Eggerthella lenta (CCUG 17323 A, DSM 2243, ATCC 25559)

Cell morphology

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_2243_1.jpg
  multimedia.multimedia content:	EM_DSM_2243_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
1003	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
1003	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
1003	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

Oxygen tolerance

Spore formation

Metabolite utilization

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

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
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	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine 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	phenylalanine arylamidase	-		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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	hydrogen production	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glycolysis	82.35	14 of 17
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	pyrimidine metabolism	75.56	34 of 45
66794	purine metabolism	75.53	71 of 94
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	alanine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	phenylalanine metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	serine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	oxidative phosphorylation	60.44	55 of 91
66794	methylglyoxal degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	citric acid cycle	57.14	8 of 14
66794	non-pathway related	55.26	21 of 38
66794	proline metabolism	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	adipate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	arginine metabolism	50	12 of 24
66794	glycine metabolism	50	5 of 10
66794	degradation of sugar alcohols	50	8 of 16
66794	glutathione metabolism	50	7 of 14
66794	vitamin B6 metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	cysteine metabolism	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	lysine metabolism	42.86	18 of 42
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	tryptophan metabolism	36.84	14 of 38
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of pentoses	32.14	9 of 28
66794	sulfate reduction	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	degradation of sugar acids	24	6 of 25
66794	ascorbate metabolism	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9

API rID32A

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AB558167 (>99% sequence identity) for Eggerthella lenta subclade from Microbeatlas

Aquatic Samples	1212
Soil Samples	49
Animal Samples	41431
Plant Samples	44
Total Samples	42736

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2426v1 assembly for Eggerthella lenta DSM 2243	complete	GCA_000024265	479437.5	644736358	479437	98.9
67770	ASM333997v1 assembly for Eggerthella lenta DSM 2243	scaffold	GCA_003339975	84112.13	8002122114	84112	64.9
124043	ASM333994v1 assembly for Eggerthella lenta UCSF2243	scaffold	GCA_003339945	84112.12		84112	64.55
67770	ASM334010v1 assembly for Eggerthella lenta ATCC 25559	scaffold	GCA_003340105	84112.19	8115164544	84112	63.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Eggerthella lenta 16S ribosomal RNA gene, partial sequence	AF292375	1500		479437
1003	Eubacterium lentum gene for 16S rRNA, partial sequence	AB011817	1472		479437
67770	Eggerthella lenta gene for 16S ribosomal RNA, partial sequence, strain: JCM 9979	AB558167	1470		84112
124043	Eggerthella lenta strain DSM 2243 16S ribosomal RNA gene, partial sequence.	ON197174	921		84112

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors.	Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJN, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ.	iScience	10.1016/j.isci.2024.110122	2024
	Enantiocomplementary Gut Bacterial Enzymes Metabolize Dietary Polyphenols.	Dong X, Bae M, Le C, Aguilar Ramos MA, Balskus EP.	J Am Chem Soc	10.1021/jacs.4c09892	2025
	Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta.	Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ.	PLoS Biol	10.1371/journal.pbio.3002125	2023
	Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators.	Dong X, Guthrie BGH, Alexander M, Noecker C, Ramirez L, Glasser NR, Turnbaugh PJ, Balskus EP.	Nat Commun	10.1038/s41467-022-33576-3	2022
	Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas.	McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS.	Cell	10.1016/j.cell.2024.05.005	2024
Pathogenicity	Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme.	Bae M, Le C, Mehta RS, Dong X, Pieper LM, Ramirez L, Alexander M, Kiamehr S, Turnbaugh PJ, Huttenhower C, Chan AT, Balskus EP.	Cell Host Microbe	10.1016/j.chom.2024.10.002	2024
	Identification of age-associated microbial changes via long-read 16S sequencing.	Toh KY, Toh TS, Chua KP, Rajakumar P, Lee JWJ, Chong CW.	Gut Pathog	10.1186/s13099-024-00650-8	2024
Metabolism	Identification of volatile metabolites produced from levodopa metabolism by different bacteria strains of the gut microbiome.	Pennington T, Eshima J, Smith BS.	BMC Microbiol	10.1186/s12866-024-03373-7	2024
	Eggerthella lenta bacteremia successfully treated with ceftizoxime: case report and review of the literature.	Jiang S, E J, Wang D, Zou Y, Liu X, Xiao H, Wen Y, Chen Z.	Eur J Med Res	10.1186/s40001-021-00582-y	2021
	The Gut-Brain-Microbiota Connection and Its Role in Autism Spectrum Disorders.	Mlynarska E, Barszcz E, Budny E, Gajewska A, Kopec K, Wasiak J, Rysz J, Franczyk B.	Nutrients	10.3390/nu17071135	2025
Genetics	Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5.	Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, Franz CMAP.	Viruses	10.3390/v14081598	2022
Genetics	A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.	Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.04.006	2020
	Simvastatin induces human gut bacterial cell surface genes.	Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ.	Mol Microbiol	10.1111/mmi.15151	2024
Genetics	Alterations in Gut Glutamate Metabolism Associated with Changes in Gut Microbiota Composition in Children with Autism Spectrum Disorder.	Wang M, Wan J, Rong H, He F, Wang H, Zhou J, Cai C, Wang Y, Xu R, Yin Z, Zhou W.	mSystems	10.1128/msystems.00321-18	2019
	CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice.	Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz CMAP, Hansen AK, Vogensen FK, Moineau S, Nielsen DS.	ISME J	10.1038/s41396-023-01358-4	2023
	CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.	Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2019.08.008	2019
	Safety evaluation of Butyricicoccus faecihominis DSM 34943.	Pitt J, Bauter MR, Kumar R, Hasselwander O, Hibberd AA, Kane H, Wang Q, Auzanneau I, Bry S, David E, Seguinot P, Burns F, Smith AB, Carnovale M.	Toxicol Rep	10.1016/j.toxrep.2025.102145	2025
	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	Human gut bacterial metabolism drives Th17 activation and colitis.	Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2021.11.001	2022
Metabolism	Microbial transformation of dietary xenobiotics shapes gut microbiome composition.	Culp EJ, Nelson NT, Verdegaal AA, Goodman AL.	Cell	10.1016/j.cell.2024.08.038	2024
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
Metabolism	Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins.	Koppel N, Bisanz JE, Pandelia ME, Turnbaugh PJ, Balskus EP.	Elife	10.7554/elife.33953	2018
Metabolism	A bacterial bile acid metabolite modulates Treg 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
	Dysbiosis of the gut microbiome in elderly patients with hepatocellular carcinoma.	Zhang W, Xu X, Cai L, Cai X.	Sci Rep	10.1038/s41598-023-34765-w	2023
Metabolism	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.	Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I.	Microbiome	10.1186/s40168-019-0689-3	2019
Phylogeny	Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD.	Larsen JS, Miller M, Oakley AJ, Dixon NE, Lewis PJ.	Microbiologyopen	10.1002/mbo3.1251	2021
Metabolism	Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12alpha-Hydroxysteroid Dehydrogenases from Bile Acid 7alpha-Dehydroxylating Human Gut Bacteria.	Doden H, Sallam LA, Devendran S, Ly L, Doden G, Daniel SL, Alves JMP, Ridlon JM.	Appl Environ Microbiol	10.1128/aem.00235-18	2018
Enzymology	Microbial Hydroxysteroid Dehydrogenases: From Alpha to Omega.	Doden HL, Ridlon JM.	Microorganisms	10.3390/microorganisms9030469	2021
	Complete Genome Sequence of Coriobacteriaceae Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract.	Looft T, Bayles DO, Alt DP, Stanton TB.	Genome Announc	10.1128/genomea.01143-15	2015
Metabolism	SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.	Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS.	Elife	10.7554/elife.82401	2023
Genetics	Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.	Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I.	Gut Microbes	10.1080/19490976.2023.2226921	2023
	Complete Genome Sequence of the Equol-Producing Bacterium Adlercreutzia equolifaciens DSM 19450T.	Toh H, Oshima K, Suzuki T, Hattori M, Morita H.	Genome Announc	10.1128/genomea.00742-13	2013
	Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells.	Cho GS, Ritzmann F, Eckstein M, Huch M, Briviba K, Behsnilian D, Neve H, Franz CM.	Front Microbiol	10.3389/fmicb.2016.00658	2016
Metabolism	Metabolism of Daidzein and Genistein by Gut Bacteria of the Class Coriobacteriia.	Soukup ST, Stoll DA, Danylec N, Schoepf A, Kulling SE, Huch M.	Foods	10.3390/foods10112741	2021
Metabolism	A Novel Locally c-di-GMP-Controlled Exopolysaccharide Synthase Required for Bacteriophage N4 Infection of Escherichia coli.	Junkermeier EH, Hengge R.	mBio	10.1128/mbio.03249-21	2021
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
Metabolism	A biosynthetic pathway for a prominent class of microbiota-derived bile acids.	Devlin AS, Fischbach MA.	Nat Chem Biol	10.1038/nchembio.1864	2015
	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
	Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations.	Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS.	Nat Ecol Evol	10.1038/s41559-022-01930-9	2023
Genetics	Towards a mechanistic understanding of reciprocal drug-microbiome interactions.	Zimmermann M, Patil KR, Typas A, Maier L.	Mol Syst Biol	10.15252/msb.202010116	2021
