	Nutrients	10.3390/nu17010035	2024
	Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis.	Zhu X, Xu P, Zhu R, Gao W, Yin W, Lan P, Zhu L, Jiao N.	Commun Biol	10.1038/s42003-023-05714-0	2024
	The Relationship between Urinary Stones and Gut Microbiomeby 16S Sequencing.	Zhou C, Li K, Zhao L, Li W, Guo Z, Xu J, Qi X, Yuan H.	Biomed Res Int	10.1155/2020/1582187	2020
	Silibinin-derived microbiota enrich (R)-2,3-dihydroxy-isovalerate and ameliorate colitis via the GAT-3/RARbeta/RORgammat axis.	Yan B, Zheng X, Lu D, Li T, Chen X, Shao Z, Fu T.	ISME J	10.1093/ismejo/wraf175	2025
	Metagenomic and metabolomic analyses reveal synergistic effects of fecal microbiota transplantation and anti-PD-1 therapy on treating colorectal cancer.	Huang J, Zheng X, Kang W, Hao H, Mao Y, Zhang H, Chen Y, Tan Y, He Y, Zhao W, Yin Y.	Front Immunol	10.3389/fimmu.2022.874922	2022
	Emodin modulates gut microbial community and triggers intestinal immunity.	Mabwi HA, Lee HJ, Hitayezu E, Mauliasari IR, Pan CH, Mwaikono KS, Komba EVG, Lee CG, Cha KH.	J Sci Food Agric	10.1002/jsfa.12221	2023
Phylogeny	Composition of the Gut Microbiota Associated with the Response to Immunotherapy in Advanced Cancer Patients: A Chinese Real-World Pilot Study.	Cheng X, Wang J, Gong L, Dong Y, Shou J, Pan H, Yu Z, Fang Y.	J Clin Med	10.3390/jcm11185479	2022
	Fecal Immunoglobulin Levels as a Modifier of the Gut Microbiome in Patients with Common Variable Immunodeficiency.	Noltner C, Bulashevska A, Hubscher K, Haberstroh H, Grimbacher B, Proietti M.	J Clin Immunol	10.1007/s10875-023-01469-9	2023
	The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins.	Szczesniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D.	mBio	10.1128/mbio.00980-23	2023
	Microbial Composition and Co-occurrence Patterns in the Gut Microbial Community of Normal and Obese Mice in Response to Astaxanthin.	Gao Y, Liu F, Li RW, Li C, Xue C, Tang Q.	Front Microbiol	10.3389/fmicb.2021.671271	2021
	Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.	Qin Y, Tong X, Mei WJ, Cheng Y, Zou Y, Han K, Yu J, Jie Z, Zhang T, Zhu S, Jin X, Wang J, Yang H, Xu X, Zhong H, Xiao L, Ding PR.	Nat Commun	10.1038/s41467-024-47523-x	2024
	Yoyo Dieting, Post-Obesity Weight Loss, and Their Relationship with Gut Health.	Phuong-Nguyen K, McGee SL, Aston-Mourney K, Mcneill BA, Mahmood MQ, Rivera LR.	Nutrients	10.3390/nu16183170	2024
Pathogenicity	Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model.	Kreis V, Toffano-Nioche C, Deneve-Larrazet C, Marvaud J-C, Garneau JR, Dumont F, van Dijk EL, Jaszczyszyn Y, Boutserin A, D'Angelo F, Gautheret D, Kansau I, Janoir C, Soutourina O.	mSystems	10.1128/msystems.00863-24	2024
Pathogenicity	Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics.	Gomez-Varela D, Xian F, Grundtner S, Sondermann JR, Carta G, Schmidt M.	Front Microbiol	10.3389/fmicb.2023.1258703	2023
Genetics	Salidroside ameliorates memory impairment following long-term ethanol intake in rats by modulating the altered intestinal microbiota content and hippocampal gene expression.	Jiao Y, Zhao Z, Li X, Li L, Xiao D, Wan S, Wu T, Li T, Li P, Zhao R.	Front Microbiol	10.3389/fmicb.2023.1172936	2023
	Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.	Chen J, Siliceo SL, Ni Y, Nielsen HB, Xu A, Panagiotou G.	Microbiome	10.1186/s40168-023-01604-z	2023
Metabolism	The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients.	Han M, Zhang N, Mao Y, Huang B, Ren M, Peng Z, Bai Z, Chen L, Liu Y, Wang S, Huang S, Cheng Z.	Front Microbiol	10.3389/fmicb.2022.839015	2022