Metabolism	Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family.	Ramanadane K, Straub MS, Dutzler R, Manatschal C.	Elife	10.7554/elife.74589	2022
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
	Evolution of endonuclease IV protein family: an in silico analysis.	Kanchan S, Sharma P, Chowdhury S.	3 Biotech	10.1007/s13205-019-1696-6	2019
Enzymology	Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes.	Lam KN, Alexander M, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2019.06.011	2019
	Deciphering microbial interactions in synthetic human gut microbiome communities.	Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.	Mol Syst Biol	10.15252/msb.20178157	2018
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
Metabolism	Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily.	Cummings JA, Vetting M, Ghodge SV, Xu C, Hillerich B, Seidel RD, Almo SC, Raushel FM.	Biochemistry	10.1021/bi401640r	2014
	Dissemination of 6S RNA among bacteria.	Wehner S, Damm K, Hartmann RK, Marz M.	RNA Biol	10.4161/rna.29894	2014
Enzymology	The desA and desB genes from Clostridium scindens ATCC 35704 encode steroid-17,20-desmolase.	Devendran S, Mythen SM, Ridlon JM.	J Lipid Res	10.1194/jlr.m083949	2018
	Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.	El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crepin A.	Front Microbiol	10.3389/fmicb.2022.828359	2022
	Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.	Fibriansah G, Kovacs AT, Pool TJ, Boonstra M, Kuipers OP, Thunnissen AM.	PLoS One	10.1371/journal.pone.0048015	2012
	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
Metabolism	Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.	Haft DH, Basu MK, Mitchell DA.	BMC Biol	10.1186/1741-7007-8-70	2010
Metabolism	Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.	Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO, Venturelli OS.	Elife	10.7554/elife.73870	2022
Metabolism	Cloning and analysis of the planosporicin lantibiotic biosynthetic gene cluster of Planomonospora alba.	Sherwood EJ, Hesketh AR, Bibb MJ.	J Bacteriol	10.1128/jb.02291-12	2013
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Phylogeny	Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.	Shlykov MA, Zheng WH, Chen JS, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2011.12.005	2012
Genetics	Genomic basis for natural product biosynthetic diversity in the actinomycetes.	Nett M, Ikeda H, Moore BS.	Nat Prod Rep	10.1039/b817069j	2009
Genetics	Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.	Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM.	BMC Microbiol	10.1186/1471-2180-12-21	2012
Genetics	Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
	A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes.	Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP.	PLoS One	10.1371/journal.pone.0030287	2012
	Defense against cannibalism: the SdpI family of bacterial immunity/signal transduction proteins.	Povolotsky TL, Orlova E, Tamang DG, Saier MH.	J Membr Biol	10.1007/s00232-010-9260-7	2010
Phylogeny	Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
	Eggerthella lenta augments preclinical autoantibody production and metabolic shift mimicking senescence in arthritis.	Balakrishnan B, Luckey D, Wright K, Davis JM, Chen J, Taneja V.	Sci Adv	10.1126/sciadv.adg1129	2023
	Hormone Replacement Therapy Reverses Gut Microbiome and Serum Metabolome Alterations in Premature Ovarian Insufficiency.	Jiang L, Fei H, Tong J, Zhou J, Zhu J, Jin X, Shi Z, Zhou Y, Ma X, Yu H, Yang J, Zhang S.	Front Endocrinol (Lausanne)	10.3389/fendo.2021.794496	2021
	Analytical Performance Characteristics of a New Transcription-Mediated Amplification Assay for Treponema pallidum.	Getman D, Lin M, Barakat N, Skvoretz R, Godornes C, Swenson P, Nenninger A, Golden MR, Lukehart SA.	J Clin Microbiol	10.1128/jcm.00511-21	2021
Metabolism	Discovery of a cyclic phosphodiesterase that catalyzes the sequential hydrolysis of both ester bonds to phosphorus.	Ghodge SV, Cummings JA, Williams HJ, Raushel FM.	J Am Chem Soc	10.1021/ja409376k	2013
Pathogenicity	In vitro antimicrobial activity of razupenem (SMP-601, PTZ601) against anaerobic bacteria.	Tran CM, Tanaka K, Yamagishi Y, Goto T, Mikamo H, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.01038-10	2011
Pathogenicity	In vitro activity of tomopenem (CS-023/RO4908463) against anaerobic bacteria.	Tanaka K, Mikamo H, Nakao K, Ichiishi T, Goto T, Yamagishi Y, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00595-08	2009
	Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum.	Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R.	Int J Bacteriol	10.1155/2013/168742	2013
	Filifactor alocis--involvement in periodontal biofilms.	Schlafer S, Riep B, Griffen AL, Petrich A, Hubner J, Berning M, Friedmann A, Gobel UB, Moter A.	BMC Microbiol	10.1186/1471-2180-10-66	2010
Enzymology	Rapid and sensitive detection of Shiga toxin-producing Escherichia coli from nonenriched stool specimens by real-time PCR in comparison to enzyme immunoassay and culture.	Grys TE, Sloan LM, Rosenblatt JE, Patel R.	J Clin Microbiol	10.1128/jcm.02013-08	2009
Pathogenicity	In vitro antianaerobic activity of DX-619, a new des-fluoro(6) quinolone.	Tanaka K, Mikamo H, Nakao K, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00639-06	2006
	Bifidobacterial lipoglycan as a new cause for false-positive platelia Aspergillus enzyme-linked immunosorbent assay reactivity.	Mennink-Kersten MA, Ruegebrink D, Klont RR, Warris A, Gavini F, Op den Camp HJ, Verweij PE.	J Clin Microbiol	10.1128/jcm.43.8.3925-3931.2005	2005
	The microbial metabolite imidazole propionate modulates hypothalamic activity and stress-induced behaviors.	Agirman G, Quicho MNB, Connelley KK, Zhang X, Lynch JB, Ha SM, Schmidt HM, Ozcan E, Liang AX, Yu KB, Ahn IS, Qian C, Paramo J, Zhang S, Espinoza A, Turnbaugh PJ, de Aguiar Vallim TQ, Yang X, Church A, Hsiao EY.	Cell Host Microbe	10.1016/j.chom.2025.10.019	2025
Metabolism	Microbial modulation of digoxin bioavailability: A pharmacomicrobiome perspective on Eggerthella lenta's role in steroid-like drug metabolism and precision therapeutics.	Ganamurali N, Sabarathinam S.	J Steroid Biochem Mol Biol	10.1016/j.jsbmb.2025.106792	2025
	Gut microbiome signatures predict cognitive impairment in older cancer survivors.	Miller BC, Haggler JA, Chaudhari DS, Shukla R, Kumar V, Mishra SP, Masternak MM, Holland P, Labyak C, Golden A, Dangiolo M, Arikawa AY, Kociolek J, Fraser A, Williams C, Agronin M, Aymat M, Pledger W, Yadav H, Jain S.	Geroscience	10.1007/s11357-025-01917-x	2025
	A gut Eggerthella lenta-derived metabolite impairs neutrophil function to aggravate bacterial lung infection.	Wang LL, Shen X, Xie Y, Ge A, Lu H, Gu S, Kong L, Narayana JK, Mattner J, Chotirmall SH, Xu JF.	Sci Transl Med	10.1126/scitranslmed.adq4409	2025
	Lutein augments the hypoglycemic effect of metformin through the gut microbiota-imidazole propionate axis in type 2 diabetic model mice.	Liu K, Han Y, Zhang J, Yin Z, Yan H, Gao W, Tong H, Zhu H, Hui S, Liang L, Yu H.	Sci Rep	10.1038/s41598-025-16133-y	2025
	Clinical and microbiological characteristics of Eggerthella lenta causing bacteremia.	Fernandez Vecilla D, Urrutikoetxea Gutierrez MJ, Roche Matheus MP, Calvo Muro FE, Diaz de Tuesta Del Arco JL.	Enferm Infecc Microbiol Clin (Engl Ed)	10.1016/j.eimce.2024.05.014	2024
	Eggerthella lenta down regulated flavone and flavonol biosynthesis promoted Kawasaki disease.	Yeh YT, Chen KD, Huang CH, Tsai JR, Kuo HC.	Virulence	10.1080/21505594.2025.2512401	2025
	Necrotizing myometritis following vaginal delivery complicated by retained placenta and uterine artery embolization: A case report.	Guo G, Zhang Y, Cao J, Fan Y, Fan L.	SAGE Open Med Case Rep	10.1177/2050313x251388740	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
	Alterations in the gut microbiome and metabolome in elderly patients with postoperative delirium: A prospective nested case-control study.	Huo J, Han S, Hao X, Zhou Z, Lou J, Li H, Cao J, Yu Y, Mi W, Liu Y.	J Clin Anesth	10.1016/j.jclinane.2025.111833	2025
Pathogenicity	Eggerthella lenta Produces a Cryptic Pro-inflammatory Lipid.	Shin YH, Bang S, Xavier R, Clardy J.	J Am Chem Soc	10.1021/jacs.5c08613	2025
	The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice.	Viehof A, Haange SB, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep	10.20517/mrr.2023.65	2024
	Clinical characteristics and antimicrobial susceptibility of Eggerthella lenta infection over a 5-year trend at a university hospital in Japan.	Mori N, Nakamura A, Hirai J, Asai N, Shibata Y, Takayama M, Kawamoto Y, Miyazaki N, Sakanashi D, Ohno T, Yamada A, Suematsu H, Koita I, Chida S, Ohta T, Mikamo H.	Nagoya J Med Sci	10.18999/nagjms.86.4.683	2024
Genetics	Metagenomics Analysis of Altered Gut Microbiome in Psoriasis and the Mediation Analysis: A Case-Control Study.	Xiao Y, Jing D, Xiao H, Mao M, Kuang Y, Shen M, Lv C, Jian X, Peng C, Chen X.	Psoriasis (Auckl)	10.2147/ptt.s505283	2025
	Reduced Sulfur Diet Reshapes the Microbiome and Metabolome in Mild-Moderate Ulcerative Colitis.	Ye J, Raman M, Taylor LM, Yousuf M, Panaccione R, Turbide C, Sinha SR, Haskey N.	Int J Mol Sci	10.3390/ijms26104596	2025
	Comparative evaluation of antimicrobial activity of spinel structured transition metal ferrites supported on reduced graphene oxide against pathogenic strains of bacteria and fungi.	Lakshmi Priya R, Dhayanithi CA, Hariprasad BS, Vidya R, Ganesh Babu S.	Nanotechnology	10.1088/1361-6528/ad4710	2024
	Otitis Media and Its Intracranial Complications: A Delicate Scenario.	Lobo M, Lopes Freitas R, Viana M, Duarte F, Camoes S.	Cureus	10.7759/cureus.76561	2024
Genetics	nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.	Guzman-Cole C, Huang AD.	Bioinformatics	10.1093/bioinformatics/btaf436	2025
	Exploring the role of acylated ghrelin and gut microbiome in delineating cognitive health in the elderly.	Rout S, Dash R, Satish V, Venugopal G, Rao BN, Bandhyopadhyay D, Bhoi SK, Ramadass B.	Aging (Albany NY)	10.18632/aging.206200	2025
	Successful Treatment of Complicated Pyogenic Spondylitis Due to Advanced Rectosigmoid Cancer Utilizing Vigorous Antibiotic Therapy and Minimally Invasive Robotic Colorectal Surgery: A Case Report.	Tanaka K, Fujikawa T, Kojima D, Nagata K, Hasegawa S.	Cureus	10.7759/cureus.67536	2024
	Polymicrobial anaerobic sepsis due to Bacteroides fragilis, Eggerthella lenta, Ruminoccocus gnavus, and Bilophila wadsworthia in a patient with myeloproliferative neoplasm.	Acker E, George M, Farooqi T, Raval M, Ramani A.	Anaerobe	10.1016/j.anaerobe.2022.102641	2022
	First periprosthetic hip infection caused by Eggerthella lenta.	Krekosch P, Jonen V, Abdelaziz H.	J Clin Orthop Trauma	10.1016/j.jcot.2023.102234	2023
	Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.	Gao Y, Zheng H, Ye M, Zhou G, Chen J, Qiang X, Bai J, Lu X, Tang Q.	J Cancer	10.7150/jca.103297	2025
	A case of bacteremia caused by Dialister micraerophilus with Enterocloster clostridioformis and Eggerthella lenta in a patient with pyometra.	Kitagawa H, Tadera K, Omori K, Nomura T, Shigemoto N, Ohge H.	BMC Infect Dis	10.1186/s12879-024-08999-6	2024
	Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.	Du J-Y, Zhang Z-J, Tan L, Yang J-Y, Yang R-N, Chen Y-L, Tan G-F, Li J, Li W-J, Yang L, Cai J, Shen D-L, Zhu H-R, Fan Z-X, Yuan M-L, Zhang W.	mBio	10.1128/mbio.02447-25	2025
	Microbial threads in the tapestry of rheumatoid arthritis.	Li J, Kuhn KA.	J Clin Invest	10.1172/jci195374	2025
	The Majority of Bacillus subtilis Strains Isolated From Blood Cultures Were Derived From Traditional Japanese Fermented Soybeans Natto: A Single-center Retrospective Study.	Sada RM, Yamamoto G, Hamaguchi S, Kuroda E, Okura A, Cai M, Nakanishi K, Abe N, Yamamoto S, Kutsuna S.	Open Forum Infect Dis	10.1093/ofid/ofaf574	2025
	Fecal microbiota transplantation for hypertension: an exploratory, multicenter, randomized, blinded, placebo-controlled trial.	Fan L, Chen J, Zhang Q, Ren J, Chen Y, Yang J, Wang L, Guo Z, Bu P, Zhu B, Zhao Y, Wang Y, Liu X, Wang W, Chen Z, Gao Q, Zheng L, Cai J.	Microbiome	10.1186/s40168-025-02118-6	2025
	An Eleven-Year Retrospective Survey of Anaerobic Bloodstream Infection in Adults in a General Hospital.	Yang R, Wang W, Yin G, Ma T, Tao J.	Infect Drug Resist	10.2147/idr.s482698	2024
	Cardiotonic Steroids as a Potential Novel Approach for Immunomodulation in Inflammatory Bowel Disease.	Cavalcante-Silva LHA, Sales-Neto JM, Soares MM, Ferreira DA, Medeiros ABA, Rodrigues-Mascarenhas S.	J Clin Med	10.3390/jcm14124132	2025
	The Role of the Gut Microbiota in Heart Failure: Pathophysiological Insights and Future Perspectives.	Epelde F.	Medicina (Kaunas)	10.3390/medicina61040720	2025
	FEATURE OF GUT MICROBIOTA IN PATIENTS WITH MIGRAINE AND HEALTHY INDIVIDUALS.	Kopchak O, Hrytsenko O.	Georgian Med News		2022
Genetics	Metagenomic association analysis of cognitive impairment in community-dwelling older adults.	Li J, Zhu S, Wang Y, Fan M, Dai J, Zhu C, Xu K, Cui M, Suo C, Jin L, Jiang Y, Chen X.	Neurobiol Dis	10.1016/j.nbd.2023.106081	2023
	Comparison of the gut microbiota in older people with and without sarcopenia: a systematic review and meta-analysis.	Ren Y, He X, Wang L, Chen N.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1480293	2025
	Dietary probiotic ingestion is associated with elevated enterolignans concentration in the United States population, evidenced by NHANES 1999-2010.	Dong J, Huang L, Wang C, Luo X, Wei J, Abuduxukuer K, Luo J, Zhou Y, Peng Q.	Front Nutr	10.3389/fnut.2025.1527029	2025
	The Role Played by Imidazole Propionic Acid in Modulating Gut-Heart Axis and the Development of Atherosclerosis: An Explorative Review.	Pinnelli VB, Ca J, Kandi V, P S, Gr M, Hussain MH, As A, R K, Jp R, T SB, Vadakedath S.	Cureus	10.7759/cureus.94362	2025
	The Gut Microbiome in Early-Onset Colorectal Cancer: Distinct Signatures, Targeted Prevention and Therapeutic Strategies.	Lauricella S, Brucchi F, Cirocchi R, Cassini D, Vitellaro M.	J Pers Med	10.3390/jpm15110552	2025
	Diversity in gut microbiota among colorectal cancer patients: findings from a case-control study conducted at a Tunisian University Hospital.	Zrelli M, Ferjani A, Nouira M, Hammami S, Ghithia N, Mouelhi L, Debbeche R, Raoult D, Boutiba Ben Boubaker I.	Discov Oncol	10.1007/s12672-024-01232-5	2024
	Fatal C-reactive Protein-less Sepsis with Anti-IL-6 Autoantibody Production after Administration of Durvalumab.	Igarashi S, Ogawa T, Kushibiki T, Ito K, Matsukida A, Kato Y, Nagao K, Kawana A, Kimizuka Y.	Intern Med	10.2169/internalmedicine.4754-24	2025
	PECULIARITIES OF THE GUT MICROBIOTA IN PATIENTS WITH MIGRAINE COMPARING TO HEALTHY INDIVIDUALS.	Kopchak OO, Hrytsenko OY, Pulyk OR.	Wiad Lek	10.36740/wlek202209207	2022
	Synthesis and Characterization of Tween-20 Capped Biosynthesized Silver Nanoparticles for Anticancer and Antimicrobial Property.	Nithya P, Raghunathan S, Prabakaran M, Antony SA, MubarakAli D.	Appl Biochem Biotechnol	10.1007/s12010-022-04069-2	2023
	Rapidly Progressive Malignant Pelvic Perivascular Epithelioid Cell Neoplasm (PEComa) Associated with Eggerthella lenta Bloodstream Infection.	Cacciatore S, Recupero C, Massaro C, Elmi D, Fusco D, Badiali V, Brandi V, Arciuolo D, Marazzi F, Landi F.	Ann Geriatr Med Res	10.4235/agmr.22.0138	2022
	Microbial Cgr2 will let your Th17 cells ROR(gammaT).	Rodriguez-Marino N, Cervantes-Barragan L.	Cell Host Microbe	10.1016/j.chom.2021.12.014	2022
	Gut bacteria and the host synergies promote resveratrol metabolism and induce tolerance in ALD mice.	Zhang SX, Hu FF, Chen H, Guo J, Xiang ZW, Ding X, Ye ML, Ye WL, Chen JH, Wang X, Han WJ, Zhou HH, Zhang W, Huang Y, Wu LL, Lian GH, Chen Y.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00766-y	2025
	The Impact of Bacterial-Fungal Interactions on Childhood Caries Pathogenesis.	Huang S, Wang H, Tian J, Qin M, Gao R, Zhao B, Wang J, Wu H, Xu H.	Pathogens	10.3390/pathogens14101033	2025
	Altered Gut Microbiota and Predicted Immune Dysregulation in Early Childhood SARS-CoV-2 Infection	Kim D, Kwak B, Cho K.	Microorganisms		2025
	Gut Microbiota Affects Mouse Social Behavior via Hippuric Acid Metabolism.	Tsukui M, Yagishita S, Tokunaga S, Wakatsuki S, Araki T.	Neurol Int	10.3390/neurolint17110185	2025
	Straining to define a healthy microbiome.	Seekatz AM.	mSphere	10.1128/msphere.00797-24	2025
Genetics	Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.	Diop K, Mbaye B, Nili S, Filin A, Benlaifaoui M, Malo J, Renaud AS, Belkaid W, Hunter S, Messaoudene M, Lee KA, Elkrief A, Routy B.	Gut Pathog	10.1186/s13099-025-00694-4	2025
Enzymology	Antimicrobial susceptibility testing of Eggerthella lenta blood culture isolates at a university hospital in Belgium from 2004 to 2018.	Declerck B, Van der Beken Y, De Geyter D, Pierard D, Wybo I.	Anaerobe	10.1016/j.anaerobe.2021.102348	2021
	Bacteremia caused by Desulfovibrio desulfuricans with the intestinal tract as the portal of entry: two case reports and a literature review.	Yamaizumi K, Kyotani M, Kenzaka T.	BMC Infect Dis	10.1186/s12879-024-09623-3	2024
	Lutein augments the hypoglycemic effect of metformin through the gut microbiota-imidazole propionate axis in type 2 diabetic model mice	Liu K, Han Y, Zhang J, Yin Z, Yan H, Gao W, Tong H, Zhu H, Hui S, Liang L, Yu H.	Sci Rep		2025
	The endogenous hydrogen gas (H2) drives women's health: a comment on "Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas".	Yang S, Zhang J, Xu L, Guan Y, Fang C, Zheng S, Yang H, Liu H, Zhang Y.	Front Endocrinol (Lausanne)	10.3389/fendo.2024.1504814	2024
	Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections.	Li X, Xu E, Shi C, Qiao G, Chen S, Xu Y, Liu Y, Bao X.	Pol J Microbiol	10.33073/pjm-2022-024	2022
	Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.	Rasoulimehrabani H, Khadem S, Hodzic A, Philipp M, Gallo R, Nikolov G, Seneca J, Ramesmayer J, Sivulic P, Berry D.	Microbiome Res Rep	10.20517/mrr.2025.29	2025
Phylogeny	Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease.	Hertz S, Anderson JM, Nielsen HL, Schachtschneider C, McCauley KE, Ozcam M, Larsen L, Lynch SV, Nielsen H.	Ann Med	10.1080/07853890.2024.2338244	2024
	Vitamin K deficiency as a cause of oral bleeding in a dog with intestinal malabsorption due to lymphocytic-plasmacytic enteritis.	Marceglia G, Petini M.	Open Vet J	10.5455/ovj.2025.v15.i5.46	2025
	Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.	Jangi S, Zhao N, Hsia K, Park YS, Michaud DS, Yoon H.	J Crohns Colitis	10.1093/ecco-jcc/jjae125	2025
	Clinical and microbiological characteristics of Eggerthella lenta bacteremia at a Japanese tertiary hospital.	Nagaoka R, Kitagawa H, Koba Y, Tadera K, Hara T, Kashiyama S, Nomura T, Omori K, Shigemoto N, Yokozaki M, Ohge H.	J Infect Chemother	10.1016/j.jiac.2021.03.019	2021
	Multi-omics technology reveals the changes in gut microbiota to stimulate aromatic amino acid metabolism in children with allergic rhinitis and constipation.	Wang C, Liu H, Li X, Kong W, Wu H, Huang C.	Front Allergy	10.3389/falgy.2025.1562832	2025
	Eggerthella lenta bacteraemia in endometrial adenocarcinoma - a case report from Pakistan.	Fatima T, Hasan R, Tariq S.	J Pak Med Assoc	10.5455/jpma.285088	2020
Enzymology	Eggerthella lenta bloodstream infections: two cases and review of the literature.	Bo J, Wang S, Bi Y, Ma S, Wang M, Du Z.	Future Microbiol	10.2217/fmb-2019-0338	2020
	A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children.	Scicchitano D, Foresto L, Laczny CC, Cinti N, Vitagliano R, Halder R, Morri G, Turroni S, D'Amico F, Palladino G, Fiori J, Wilmes P, Rampelli S, Candela M.	One Health	10.1016/j.onehlt.2024.100902	2024
	Metagenomic Next-Generation Sequencing Direct Diagnosis of Mixed Bacterial Meningitis in a Child: A Case Report.	Wang W, Wang Y, Xin X, Yin Y, Zhao C, Jin Y.	Infect Drug Resist	10.2147/idr.s476781	2024
	The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice	Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep		2024
	Targeted Gut Microbiota Modulation Enhances Levodopa Bioavailability and Motor Recovery in MPTP Parkinson's Disease Models.	Ai P, Xu S, Yuan Y, Xu Z, He X, Mo C, Zhang Y, Yang X, Xiao Q.	Int J Mol Sci	10.3390/ijms26115282	2025
	Exploring the causal role of gut microbiota and inflammatory proteins in neuromyelitis optica spectrum disorder: A Mendelian randomization study with mediation analysis.	Yin Z, Qiu Y, Yang Y, Yue S, Chen Z, Wu J.	Medicine (Baltimore)	10.1097/md.0000000000043967	2025