Phylogeny	DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.	Sun Y, Kong L, Wu G, Cao B, Pang X, Deng Z, Dedon PC, Zhang C, You D.	Biomolecules	10.3390/biom10081175	2020
	Roseburia intestinalis-derived extracellular vesicles ameliorate colitis by modulating intestinal barrier, microbiome, and inflammatory responses.	Han HS, Hwang S, Choi SY, Hitayezu E, Humphrey MA, Enkhbayar A, Song DG, Kim M, Park JS, Park YT, Park JS, Cha KH, Choi KY.	J Extracell Vesicles	10.1002/jev2.12487	2024
	Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria.	Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S, Buhl EM, Abt B, Neuhaus K, Velge P, Overmann J, Kaspers B, Clavel T.	mSystems	10.1128/msystems.01300-20	2021
Metabolism	Glucose Metabolism-Modifying Natural Materials for Potential Feed Additive Development.	Lin WC, Hoe BC, Li X, Lian D, Zeng X.	Pharmaceutics	10.3390/pharmaceutics16091208	2024
	Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity.	Wang H, Ainiwaer A, Song Y, Qin L, Peng A, Bao H, Qin H.	Microbiome	10.1186/s40168-022-01443-4	2023
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
Pathogenicity	Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial.	Yacoub R, Nugent M, Cai W, Nadkarni GN, Chaves LD, Abyad S, Honan AM, Thomas SA, Zheng W, Valiyaparambil SA, Bryniarski MA, Sun Y, Buck M, Genco RJ, Quigg RJ, He JC, Uribarri J.	PLoS One	10.1371/journal.pone.0184789	2017
Genetics	Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.	Zhang Z, Xiao J, Wang H, Yang C, Huang Y, Yue Z, Chen Y, Han L, Yin K, Lyu A, Fang X, Zhang L.	Nat Commun	10.1038/s41467-024-49060-z	2024
Phylogeny	A 4-Week Diet Low or High in Advanced Glycation Endproducts Has Limited Impact on Gut Microbial Composition in Abdominally Obese Individuals: The deAGEing Trial.	Linkens AMA, van Best N, Niessen PM, Wijckmans NEG, de Goei EEC, Scheijen JLJM, van Dongen MCJM, van Gool CCJAW, de Vos WM, Houben AJHM, Stehouwer CDA, Eussen SJMP, Penders J, Schalkwijk CG.	Int J Mol Sci	10.3390/ijms23105328	2022
	Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review.	Imade EE, Obayagbona NO.	Gut Microbiome (Camb)	10.1017/gmb.2024.3	2024
	A Profile of Avelumab Plus Axitinib in the Treatment of Renal Cell Carcinoma.	Tiako Meyo M, Chen J, Goldwasser F, Hirsch L, Huillard O.	Ther Clin Risk Manag	10.2147/tcrm.s263832	2022
	The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health.	Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A.	Front Immunol	10.3389/fimmu.2020.00906	2020
	Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits.	Chen Y, Zhao B, Wu Y, Hu S, Mu L, Zhu C, Pan Y, Wu X.	PeerJ	10.7717/peerj.4100	2017
	Xylanase impact beyond performance: A microbiome approach in laying hens.	Van Hoeck V, Somers I, Abdelqader A, Wealleans AL, Van de Craen S, Morisset D.	PLoS One	10.1371/journal.pone.0257681	2021
	The effect of intestinal flora on immune checkpoint inhibitors in tumor treatment: a narrative review.	Wang D, Hao H, Li X, Wang Z.	Ann Transl Med	10.21037/atm-20-4535	2020
Genetics	Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.	Vasco K, Guevara N, Mosquera J, Zapata S, Zhang L.	Anim Microbiome	10.1186/s42523-022-00218-4	2022
	Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart.	Shi B, Zhang X, Song Z, Dai Z, Luo K, Chen B, Zhou Z, Cui Y, Feng B, Zhu Z, Zheng J, Zhang H, He X.	Sci Adv	10.1126/sciadv.adg7417	2023
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
	Screening for chronic prostatitis pathogens using high-throughput next-generation sequencing.	Wu Y, Jiang H, Tan M, Lu X.	Prostate	10.1002/pros.23971	2020
	Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.	Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK.	Gut	10.1136/gutjnl-2019-319706	2021
Pathogenicity	Tipping the Balance: Vitamin D Inadequacy in Children Impacts the Major Gut Bacterial Phyla.	Singh P, Rawat A, Saadaoui M, Elhag D, Tomei S, Elanbari M, Akobeng AK, Mustafa A, Abdelgadir I, Udassi S, Hendaus MA, Al Khodor S.	Biomedicines	10.3390/biomedicines10020278	2022
	Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors.	Rezasoltani S, Yadegar A, Asadzadeh Aghdaei H, Reza Zali M.	Cancer Med	10.1002/cam4.3694	2021
	Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China.	Li J, Hou Q, Zhang J, Xu H, Sun Z, Menghe B, Zhang H.	Front Microbiol	10.3389/fmicb.2017.00484	2017
	A review of cancer immunotherapy: from the past, to the present, to the future.	Esfahani K, Roudaia L, Buhlaiga N, Del Rincon SV, Papneja N, Miller WH.	Curr Oncol	10.3747/co.27.5223	2020
	The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies.	Gong J, Chehrazi-Raffle A, Placencio-Hickok V, Guan M, Hendifar A, Salgia R.	Clin Transl Med	10.1186/s40169-019-0225-x	2019
Genetics	Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread.	Abbondio M, Palomba A, Tanca A, Fraumene C, Pagnozzi D, Serra M, Marongiu F, Laconi E, Uzzau S.	Front Microbiol	10.3389/fmicb.2019.01733	2019
	Human gut microbial communities dictate efficacy of anti-PD-1 therapy in a humanized microbiome mouse model of glioma.	Dees KJ, Koo H, Humphreys JF, Hakim JA, Crossman DK, Crowley MR, Nabors LB, Benveniste EN, Morrow CD, McFarland BC.	Neurooncol Adv	10.1093/noajnl/vdab023	2021
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
Metabolism	Bruton's tyrosine kinase regulates gut immune homeostasis through attenuating Th1 response.	Guan D, Wang Z, Huo J, Xu S, Lam KP.	Cell Death Dis	10.1038/s41419-021-03702-y	2021
Phylogeny	Postmenopausal breast cancer and oestrogen associations with the IgA-coated and IgA-noncoated faecal microbiota.	Goedert JJ, Hua X, Bielecka A, Okayasu I, Milne GL, Jones GS, Fujiwara M, Sinha R, Wan Y, Xu X, Ravel J, Shi J, Palm NW, Feigelson HS.	Br J Cancer	10.1038/bjc.2017.435	2018
Metabolism	Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism.	Kayser BD, Prifti E, Lhomme M, Belda E, Dao MC, Aron-Wisnewsky J, MICRO-Obes Consortium, Kontush A, Zucker JD, Rizkalla SW, Dugail I, Clement K.	Metabolomics	10.1007/s11306-019-1596-0	2019
	Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids.	Lucas LN, Barrett K, Kerby RL, Zhang Q, Cattaneo LE, Stevenson D, Rey FE, Amador-Noguez D.	mSystems	10.1128/msystems.00805-21	2021
	Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients.	Hoang T, Kim MJ, Park JW, Jeong SY, Lee J, Shin A.	BMC Cancer	10.1186/s12885-022-09735-6	2022
Pathogenicity	Gut Microbiota-Mediated Inflammation and Gut Permeability in Patients with Obesity and Colorectal Cancer.	Sanchez-Alcoholado L, Ordonez R, Otero A, Plaza-Andrade I, Laborda-Illanes A, Medina JA, Ramos-Molina B, Gomez-Millan J, Queipo-Ortuno MI.	Int J Mol Sci	10.3390/ijms21186782	2020
Genetics	Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.	Shao L, Ling Z, Chen D, Liu Y, Yang F, Li L.	Front Microbiol	10.3389/fmicb.2018.03166	2018
	Integrated gut virome and bacteriome dynamics in COVID-19 patients.	Cao J, Wang C, Zhang Y, Lei G, Xu K, Zhao N, Lu J, Meng F, Yu L, Yan J, Bai C, Zhang S, Zhang N, Gong Y, Bi Y, Shi Y, Chen Z, Dai L, Wang J, Yang P.	Gut Microbes	10.1080/19490976.2021.1887722	2021