	A Narrative Review of Intestinal Microbiota's Impact on Migraine with Psychopathologies.	Francavilla M, Facchetti S, Demartini C, Zanaboni AM, Amoroso C, Bottiroli S, Tassorelli C, Greco R.	Int J Mol Sci	10.3390/ijms25126655	2024
	Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.	Marcos-Zambrano LJ, Lacruz-Pleguezuelos B, Aguilar-Aguilar E, Marcos-Pasero H, Valdes A, Loria-Kohen V, Cifuentes A, Ramirez de Molina A, Diaz-Ruiz A, Pancaldi V, Carrillo de Santa Pau E.	mSystems	10.1128/msystems.00143-25	2025
	Epidemiology and antibiotic susceptibility in anaerobic bacteraemia: a 15-year retrospective study in South-Eastern Hungary.	Sarvari KP, Racz NB, Burian K.	Infect Dis (Lond)	10.1080/23744235.2021.1963469	2022
Pathogenicity	SARS-CoV-2 infection is associated with intestinal permeability, systemic inflammation, and microbial dysbiosis in hospitalized patients.	Basting CM, Langat R, Broedlow CA, Guerrero CR, Bold TD, Bailey M, Velez A, Schroeder T, Short-Miller J, Cromarty R, Mayer ZJ, Southern PJ, Schacker TW, Safo SE, Bramante CT, Tignanelli CJ, Schifanella L, Klatt NR.	Microbiol Spectr	10.1128/spectrum.00680-24	2024
	Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.	Hussan H, Ali MR, Lyo V, Webb A, Pietrzak M, Zhu J, Choueiry F, Li H, Cummings BP, Marco ML, Medici V, Clinton SK.	Obes Surg	10.1007/s11695-024-07420-0	2024
	Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.	Riva A, Rasoulimehrabani H, Cruz-Rubio JM, Schnorr SL, von Baeckmann C, Inan D, Nikolov G, Herbold CW, Hausmann B, Pjevac P, Schintlmeister A, Spittler A, Palatinszky M, Kadunic A, Hieger N, Del Favero G, von Bergen M, Jehmlich N, Watzka M, Lee KS, Lee KS, Wiesenbauer J, Khadem S, Viernstein H, Stocker R, Wagner M, Kaiser C, Richter A, Kleitz F, Berry D.	Nat Commun	10.1038/s41467-023-43448-z	2023
	Characterization of bacterial composition of surgical site infections after gynecologic surgery.	Cowley ES, Jacques L, Powell AM, Al-Niaimi A, Pop-Vicas A.	Am J Obstet Gynecol	10.1016/j.ajog.2022.02.033	2022
	National antibiotic consumption is strongly related to the prevalence of antibiotic resistance across bacterial clades.	Louca S.	iScience	10.1016/j.isci.2024.111712	2025
	Microbial Features Linked to Medication Strategies in Cardiometabolic Disease Management.	Shearer J, Shah S, Shen-Tu G, Schlicht K, Laudes M, Mu C.	ACS Pharmacol Transl Sci	10.1021/acsptsci.3c00261	2024
Phylogeny	Deciphering Bacterial Community Succession and Pathogen Dynamics in ICU Ventilator Circuits Through Full-Length 16S rRNA Sequencing for Mitigating the Risk of Nosocomial Infections.	Tsai HC, Chen JS, Hsu GJ, Hussain B, Lin IC, Hsu TK, Han J, Huang SW, Wu CC, Hsu BM.	Microorganisms	10.3390/microorganisms13091982	2025
	Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.	Dike CR, Duan Q, Ahmed F, Denson LA, Haslam D, Minar P, Ollberding NJ, Papachristou GI, Setchell KDR, Thompson T, Vitale DS, Zhao X, Abu-El-Haija M.	J Pediatr Gastroenterol Nutr	10.1002/jpn3.70135	2025
	Clinical evaluation of an in-house Xpert Lysate-based Method combined with MALDI-TOF MS for the rapid identification of positive blood cultures.	Ping Y, Chen Q, Sun X, Wang H, Lin S, Zhu B, Wang Z, Lu J, Cao J.	BMC Microbiol	10.1186/s12866-025-03996-4	2025
	Longitudinal Fecal Microbiota Profiles in A Cohort of Non-Hospitalized Adolescents and Young Adults with COVID-19: Associations with SARS-CoV-2 Status and Long-Term Fatigue.	Olbjorn C, Hagen M, Moen AEF, Havdal LB, Sommen SL, Berven LL, Thiis-Evensen E, Stiansen-Sonerud T, Selvakumar J, Wyller VBB.	Pathogens	10.3390/pathogens13110953	2024
	Hawai'i's First Published Case of Eggerthella lenta Sepsis.	Peter-Bibb TK, Tokeshi J.	Hawaii J Health Soc Welf		2020
	Gut microbiota changes associated with frailty in older adults: A systematic review of observational studies.	Wen NN, Sun LW, Geng Q, Zheng GH.	World J Clin Cases	10.12998/wjcc.v12.i35.6815	2024
	Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.	Ke S, Villafuerte Galvez JA, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu YY.	J Infect Dis	10.1093/infdis/jiae470	2025
	A retrospective study of the detection of sepsis pathogens comparing blood culture and culture-independent digital PCR.	Zhao Z, Wang Y, Kang Y, Wu G, He J, Wang Z, Yang J, Wang Y, Yang X, Jia W.	Heliyon	10.1016/j.heliyon.2024.e27523	2024
	Preliminary Study to Understand the Role of Gut Microbiota in Coronary Slow Flow Phenomenon (CSFP).	Gurol T, Karaman T, Gurol Y, Sezerman OU, Oktem Okullu S.	Metabolites	10.3390/metabo15070475	2025
Genetics	Bacteraemia Associated with Bilophila wadsworthia: A Rare Case Presentation from Hungary.	Kovacs R, Arokszallasi T, Bozo A, Jakab A, Babel KS, Heja M, Kovacs KB, Balazs B, Vitalis E, Majoros L, Toth Z.	Pathogens	10.3390/pathogens13090749	2024
	Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.	Lee YQ, Choi YM, Park SY, Kim SK, Lee M, Kim D, Koduru L, Lakshmanan M, Jung S, Kim MJ, Choe YH, Lee DY.	NPJ Syst Biol Appl	10.1038/s41540-025-00555-5	2025
	The Causal Role of Esophageal Cancer and Gut Microbiota: A Bidirectional Mendelian Randomization Study.	Su W, Chen H, Hu D, Ye B, Zhang W, Zhang G, Si X, Zhou X.	J Evid Based Integr Med	10.1177/2515690x251324793	2025
	Flavonifractor plautii Bacteremia With Generalized Peritonitis: A Case Report and Literature Review.	Saito S, Baba S, Nikai H, Fujisawa R, Fujiwara T.	Cureus	10.7759/cureus.63890	2024
	Levofloxacin prophylaxis and parenteral nutrition have a detrimental effect on intestinal microbial networks in pediatric patients undergoing HSCT.	Fabbrini M, D'Amico F, Leardini D, Muratore E, Barone M, Belotti T, Forchielli ML, Zama D, Pession A, Prete A, Brigidi P, Rampelli S, Candela M, Turroni S, Masetti R.	Commun Biol	10.1038/s42003-023-04436-7	2023
	A rare case of an infected aortoiliac graft complicated with Eggerthella lenta bacteremia and septic shock.	Alataby HA, Muzangwa LG, Atere MK, Bibawy J, Diaz KT, Nfonoyim JM.	J Community Hosp Intern Med Perspect	10.1080/20009666.2020.1809260	2020
Pathogenicity	The Impact of a 10-Month Synbiotic Intake on eGFR, Uremic Toxins, Oxidative Stress, and Inflammatory Markers in Non-Dialysis Chronic Kidney Disease Patients: A Prospective, Non-Randomized, Placebo-Controlled Study.	Kuskunov T, Tilkiyan E, Zdravkova I, Valova S, Boyanov K, Bivolarska A.	Medicina (Kaunas)	10.3390/medicina61071199	2025
	Bacteremia Caused by the Eggerthella lenta in a Previously Healthy 30-Year-Old Man with Acute Suppurative Appendicitis: A Case Report from China.	Jiang J, She B, Zheng R.	Infect Drug Resist	10.2147/idr.s274494	2020
	Unravelling the gut-brain connection: a systematic review of migraine and the gut microbiome.	Mugo CW, Church E, Horniblow RD, Mollan SP, Botfield H, Hill LJ, Sinclair AJ, Grech O.	J Headache Pain	10.1186/s10194-025-02039-7	2025
	Interaction between gut microbiota and immunity in health and intestinal disease.	Wang Q, Meng Q, Chen Y, Liu Y, Li X, Zhou J, Ma Y, Yu Z, Chen X.	Front Immunol	10.3389/fimmu.2025.1673852	2025
Enzymology	Septic shock caused by the under-recognized bacterium Eggerthella lenta in a 61-year-old male with a periurethral abscess: a case report.	Cordoba G, Kim ML, Sharma S, Paniagua J, Folgarait G, Berger J.	Rev Soc Bras Med Trop	10.1590/0037-8682-0081-2019	2019
	Polyphenols and Microbiota Modulation: Insights from Swine and Other Animal Models for Human Therapeutic Strategies.	Anghel AC, Taranu I, Ortan A, Marcu Spinu S, Dragoi Cudalbeanu M, Rosu PM, Babeanu NE.	Molecules	10.3390/molecules29246026	2024
	Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.	Guo Y, Yuan W, Lyu N, Pan Y, Cao X, Wang Y, Han Y, Zhu B.	Microorganisms	10.3390/microorganisms11030546	2023
	Microbes and GFR in Health and CKD in Mice.	Xu J, Verma E, Sanchez J, Gharaie S, Jeong S, Patel SK, Gooya M, Rosa X, Gupta K, Rinschen MM, Rabb H, Pluznick JL.	J Am Soc Nephrol	10.1681/asn.0000000814	2025
	Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C).	Suskun C, Kilic O, Yilmaz Ciftdogan D, Guven S, Karbuz A, Ozkaya Parlakay A, Kara Y, Kacmaz E, Sahin A, Boga A, Kizmaz Isancli D, Gulhan B, Kanik-Yuksek S, Kiral E, Bozan G, Arslanoglu MO, Kizil MC, Dinleyici M, Us T, Varis A, Kaya M, Vandenplas Y, Dinleyici EC.	Eur J Pediatr	10.1007/s00431-022-04494-9	2022
	Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda.	Agudelo C, Kateete DP, Nasinghe E, Kamulegeya R, Lubega C, Mbabazi M, Baker N, Lin KY, Liu CC, Kasambula AS, Kigozi E, Komakech K, Mukisa J, Mulumba K, Mwachan P, Nakalanda BS, Nalubega GP, Nsubuga J, Sitenda D, Ssenfuka H, Cirolia GT, Gustafson JT, Wang R, Nsubuga ML, Yiga F, Stanley SA, Bagaya BS, Elliott A, Joloba M, Wolf AR.	Gut Pathog	10.1186/s13099-025-00678-4	2025
Pathogenicity	Cytokine release and NLRP3 inflammasome activation induced by low-abundance oral bacterial biofilms.	Karched M, Guleri Bhardwaj R, Abu Al-Melh M, Qudeimat MA.	J Oral Microbiol	10.1080/20002297.2025.2552167	2025
	Postpartum endometritis and obstetrical sepsis associated with Eggerthella lenta. Case report and review of the literature.	Priputnevich T, Lyubasovskaya L, Muravieva V, Kondrakhin A, Ignateva A, Gordeev A, Shmakov R, Sukhikh G, Yarotskaya E.	J Matern Fetal Neonatal Med	10.1080/14767058.2019.1602602	2021
	Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.	Wong MK, Armstrong E, Heirali AA, Schneeberger PHH, Chen H, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	mBio	10.1128/mbio.01904-25	2025
	Supplementation with a cranberry extract favors the establishment of butyrogenic guilds in the human fermentation SHIME system.	Cattero V, Roussel C, Lessard-Lord J, Roy D, Desjardins Y.	Microbiome Res Rep	10.20517/mrr.2024.17	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
	microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.	Zafeiropoulos H, Delopoulos EIM, Erega A, Schneider A, Geirnaert A, Morris J, Faust K.	Genome Biol	10.1186/s13059-025-03769-2	2025
	The Role of the Microbiome in Gastroentero-Pancreatic Neuroendocrine Neoplasms (GEP-NENs).	Mohamed A, Asa SL, McCormick T, Al-Shakhshir H, Dasari A, Mauricio R, Salem I, Ocuin LM, Bajor D, Lee RT, Selfridge JE, Kardan A, Lee Z, Avril N, Kopp S, Winter JM, Hardacre JM, Ammori JB, Ghannoum MA.	Curr Issues Mol Biol	10.3390/cimb44050136	2022
Pathogenicity	Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.	Brar AS, Vemula SL, Yanamaladoddi V, Sodhi S, Hatwal J, Sohal A, Batta A.	World J Cardiol	10.4330/wjc.v17.i6.107386	2025
	Comprehensive retrospect and future perspective on bacteriophage and cancer.	Liping Z, Sheng Y, Yinhang W, Yifei S, Jiaqun H, Xiaojian Y, Shuwen H, Jing Z.	Virol J	10.1186/s12985-024-02553-1	2024
	Draft Genome Sequences of 13 Isolates of Adlercreutzia equolifaciens, Eggerthella lenta, and Gordonibacter urolithinfaciens, Isolated from Human Fecal Samples in Karlsruhe, Germany.	Danylec N, Stoll DA, Gobl A, Huch M.	Microbiol Resour Announc	10.1128/mra.00017-20	2020
	Gut dysbiosis in patients with chronic pain: a systematic review and meta-analysis.	Goudman L, Demuyser T, Pilitsis JG, Billot M, Roulaud M, Rigoard P, Moens M.	Front Immunol	10.3389/fimmu.2024.1342833	2024
	Red meat consumption in higher healthy eating index diets is associated with brain health critical nutritional adequacy, and fecal microbial diversity.	Dhakal S, Hossain M, Parajuli S.	Sci Rep	10.1038/s41598-025-18907-w	2025
	A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.	Sun W, Zhang Y, Guo R, Sha S, Chen C, Ullah H, Zhang Y, Ma J, You W, Meng J, Lv Q, Cheng L, Fan S, Li R, Mu X, Li S, Yan Q.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00567-9	2024
	Vancomycin-Resistant Enterococci: Screening Efficacy and the Risk of Bloodstream Infections in a Specialized Healthcare Setting.	Navarra A, Cicalini S, D'Arezzo S, Pica F, Selleri M, Nisii C, Venditti C, Cannas A, Mazzarelli A, Vulcano A, Carrara S, Vincenti D, Bartolini B, Giacomini P, Bocci MG, Fontana C.	Antibiotics (Basel)	10.3390/antibiotics14030304	2025
	[Gut microbiota and systemic inflammation in patients with chronic heart failure].	Vlasov AA, Salikova SP, Grinevich VB, Bystrova OV, Osipov GA, Meshkova ME.	Kardiologiia	10.18087/cardio.2020.5.n859	2020
	Pharmacomicrobiomics: a new field contributing to optimizing drug therapy in Parkinson's disease.	Zhang Y, Mo C, Ai P, He X, Xiao Q, Yang X.	Gut Microbes	10.1080/19490976.2025.2454937	2025
	Deciphering the impact of dietary habits and behavioral patterns on colorectal cancer.	Yuan Q, Liu J, Wang X, Du C, Zhang Y, Lin L, Wang C, Hong Z.	Int J Surg	10.1097/js9.0000000000002229	2025
Genetics	StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.	Heber K, Tian S, Betancurt-Anzola D, Koo H, Bisanz JE.	Bioinformatics	10.1093/bioinformatics/btaf440	2025
Metabolism	Gut microbiota and metabolites of alpha-synuclein transgenic monkey models with early stage of Parkinson's disease.	Yan Y, Ren S, Duan Y, Lu C, Niu Y, Wang Z, Inglis B, Ji W, Zheng Y, Si W.	NPJ Biofilms Microbiomes	10.1038/s41522-021-00242-3	2021
	Different Fecal Microbiota in Hirschsprung's Patients With and Without Associated Enterocolitis.	Arnaud AP, Cousin I, Schmitt F, Petit T, Parmentier B, Levard G, Podevin G, Guinot A, DeNapoli S, Hervieux E, Flaum V, De Vries P, Randuineau G, David-Le Gall S, Buffet-Bataillon S, Boudry G.	Front Microbiol	10.3389/fmicb.2022.904758	2022
	Association between Fecal Bile Acids and Levodopa Response in Patients with Parkinson's Disease.	He X, Lai Y, Mo C, Zhang Y, Ai P, Xu S, Qian Y, Xiao Q, Yang X.	Microorganisms	10.3390/microorganisms12071432	2024
	Accounting Gut Microbiota as the Mediator of Beneficial Effects of Dietary (Poly)phenols on Skeletal Muscle in Aging.	Ticinesi A, Nouvenne A, Cerundolo N, Parise A, Meschi T.	Nutrients	10.3390/nu15102367	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
	mNFE: microbiome network flow entropy for detecting pre-disease states of type 1 diabetes.	Gao R, Li P, Ni Y, Peng X, Ren J, Chen L.	Gut Microbes	10.1080/19490976.2024.2327349	2024
	Eggerthella lenta Bloodstream Infections Are Associated With Increased Mortality Following Empiric Piperacillin-Tazobactam (TZP) Monotherapy: A Population-based Cohort Study.	Ugarte-Torres A, Gillrie MR, Griener TP, Church DL.	Clin Infect Dis	10.1093/cid/ciy057	2018
	Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity.	Valdes AM, Louca P, Visconti A, Asnicar F, Bermingham K, Nogal A, Wong K, Michelotti GA, Wolf J, Segata N, Spector TD, Berry SE, Falchi M, Menni C.	BMC Med	10.1186/s12916-024-03543-4	2024
	Pelvic abscess caused by a slow growing anaerobic bacterium, Eggerthella lenta: First case report from Pakistan.	Mal PB, Rafiq I, Iftikhar I, Irfan S.	J Pak Med Assoc		2017
Pathogenicity	Antimicrobial susceptibility profiles of anaerobic bacteria, isolated from human clinical specimens, within different European and surrounding countries. A joint ESGAI study.	Veloo ACM, Tokman HB, Jean-Pierre H, Dumont Y, Jeverica S, Lienhard R, Novak A, Rodloff A, Rotimi V, Wybo I, Nagy E, ESGAI study group.	Anaerobe	10.1016/j.anaerobe.2019.102111	2020
	Lactiplantibacillus plantarum P470 Isolated from Fermented Chinese Chives Has the Potential to Improve In Vitro the Intestinal Microbiota and Biological Activity in Feces of Coronary Heart Disease (CHD) Patients.	Yang L, Wu Y, Yang J, Li Y, Zhao X, Liang T, Li L, Jiang T, Zhang T, Zhang J, Zhong H, Xie X, Wu Q.	Nutrients	10.3390/nu16172945	2024
Phylogeny	Evaluation of the Correlation between Gut Microbiota and Renal Function in Chronic Kidney Disease Patients.	Xi J, Xu J, Sun J, Li H, Zhang S, Xie H, Wang H, Zhang R, Zhao M, Wang M, Zheng T.	J Microbiol Biotechnol	10.4014/jmb.2502.02039	2025
Pathogenicity	Tuo-Min-Ding-Chuan Decoction Alleviates Asthma via Spatial Regulation of Gut Microbiota and Treg Cell Promotion.	Hong Y, Yang Z, Liu Z, Li N, Qin J, Ge D, Peng G, Wang J, Wang Q.	Pharmaceuticals (Basel)	10.3390/ph18050646	2025
	High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.	Slager J, Simpson HL, Gacesa R, Chen L, Tan IL, Gelderloos J, Maatman A, Wijmenga C, Zhernakova A, Fu J, Weersma RK, Gonera G, Jonkers IH, Withoff S.	Gut Microbes	10.1080/19490976.2025.2489071	2025
	Exploring bacterial key genes and therapeutic agents for breast cancer among the Ghanaian female population: Insights from In Silico analyses.	Kibria MK, Ali MA, Mollah MNH.	PLoS One	10.1371/journal.pone.0312493	2024
	Antimicrobial Susceptibility Profile of Rare Anaerobic Bacteria.	Wolf LJ, Stingu CS.	Antibiotics (Basel)	10.3390/antibiotics12010063	2022
	Effects of N-Carbamylglutamate supplementation on cecal morphology, microbiota composition, and short-chain fatty acids contents of broiler breeder roosters.	Liu N, Zhang Z, Zhang J, Ma W, Wang C.	Sci Rep	10.1038/s41598-025-91577-w	2025
Metabolism	Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes.	Lamichhane S, Sen P, Dickens AM, Alves MA, Harkonen T, Honkanen J, Vatanen T, Xavier RJ, Hyotylainen T, Knip M, Oresic M.	Cell Rep Med	10.1016/j.xcrm.2022.100762	2022
	Eggerthella lenta Bacteremia in a Middle-Aged Healthy Man with Acute Hepatic Abscess: Case Report and Literature Review, 1970-2020.	Wang J, Guo R, Ma W, Dong X, Yan S, Xie W.	Infect Drug Resist	10.2147/idr.s321282	2021
Metabolism	Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites.	Bai X, Wei H, Liu W, Coker OO, Gou H, Liu C, Zhao L, Li C, Zhou Y, Wang G, Kang W, Ng EK, Yu J.	Gut	10.1136/gutjnl-2021-325021	2022
Phylogeny	Changes in the Gut and Oral Microbiome in Children with Phenylketonuria in the Context of Dietary Restrictions-A Preliminary Study.	Ostrowska M, Nowosad K, Mikoluc B, Szczerba H, Komon-Janczara E.	Nutrients	10.3390/nu16223915	2024
	Gut microbiota analysis reveals microbial signature for multi-autoimmune diseases based on machine learning model.	An T, Zhang S, Li J, Wang H, Chen L, Shi Y, Wang J, Han S, Wang R, Wang L, Huan Z, Yang R, Hao D, Liu Y, Liu X, Yuan C.	Front Microbiol	10.3389/fmicb.2025.1660775	2025
Genetics	The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.	Kulecka M, Jaworski P, Zeber-Lubecka N, Balabas A, Piatkowska M, Czarnowski P, Fraczek B, Tarnowski W, Mikula M, Ostrowski J.	Nutrients	10.3390/nu17142320	2025
Pathogenicity	Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.	Wang Y, Lu J, Dai W, Yang S.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1526863	2025
	DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy.	Oh M, Zhang L.	Sci Rep	10.1038/s41598-023-31210-w	2023
Genetics	Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.	Luo L, Chen B, Zeng S, Li Y, Chen X, Zhang J, Guo X, Li S, Ruan L, Zhu S, Gao C, Zhang C, Li T.	Front Microbiol	10.3389/fmicb.2025.1586195	2025
	To analyze the relationship between gut microbiota, metabolites and migraine: a two-sample Mendelian randomization study.	Qu K, Li MX, Gan L, Cui ZT, Li JJ, Yang R, Dong M.	Front Microbiol	10.3389/fmicb.2024.1325047	2024
Genetics	Pathogenesis diagnosis of a pediatric patient suffering from multi-organ abscesses.	Wu M, Xiao H, Xiao Y, Chen T, Wang X, Xiao X, Wang Y, Wang J, Ren L, Liu G.	Diagn Pathol	10.1186/s13000-023-01360-6	2023
	A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.	Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD.	Nat Commun	10.1038/s41467-025-64822-z	2025
Pathogenicity	Associations Between Uraemic Toxins and Gut Microbiota in Adults Initiating Peritoneal Dialysis.	James P, Stanford J, Dixit OVA, Nicdao MA, McWhinney B, Sud K, Ryan M, Read S, Ahlenstiel G, Lambert K, O'Brien C, Chau K.	Toxins (Basel)	10.3390/toxins17070334	2025
Phylogeny	The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery.	Yang Y, Zhou HY, Zhou GM, Chen J, Ming R, Zhang D, Jiang HW.	Front Microbiol	10.3389/fmicb.2024.1494049	2024
Genetics	Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.	Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Longhi G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M.	Front Microbiol	10.3389/fmicb.2024.1349391	2024
Enzymology	Eggerthella lenta bacteremia in solid tumor cancer patients: Pathogen or witness of frailty?	Woerther PL, Antoun S, Chachaty E, Merad M.	Anaerobe	10.1016/j.anaerobe.2017.04.010	2017
	High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation.	Ricaurte D, Huang Y, Sheth RU, Gelsinger DR, Kaufman A, Wang HH.	Nat Microbiol	10.1038/s41564-023-01581-x	2024
Genetics	A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.	Feng M, Chai Y, Li J, Wang Q, Zhang D.	Front Genet	10.3389/fgene.2025.1619911	2025
	Investigating causal relationships between the gut microbiota and allergic diseases: A mendelian randomization study.	Wang Y, Liu T, Wan Z, Wang L, Hou J, Shi M, Tsui SKW.	Front Genet	10.3389/fgene.2023.1153847	2023