Genetics	Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?	Tidjani Alou M, Million M, Traore SI, Mouelhi D, Khelaifia S, Bachar D, Caputo A, Delerce J, Brah S, Alhousseini D, Sokhna C, Robert C, Diallo BA, Diallo A, Parola P, Golden M, Lagier JC, Raoult D.	Front Microbiol	10.3389/fmicb.2017.00899	2017
Pathogenicity	Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease.	Singh Y, Trautwein C, Romani J, Salker MS, Neckel PH, Fraccaroli I, Abeditashi M, Woerner N, Admard J, Dhariwal A, Dueholm MKD, Schafer KH, Lang F, Otzen DE, Lashuel HA, Riess O, Casadei N.	Mol Neurodegener	10.1186/s13024-023-00628-1	2023
Metabolism	Microbiota regulate innate immune signaling and protective immunity against cancer.	Xing C, Wang M, Ajibade AA, Tan P, Fu C, Chen L, Zhu M, Hao ZZ, Chu J, Yu X, Yin B, Zhu J, Shen WJ, Duan T, Wang HY, Wang RF.	Cell Host Microbe	10.1016/j.chom.2021.03.016	2021
	Aryl Hydrocarbon Receptor Deficiency in Intestinal Epithelial Cells Aggravates Alcohol-Related Liver Disease.	Qian M, Liu J, Zhao D, Cai P, Pan C, Jia W, Gao Y, Zhang Y, Zhang N, Zhang Y, Zhang Q, Wu D, Shan C, Zhang M, Schnabl B, Yang S, Shen X, Wang L.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2021.08.014	2022
Genetics	Strain/species identification in metagenomes using genome-specific markers.	Tu Q, He Z, Zhou J.	Nucleic Acids Res	10.1093/nar/gku138	2014
Metabolism	Defective humoral immunity disrupts bile acid homeostasis which promotes inflammatory disease of the small bowel.	Mohammed AD, Mohammed Z, Roland MM, Chatzistamou I, Jolly A, Schoettmer LM, Arroyo M, Kakar K, Tian Y, Patterson A, Nagarkatti M, Nagarkatti P, Kubinak JL.	Nat Commun	10.1038/s41467-022-28126-w	2022
	Impact of Altered Intestinal Microbiota on Chronic Kidney Disease Progression.	Castillo-Rodriguez E, Fernandez-Prado R, Esteras R, Perez-Gomez MV, Gracia-Iguacel C, Fernandez-Fernandez B, Kanbay M, Tejedor A, Lazaro A, Ruiz-Ortega M, Gonzalez-Parra E, Sanz AB, Ortiz A, Sanchez-Nino MD.	Toxins (Basel)	10.3390/toxins10070300	2018
Metabolism	16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.	Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.	PLoS One	10.1371/journal.pone.0213869	2019
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
	Extensive microbial and functional diversity within the chicken cecal microbiome.	Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ.	PLoS One	10.1371/journal.pone.0091941	2014
	Proteomic indicators of oxidation and hydration state in colorectal cancer.	Dick JM.	PeerJ	10.7717/peerj.2238	2016
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
Pathogenicity	Adjusting for age improves identification of gut microbiome alterations in multiple diseases.	Ghosh TS, Das M, Jeffery IB, O'Toole PW.	Elife	10.7554/elife.50240	2020
Genetics	Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.	Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3336746	2013
Phylogeny	Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces.	Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R	Int J Syst Evol Microbiol	10.1099/ijs.0.014571-0	2009

References

#16377	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22520
#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 )
#25907	IJSEM 1296 2010 ( DOI 10.1099/ijs.0.014571-0 , PubMed 19667375 )
#29508	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25907
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Alistipes indistinctus (DSM 22520, JCM 16068, YIT 12060)

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