	Lactiplantibacillus plantarum Interstrain Variability in the Production of Bioactive Phenolic Metabolites from Flavan-3-ols.	Pulido-Mateos EC, Lessard-Lord J, Desjardins Y, Roy D.	J Agric Food Chem	10.1021/acs.jafc.4c07890	2024
Pathogenicity	Assembled human microbiome and metabolome in chronic kidney disease: Dysbiosis a double-edged sword interlinking Circ-YAP1, Circ-APOE & Circ-SLC8A1.	Zaki EA, Afifi SM, Ammar NM, Kadry MO.	Toxicol Rep	10.1016/j.toxrep.2025.102058	2025
	Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice.	Balakrishnan B, Luckey D, Taneja V.	Mil Med	10.1093/milmed/usy309	2019
	Streptomyces uses both polar and dispersed cell wall synthesis during exploratory growth.	Zambri MP, Baglio CR, Irazoki O, Jones SE, Garner EC, Cava F, Elliot MA.	Nat Microbiol	10.1038/s41564-025-02080-x	2025
	Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery.	Xu J, Dai D, Yang Y, Gao S, Yang J, Dong C, Yang W, Yuan J, Wang T, Tian T, Yang Y, Luo F, Jiang P, Wu C, Sun X, Sui Y, Gao G, Ma W, Wu Y, Zhang J, Li J, Guo C, Cui C, Guo T, Zhao X, Yuan J, Qiao S, Hu F, Gao X, Luo X, Peng H, Wang D, Wu J, Wu C, He J, Chen WH, Yang Y, Fu J.	Imeta	10.1002/imt2.70079	2025
Genetics	Association between gut microbiota and central retinal artery occlusion: A two-sample Mendelian randomization study.	Chen J, Wang X, Yang J, Huang J, Xie M, Su Z, Jiang F.	Indian J Ophthalmol	10.4103/ijo.ijo_3304_23	2024
	Causal effects of gut microbiota on diabetic retinopathy: A Mendelian randomization study.	Liu K, Zou J, Fan H, Hu H, You Z.	Front Immunol	10.3389/fimmu.2022.930318	2022
	MagMD: Database summarizing the metabolic action of gut microbiota to drugs.	Zhou J, Ouyang J, Gao Z, Qin H, Jun W, Shi T.	Comput Struct Biotechnol J	10.1016/j.csbj.2022.11.021	2022
	Consumption of only wild foods induces large scale, partially persistent alterations to the gut microbiome.	Rampelli S, Pomstra D, Barone M, Fabbrini M, Turroni S, Candela M, Henry AG.	Sci Rep	10.1038/s41598-025-00319-5	2025
	Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.	Vazquez-Castellanos JF, Maciel LF, Wauters L, Gregory A, Van Oudenhove L, Geboers K, Verbeke K, Smokvina T, Tack J, Vanuytsel T, Derrien M, Raes J.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00776-w	2025
	Molecular Mechanisms and Emerging Precision Therapeutics in the Gut Microbiota-Cardiovascular Axis.	Ponce Alencastro JA, Salinas Lucero DA, Solis RP, Herrera Giron CG, Estrella Lopez AS, Anda Suarez PX.	Cureus	10.7759/cureus.83022	2025
	A plug-and-play system for polycyclic tetramate macrolactam production and functionalization.	Glockle A, Schuler S, Einsiedler M, Gulder TAM.	Microb Cell Fact	10.1186/s12934-024-02630-8	2025
	Bibliometric analysis of mucosal immunity in IgA nephropathy from 1990 to 2022.	Chen X, Yan Z, Pan Q, Zhang C, Chen Y, Liang X, Li S, Wu G.	Immun Inflamm Dis	10.1002/iid3.1156	2024
	In Vitro Activity of Gepotidacin against Gram-Negative and Gram-Positive Anaerobes.	Hackel MA, Karlowsky JA, Canino MA, Sahm DF, Scangarella-Oman NE.	Antimicrob Agents Chemother	10.1128/aac.02165-21	2022
	Functional recovery outcomes following acute stroke is associated with abundance of gut microbiota related to inflammation, butyrate and secondary bile acid.	Hammond TC, Powell E, Green SJ, Chlipala G, Frank J, Yackzan AT, Yanckello LM, Chang YH, Xing X, Heil S, Springer JE, Pennypacker K, Stromberg A, Sawaki L, Lin AL.	Front Rehabil Sci	10.3389/fresc.2022.1017180	2022
Enzymology	Relative abundance of Megamonas hypermegale and Butyrivibrio species decreased in the intestine and its possible association with the T cell aberration by metabolite alteration in patients with Behcet's disease (210 characters).	Shimizu J, Kubota T, Takada E, Takai K, Fujiwara N, Arimitsu N, Ueda Y, Wakisaka S, Suzuki T, Suzuki N.	Clin Rheumatol	10.1007/s10067-018-04419-8	2019
	Potential risk factors and outcomes of infection with multidrug resistance among diabetic patients having ulcers: 7 years study.	Zubair M, Ahmad J.	Diabetes Metab Syndr	10.1016/j.dsx.2018.10.014	2019
	Effects of live and pasteurized forms of Lactobacillus casei Zhang on acute kidney injury and chronic renal fibrosis.	Wang X, Shi M, Cao C, Zeng R, Yao Y.	Braz J Microbiol	10.1007/s42770-024-01491-y	2024
	Integration of Pseudotargeted Metabolomics and Microbiomics Reveals That Hugan Tablets Ameliorate NASH with Liver Fibrosis in Mice by Modulating Bile Acid Metabolism via the Gut Microbiome.	Dong W, Wang Y, Li H, Ma H, Gong Y, Luo G, Gao X.	Metabolites	10.3390/metabo15070433	2025
	Prediction of microbe-drug associations based on a modified graph attention variational autoencoder and random forest.	Wang B, Ma F, Du X, Zhang G, Li J.	Front Microbiol	10.3389/fmicb.2024.1394302	2024
Metabolism	Gut microbiota-derived arginine metabolism mitigates intestinal ischemia-reperfusion injury.	Li X, Hou M, Lyu J, Min X, Han X, Wang X, Liu Z, Leng Y.	J Transl Med	10.1186/s12967-025-07225-4	2025
	Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.	Wang H, Xue W, Cheng J, He Y, Song Y, Hu D, Peng A, Li C, Bao H.	Microbiol Spectr	10.1128/spectrum.03166-24	2025
Metabolism	Relationship Between Gut Bacteria and Levodopa Metabolism.	Xu K, Sheng S, Zhang F.	Curr Neuropharmacol	10.2174/1570159x21666221019115716	2023
Phylogeny	Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity.	Buttimer C, Bottacini F, Shkoporov AN, Draper LA, Ross P, Hill C.	Microorganisms	10.3390/microorganisms10010195	2022
	Gut Bacterial Dysbiosis in Children with Intractable Epilepsy.	Lee K, Kim N, Shim JO, Kim GH.	J Clin Med	10.3390/jcm10010005	2020
	Bifidobacterium as a Potential Biomarker of Sarcopenia in Elderly Women.	Wang Z, Xu X, Deji Y, Gao S, Wu C, Song Q, Shi Z, Xiang X, Zang J, Su J.	Nutrients	10.3390/nu15051266	2023
Metabolism	Computational analysis of the gut microbiota-mediated drug metabolism.	Chum S, Naveira Montalvo A, Hassoun S.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.03.016	2025
	Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis.	Cai J, Sun L, Gonzalez FJ.	Cell Host Microbe	10.1016/j.chom.2022.02.004	2022
	The gut microbiota during tamoxifen therapy in patients with breast cancer.	Hillege LE, Barnett DJM, Ziemons J, Aarnoutse R, de Vos-Geelen J, van Geel R, de Boer M, van Riet YEA, Vincent J, Penders J, Smidt ML.	Sci Rep	10.1038/s41598-025-91734-1	2025
	Expansion of Colorectal Cancer Biomarkers Based on Gut Bacteria and Viruses.	Zhang J, He Y, Xia L, Yi J, Wang Z, Zhao Y, Song X, Li J, Liu H, Liang X, Nie S, Liu L.	Cancers (Basel)	10.3390/cancers14194662	2022
Pathogenicity	Metabolic modeling of host-microbe interactions.	Srinak N, Kruger F, Kaleta C, Taubenheim J.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.10.006	2025
	Targeted high-level production of chuangxinmycin and its halogenated derivatives with antitubercular activity.	Zhao X, Lu Y, Zhang X, Zhang X, Du Y, Han X, Zhu Y, Yu W, Wu L, Li X, Shi Y, Zhang T, Hong B.	Microb Cell Fact	10.1186/s12934-025-02740-x	2025
	Oral administration of pioglitazone inhibits pulmonary hypertension by regulating the gut microbiome and plasma metabolome in male rats.	Zhang Z, Liang Y, Mo S, Zhao M, Li Y, Zhang C, Shan X, Liu S, Liao J, Luo X, Zhu J, Wang C, Jiang Q, Hou C, Hong W, Lai N, Chen Y, Xu L, Lu W, Wang J, Wang Z, Yang K.	Physiol Rep	10.14814/phy2.70174	2025
	Correlation between postmortem microbial signatures and substance abuse disorders.	Javan GT, Wells T, Allen J, Visona S, Moretti M, Tipton C, Scott L, Finley SJ.	PLoS One	10.1371/journal.pone.0274401	2022
Metabolism	Multi-Omics Analysis Reveals Aberrant Gut-Metabolome-Immune Network in Schizophrenia.	Fan Y, Gao Y, Ma Q, Yang Z, Zhao B, He X, Yang J, Yan B, Gao F, Qian L, Wang W, Zhu F, Ma X.	Front Immunol	10.3389/fimmu.2022.812293	2022
	Early assessment of blood culture negativity as a potential support tool for antimicrobial stewardship.	Menchinelli G, Oliveti A, Fiori B, D'Inzeo T, Spanu T, Murri R, Fantoni M, Sanguinetti M, Posteraro B, De Angelis G.	Heliyon	10.1016/j.heliyon.2024.e27849	2024
Phylogeny	A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing.	Neuenschwander SM, Terrazos Miani MA, Amlang H, Perroulaz C, Bittel P, Casanova C, Droz S, Flandrois JP, Leib SL, Suter-Riniker F, Ramette A.	J Clin Microbiol	10.1128/jcm.00060-20	2020
Enzymology	Microbiological diagnosis of Eggerthella lenta blood culture isolates in a Swedish tertiary hospital: Rapid identification and antimicrobial susceptibility profile.	Liderot K, Ratcliffe P, Luthje P, Thidholm E, Ozenci V.	Anaerobe	10.1016/j.anaerobe.2015.11.005	2016
	Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome.	Chang B, Zhang W, Wang Y, Zhang Y, Zhong S, Gao P, Wang L, Zhao Z.	BMC Microbiol	10.1186/s12866-024-03211-w	2024
	Predicting microbial interactions with approaches based on flux balance analysis: an evaluation.	Joseph C, Zafeiropoulos H, Bernaerts K, Faust K.	BMC Bioinformatics	10.1186/s12859-024-05651-7	2024
	Clinical evidence of the link between gut microbiome and myalgic encephalomyelitis/chronic fatigue syndrome: a retrospective review.	Wang JH, Choi Y, Lee JS, Hwang SJ, Gu J, Son CG.	Eur J Med Res	10.1186/s40001-024-01747-1	2024
	Application of artificial intelligence approaches to predict the metabolism of xenobiotic molecules by human gut microbiome.	Malwe AS, Sharma VK.	Front Microbiol	10.3389/fmicb.2023.1254073	2023
Pathogenicity	[Effect of silver nanoparticles on anaerobic bacteria].	Vecerova R, Panacek A, Kolar M.	Klin Mikrobiol Infekc Lek		2017
	Microbiological Assessment of the FilmArray Blood Culture Identification 2 Panel: Potential Impact in Critically Ill Patients.	Mauri C, Consonni A, Briozzo E, Giubbi C, Meroni E, Tonolo S, Luzzaro F.	Antibiotics (Basel)	10.3390/antibiotics12081247	2023
Phylogeny	Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples.	Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA.	Front Microbiol	10.3389/fmicb.2023.1148097	2023
	Exploring the role of gut microbiota in advancing personalized medicine.	Huang G, Khan R, Zheng Y, Lee PC, Li Q, Khan I.	Front Microbiol	10.3389/fmicb.2023.1274925	2023
	Blood lipids mediate the effects of gut microbiome on endometriosis: a mendelian randomization study.	Su C, Wan S, Ding J, Ni G, Ding H.	Lipids Health Dis	10.1186/s12944-024-02096-y	2024
Genetics	Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.	Millard SA, Vendrov KC, Young VB, Seekatz AM.	mBio	10.1128/mbio.01108-25	2025
	Severe Cognitive Decline in Long-term Care Is Related to Gut Microbiome Production of Metabolites Involved in Neurotransmission, Immunomodulation, and Autophagy.	Shoubridge AP, Carpenter L, Flynn E, Papanicolas LE, Collins J, Gordon D, Lynn DJ, Whitehead C, Leong LEX, Cations M, De Souza DP, Narayana VK, Choo JM, Wesselingh SL, Crotty M, Inacio MC, Ivey K, Taylor SL, Rogers GB.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glaf053	2025
	Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.	Myers T, Song SJ, Chen Y, De Pessemier B, Khatib L, McDonald D, Huang S, Gallo R, Callewaert C, Havulinna AS, Lahti L, Roeselers G, Laiola M, Shetty SA, Kelley ST, Knight R, Bartko A.	Commun Biol	10.1038/s42003-025-08590-y	2025
Pathogenicity	Bibliometric and visual analysis of human microbiome-breast cancer interactions: current insights and future directions.	Zhou Y, Jiang M, Li X, Shen K, Zong H, Lv Q, Shen B.	Front Microbiol	10.3389/fmicb.2024.1490007	2024
Genetics	Metagenomics-based systematic analysis reveals that gut microbiota Gd-IgA1-associated enzymes may play a key role in IgA nephropathy.	Liang X, Zhang S, Zhang D, Hu L, Zhang, Peng Y, Xu Y, Hou H, Zou C, Liu X, Chen Y, Lu F.	Front Mol Biosci	10.3389/fmolb.2022.970723	2022
	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	Cocoa Polyphenols Alter the Fecal Microbiome Without Mitigating Colitis in Mice Fed Healthy or Western Basal Diets	Stewart E, Almatani M, Hayden M, Rompato G, Case J, Rice S, Hintze K, Benninghoff A.	Nutrients		2025
	Exploring substrate-microbe interactions: a metabiotic approach toward developing targeted synbiotic compositions.	Speckmann B, Ehring E, Hu J, Rodriguez Mateos A.	Gut Microbes	10.1080/19490976.2024.2305716	2024
	Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs.	Ren H, Shi Z, Yang F, Wang S, Yuan F, Li T, Li M, Zhu J, Li J, Wu K, Zhang Y, Ning G, Kristiansen K, Wang W, Gu Y, Zhong H.	Imeta	10.1002/imt2.179	2024
Pathogenicity	Alterations in Gut Microbiota and Serum Metabolites in Children with Mycoplasma pneumoniae Pneumonia.	Wang S, Liu C, Ding R, Wang S, Ye Y, He M.	Infect Drug Resist	10.2147/idr.s490547	2024
	Participation of gut microbiota and bacterial translocation in chronic systemic inflammation in recently diagnosed rheumatoid arthritis patients.	Dunyach-Remy C, Pouget C, Pers YM, Gaujoux-Viala C, Demattei C, Salipante F, Grenga L, Armengaud J, Lavigne JP, Jorgensen C.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100366	2025
	Stimulation of Codonopsis pilosula Polysaccharide on Bifidobacterium of Human Gut Bacteria In Vitro.	Li J, Dong L, Liu Y, Gao J.	Evid Based Complement Alternat Med	10.1155/2021/9524913	2021
Pathogenicity	The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.	Bayne J, Charavaryamath C, Hu Y, Yousefi F, Murphy M, Law A, Michael A, Muyyarikkandy MS, Nibbering B, Smits WK, Kuijper E, Opriessnig T, Sauer M, Scaria J, Sponseller B, Ramirez A, Mooyottu S.	Gut Microbes	10.1080/19490976.2025.2568706	2025
	Smoking-induced gut microbial dysbiosis mediates cancer progression through modulation of anti-tumor immune response.	Sharma P, Jain T, Sorgen A, Iyer S, Tarique M, Roy P, Kurtom S, Sethi V, Bava EP, Gutierrez-Garcia AK, Vaish U, Suresh DS, Sahay P, Edwards D, Afghani J, Putluri S, Reddy KRK, Amara CS, Kamal AHM, Fodor A, Dudeja V.	iScience	10.1016/j.isci.2025.112002	2025
	Echinacea purpurea (L.) Moench Polysaccharide Alleviates DSS-Induced Colitis in Rats by Restoring Th17/Treg Balance and Regulating Intestinal Flora.	Li Y, Lin Y, Zheng X, Zheng X, Yan M, Wang H, Liu C.	Foods	10.3390/foods12234265	2023
	The Microbiome-Gut-Brain axis regulates social cognition & craving in young binge drinkers.	Carbia C, Bastiaanssen TFS, Iannone LF, Garcia-Cabrerizo R, Boscaini S, Berding K, Strain CR, Clarke G, Stanton C, Dinan TG, Cryan JF.	EBioMedicine	10.1016/j.ebiom.2023.104442	2023
	The gut microbiome, chronic kidney disease, and sarcopenia.	Zheng G, Cao J, Wang XH, He W, Wang B.	Cell Commun Signal	10.1186/s12964-024-01922-1	2024
	Antimicrobial Susceptibility Patterns and Wild-Type MIC Distributions of Anaerobic Bacteria at a German University Hospital: A Five-Year Retrospective Study (2015-2019).	Badr MT, Blumel B, Baumgartner S, Komp JMA, Hacker G.	Antibiotics (Basel)	10.3390/antibiotics9110823	2020
Phylogeny	The influence of blood on the human gut microbiome.	Chenard T, Malick M, Dube J, Masse E.	BMC Microbiol	10.1186/s12866-020-01724-8	2020
Enzymology	Performance of two blood culture systems to detect anaerobic bacteria. Is there any difference?	Mueller-Premru M, Jeverica S, Papst L, Nagy E.	Anaerobe	10.1016/j.anaerobe.2017.03.006	2017
Metabolism	The influence of the gut microbiome on BCG-induced trained immunity.	Strazar M, Mourits VP, Koeken VACM, de Bree LCJ, Moorlag SJCFM, Joosten LAB, van Crevel R, Vlamakis H, Netea MG, Xavier RJ.	Genome Biol	10.1186/s13059-021-02482-0	2021
	Precision microbiota therapy for IBD: premise and promise.	Nagayama M, Gogokhia L, Longman RS.	Gut Microbes	10.1080/19490976.2025.2489067	2025
	Bacterial pathogens in pediatric appendicitis: a comprehensive retrospective study.	Felber J, Gross B, Rahrisch A, Waltersbacher E, Trips E, Schrottner P, Fitze G, Schultz J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1027769	2023
	Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome.	Brushett S, Gacesa R, Vich Vila A, Brandao Gois MF, Andreu-Sanchez S, Swarte JC, Klaassen MAY, Collij V, Sinha T, Bolte LA, Wu J, Swertz M, de Kroon MLA, Reijneveld SA, Wijmenga C, Weersma RK, Fu J, van Loo HM, Kurilshikov A, Zhernakova A.	Gut Microbes	10.1080/19490976.2023.2281360	2023
Genetics	Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China.	Sun S, Wang H, Howard AG, Zhang J, Su C, Wang Z, Du S, Fodor AA, Gordon-Larsen P, Zhang B.	mSystems	10.1128/msystems.00200-22	2022
	Intestinal microbiome and maternal mental health: preventing parental stress and enhancing resilience in mothers.	Matsunaga M, Takeuchi M, Watanabe S, Takeda AK, Kikusui T, Mogi K, Nagasawa M, Hagihara K, Myowa M.	Commun Biol	10.1038/s42003-024-05884-5	2024
	Astragalus Polysaccharide Modulates the Gut Microbiota and Metabolites of Patients with Type 2 Diabetes in an In Vitro Fermentation Model.	Zhang X, Jia L, Ma Q, Zhang X, Chen M, Liu F, Zhang T, Jia W, Zhu L, Qi W, Wang N.	Nutrients	10.3390/nu16111698	2024
Genetics	Quercetin positively affects gene expression profiles and metabolic pathway of antibiotic-treated mouse gut microbiota.	Mi W, Hu Z, Xu L, Bian X, Lian W, Yin S, Zhao S, Gao W, Guo C, Shi T.	Front Microbiol	10.3389/fmicb.2022.983358	2022
	Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome.	De Filippis F, Valentino V, Sequino G, Borriello G, Riccardi MG, Pierri B, Cerino P, Pizzolante A, Pasolli E, Esposito M, Limone A, Ercolini D.	Nat Commun	10.1038/s41467-024-48739-7	2024
	Enteric Fistulous Communication with an Aortobifemoral Graft Permitting for Eggerthella Lenta Colonization.	Jehangir W, Sanabria F, Singh Z, Enakuaa S, Bedran KH, Raoof N, Yousif A.	J Glob Infect Dis	10.4103/0974-777x.170506	2015
	Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances.	Lindell AE, Griesshammer A, Michaelis L, Papagiannidis D, Ochner H, Kamrad S, Guan R, Blasche S, Ventimiglia LN, Ramachandran B, Ozgur H, Zelezniak A, Beristain-Covarrubias N, Yam-Puc JC, Roux I, Barron LP, Richardson AK, Martin MG, Benes V, Morone N, Thaventhiran JED, Bharat TAM, Savitski MM, Maier L, Patil KR.	Nat Microbiol	10.1038/s41564-025-02032-5	2025
	Synthesis of versatile neuromodulatory molecules by a gut microbial glutamate decarboxylase.	Dadi P, Pauling CW, Shrivastava A, Shah DD.	iScience	10.1016/j.isci.2025.112289	2025
	Personalized modeling of gut microbiome metabolism throughout the first year of life.	Shaaban R, Busi SB, Wilmes P, Gueant JL, Heinken A.	Commun Med (Lond)	10.1038/s43856-024-00715-4	2024
	Determination of Glycopeptide Resistance Genes and Virulence Factors in Vancomycin-Resistant Enterococci Isolates and the Relationship Between Glycopeptide Resistance Genes and Endogenous/Exogenous Flora.	Orak F, Yalcinkaya KT, Aydin F, Karakaya E, Doganer A, Mustak IB, Aral M, Ipek S.	J Clin Pract Res	10.14744/cpr.2024.03419	2024
	Characteristics of Intestinal Microbiota in Japanese Patients with Mild Cognitive Impairment and a Risk-Estimating Method for the Disorder.	Hatayama K, Ebara A, Okuma K, Tokuno H, Hasuko K, Masuyama H, Ashikari I, Shirasawa T.	Biomedicines	10.3390/biomedicines11071789	2023
Genetics	Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes.	Ren Y, Chen L, Guo R, Ma S, Li S, Zhang Y, Jiang H, Shi H, Zhang P.	J Transl Med	10.1186/s12967-024-05004-1	2024
Genetics	Changes in Gut Microbiota of Patients with Atopic Dermatitis During Balneotherapy.	Thirion F, Guilly S, Fromentin S, Plaza Onate F, Alvarez AS, Le Chatelier E, Pons N, Levenez F, Quinquis B, Ehrlich S, Dore J, Martin R, Seite S.	Clin Cosmet Investig Dermatol	10.2147/ccid.s342104	2022
	The importance of personalization in high altitude protocols for hematologic and metabolic benefits in sports: A multi-dimensional N-of-1 case study.	Lili L, Meydan C, Rickard N, Zhang B.	Heliyon	10.1016/j.heliyon.2023.e23159	2024
	Causal effects of the gut microbiome on COVID-19 susceptibility and severity: a two-sample Mendelian randomization study.	Zhong MM, Xie JH, Feng Y, Zhang SH, Xia JN, Tan L, Chen NX, Su XL, Zhang Q, Feng YZ, Guo Y.	Front Immunol	10.3389/fimmu.2023.1173974	2023
Metabolism	Systematic identification of secondary bile acid production genes in global microbiome.	Yang Y, Gao W, Zhu R, Tao L, Chen W, Zhu X, Shen M, Xu T, Zhao T, Zhang X, Zhu L, Jiao N.	mSystems	10.1128/msystems.00817-24	2025
	The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Kim EH, Choi J, Choi Y, Yoon H, Lee SM, Seok YJ.	Gut Liver	10.5009/gnl230385	2024
Enzymology	Gut microbiota and cardiac arrhythmia: a pharmacokinetic scope.	Nabeh OA.	Egypt Heart J	10.1186/s43044-022-00325-2	2022
	The gut-kidney axis in high-altitude hypoxia: pathophysiological mechanisms and the central role of hypoxia inducible factor.	Wu P, Li X, Long W, Ma Y, Xue B, Xie W, Ma X.	Ann Med	10.1080/07853890.2025.2557514	2025
	Urinary Metabolic Profiling During Epileptogenesis in Rat Model of Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.	Antmen FM, Matpan E, Dongel Dayanc E, Savas EO, Eken Y, Acar D, Ak A, Ozefe B, Sakar D, Canozer U, Sancak SN, Ozdemir O, Sezerman OU, Baykal AT, Serteser M, Suyen G.	Biomedicines	10.3390/biomedicines13030588	2025
	Gut Microbiota and Related Electronic Multisensorial System Changes in Subjects With Symptomatic Uncomplicated Diverticular Disease Undergoing Rifaximin Therapy.	De Vincentis A, Santonico M, Del Chierico F, Altomare A, Marigliano B, Laudisio A, Reddel S, Grasso S, Zompanti A, Pennazza G, Putignani L, Guarino MPL, Cicala M, Antonelli Incalzi R.	Front Med (Lausanne)	10.3389/fmed.2021.655474	2021
Metabolism	Rapid analysis of bile acids in different biological matrices using LC-ESI-MS/MS for the investigation of bile acid transformation by mammalian gut bacteria.	Wegner K, Just S, Gau L, Mueller H, Gerard P, Lepage P, Clavel T, Rohn S.	Anal Bioanal Chem	10.1007/s00216-016-0048-1	2017
	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
Pathogenicity	Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.	Kumbhari A, Cheng TNH, Ananthakrishnan AN, Kochar B, Burke KE, Shannon K, Lau H, Xavier RJ, Smillie CS.	Cell Host Microbe	10.1016/j.chom.2024.05.022	2024
Pathogenicity	Microbiome in Chronic Kidney Disease (CKD): An Omics Perspective.	Lohia S, Vlahou A, Zoidakis J.	Toxins (Basel)	10.3390/toxins14030176	2022
Pathogenicity	Perturbed gut microbiota and serum metabolites are associated with progressive renal fibrosis.	Wang RX, Zhou HB, Gao JX, Li XH, Bai WF, Wang J, Bai YC, Fan LY, Chang H, Shi SL.	Front Med (Lausanne)	10.3389/fmed.2025.1489100	2025
Enzymology	Dynamics and diversity of the 'Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of 'Atopobium cluster' isolates.	Thorasin T, Hoyles L, McCartney AL.	Microbiology (Reading)	10.1099/mic.0.000016	2015
	Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study.	Ivashkin V, Shifrin O, Maslennikov R, Poluektova E, Korolev A, Kudryavtseva A, Krasnov G, Benuni N, Barbara G.	BMC Gastroenterol	10.1186/s12876-023-02690-x	2023
	Myricetin alleviates diabetic cardiomyopathy by regulating gut microbiota and their metabolites.	Zhu J, Bao Z, Hu Z, Wu S, Tian C, Zhou Y, Ding Z, Tan X.	Nutr Diabetes	10.1038/s41387-024-00268-4	2024
	Advances in understanding the role of gut microbiota in fat deposition and lipid metabolism.	Zhong Y, Lei Y, Jiang S, Chen D, Wang X, Wang K, Liao T, Liao R, Gan M, Niu L, Zhao Y, Chen L, Zhou X, Wang Y, Zhu L, Shen L.	J Anim Sci Biotechnol	10.1186/s40104-025-01284-9	2025
	Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria.	Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E, Mangalam AK.	Sci Rep	10.1038/s41598-023-27436-3	2023
	Gut microbiota: a crucial player in the combat against tuberculosis.	Lin J, Chen D, Yan Y, Pi J, Xu J, Chen L, Zheng B.	Front Immunol	10.3389/fimmu.2024.1442095	2024
	Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model.	Schumacher J, Muller P, Sulzer J, Faber F, Molitor B, Maier L.	Gut Microbes	10.1080/19490976.2025.2519697	2025
	Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration.	Little AS, Younker IT, Schechter MS, Bernardino PN, Meheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramaswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH.	Nat Microbiol	10.1038/s41564-023-01560-2	2024
Metabolism	Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents.	Wang X, Yang S, Li S, Zhao L, Hao Y, Qin J, Zhang L, Zhang C, Bian W, Zuo L, Gao X, Zhu B, Lei XG, Gu Z, Cui W, Xu X, Li Z, Zhu B, Li Y, Chen S, Guo H, Zhang H, Sun J, Zhang M, Hui Y, Zhang X, Liu X, Sun B, Wang L, Qiu Q, Zhang Y, Li X, Liu W, Xue R, Wu H, Shao D, Li J, Zhou Y, Li S, Yang R, Pedersen OB, Yu Z, Ehrlich SD, Ren F.	Gut	10.1136/gutjnl-2019-319766	2020
	Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor.	Oliphant K, Cruz Ayala W, Ilyumzhinova R, Mbayiwa K, Sroka A, Xie B, Andrews B, Keenan K, Claud EC.	Gut Microbes	10.1080/19490976.2023.2298697	2024
	Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.	Yang Y, Han Z, Gao Z, Chen J, Song C, Xu J, Wang H, Huang A, Shi J, Gu J.	Chin Med J (Engl)	10.1097/cm9.0000000000002421	2023
	Associations of fruit, whole grain, and total energy intakes with gut microbiome diversity and composition.	Wang Y, Zhang K, Dai L, Sun F, Wang D, Meng S, Zhao J, Liu Y, Liu W, Li C, Wang Y, Lu W, Zhu Y.	Food Nutr Res	10.29219/fnr.v67.9725	2023
Pathogenicity	Third-party fecal microbiota transplantation for high-risk treatment-naïve acute GVHD of the lower GI tract.	DeFilipp Z, Damania AV, Kim HT, Chang CC, El-Jawahri A, McAfee SL, Bottoms AS, Toncheva V, Smith MM, Dolaher M, Perry L, White M, Diana B, Connolly S, Dey BR, Frigault MJ, Newcomb RA, O'Donnell PV, Spitzer TR, Mansour MK, Weber D, Ajami NJ, Hohmann E, Jenq RR, Chen YB.	Blood Adv	10.1182/bloodadvances.2024012556	2024
	Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections.	Camelena F, Pean de Ponfilly G, Pailhories H, Bonzon L, Alanio A, Poncin T, Lafaurie M, Depret F, Cambau E, Godreuil S, Chenouard R, Le Monnier A, Jacquier H, Bercot B.	Microbiol Spectr	10.1128/spectrum.02547-22	2023
	Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel.	Kommedal O, Eagan TM, Flotten O, Leegaard TM, Siljan W, Fardal H, Bo B, Grovan F, Larssen KW, Kildahl-Andersen A, Hjetland R, Tilseth R, Hareide SKO, Tellevik M, Dyrhovden R.	Microbiol Spectr	10.1128/spectrum.03510-23	2024
Genetics	Investigating Multi-Omic Signatures of Ethnicity and Dysglycaemia in Asian Chinese and European Caucasian Adults: Cross-Sectional Analysis of the TOFI_Asia Study at 4-Year Follow-Up.	Faraj S, Joblin-Mills A, Sequeira-Bisson IR, Leiu KH, Tung T, Wallbank JA, Fraser K, Miles-Chan JL, Poppitt SD, Taylor MW.	Metabolites	10.3390/metabo15080522	2025
	Randomised, Placebo-Controlled Investigation of the Impact of Probiotic Consumption on Gut Microbiota Diversity and the Faecal Metabolome in Seniors.	van Zanten GC, Madsen AL, Yde CC, Krych L, Yeung N, Saarinen MT, Kot W, Jensen HM, Rasmussen MA, Ouwehand AC, Nielsen DS.	Microorganisms	10.3390/microorganisms12040796	2024
	Intestinal Metabolome for Diagnosing and Prognosing Autism Spectrum Disorder in Children: A Systematic Review.	Suarez-Jaramillo A, Cifuentes SG, Baldeon M, Cardenas P.	Metabolites	10.3390/metabo15040213	2025
	Unraveling the key drivers of bacterial progesterone degradation.	Hernandez-Fernandez G, Ibero J, Garcia JL, Galan B.	mBio	10.1128/mbio.01077-25	2025
	Application of MALDI-TOF MS to assess clinical characteristics, risk factors, and outcomes associated with anaerobic bloodstream infection: a retrospective observational study.	Watanabe T, Hara Y, Yoshimi Y, Yokoyama-Kokuryo W, Fujita Y, Yokoe M, Noguchi Y.	Ann Clin Microbiol Antimicrob	10.1186/s12941-021-00449-4	2021
	Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.	Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnusdottir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I.	Nat Biotechnol	10.1038/s41587-022-01628-0	2023
Genetics	Next-generation diagnostics of bloodstream infections enabled by rapid whole-genome sequencing of bacterial cells purified from blood cultures.	Di Pilato V, Bonaiuto C, Morecchiato F, Antonelli A, Giani T, Rossolini GM.	EBioMedicine	10.1016/j.ebiom.2025.105633	2025
Genetics	Butyric Acid Supplementation Reduces Changes in the Taxonomic and Functional Composition of Gut Microbiota Caused by H. pylori Eradication Therapy.	Abdulkhakov S, Markelova M, Safina D, Siniagina M, Khusnutdinova D, Abdulkhakov R, Grigoryeva T.	Microorganisms	10.3390/microorganisms12020319	2024
Enzymology	A metagenome-wide association study of gut microbiota in asthma in UK adults.	Wang Q, Li F, Liang B, Liang Y, Chen S, Mo X, Ju Y, Zhao H, Jia H, Spector TD, Xie H, Guo R.	BMC Microbiol	10.1186/s12866-018-1257-x	2018
	Mitigating gut microbial degradation of levodopa and enhancing brain dopamine: Implications in Parkinson's disease.	Cheng G, Hardy M, Hillard CJ, Feix JB, Kalyanaraman B.	Commun Biol	10.1038/s42003-024-06330-2	2024
Phylogeny	Host-Microbiome Interactions Mediated by Phenolic Metabolites in Chronically Critically Ill Patients.	Chernevskaya E, Klimenko N, Pautova A, Buyakova I, Tyakht A, Beloborodova N.	Metabolites	10.3390/metabo11020122	2021
	Polyphenol-Rich Cranberry Beverage Positively Affected Skin Health, Skin Lipids, Skin Microbiome, Inflammation, and Oxidative Stress in Women in a Randomized Controlled Trial.	Christman L, De Benedetto A, Johnson E, Khoo C, Gu L.	Nutrients	10.3390/nu16183126	2024
Phylogeny	Microbiota profiling reveals alteration of gut microbial neurotransmitters in a mouse model of autism-associated 16p11.2 microduplication.	Fu Z, Yang X, Jiang Y, Mao X, Liu H, Yang Y, Chen J, Chen Z, Li H, Zhang XS, Mao X, Li N, Wang D, Jiang J.	Front Microbiol	10.3389/fmicb.2024.1331130	2024
Pathogenicity	Causal associations of genetically predicted gut microbiota and blood metabolites with inflammatory states and risk of infections: a Mendelian randomization analysis.	Liu Y, Zhu Q, Guo G, Xie Z, Li S, Lai C, Wu Y, Wang L, Zhong S.	Front Microbiol	10.3389/fmicb.2024.1342653	2024
Genetics	Framework for exploring the sensory repertoire of the human gut microbiota.	Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB.	mBio	10.1128/mbio.01039-24	2024
Pathogenicity	Innovative engineering approaches to model host-microbiome interactions in vitro.	Mancera Azamar KM, Sudi SD, Mohammadalizadeh Z, Coffin C, Parker IK, Porras AM.	Adv Drug Deliv Rev	10.1016/j.addr.2025.115677	2025
Enzymology	Impact of Physical Exercise on Levodopa Therapy Across Parkinson's Disease Stages.	Figura M, Mrozowicz A, Milanowski L, Szlufik S, Rackowska E, Lypkan H, Friedman A, Koziorowski D, Giebultowicz J.	J Parkinsons Dis	10.3233/jpd-230384	2024
	Comparison of fidaxomicin, thuricin CD, vancomycin and nisin highlights the narrow spectrum nature of thuricin CD.	Walsh L, Lavelle A, O'Connor PM, Hill C, Ross RP.	Gut Microbes	10.1080/19490976.2024.2342583	2024
Genetics	Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.	Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J.	Gut Microbes	10.1080/19490976.2022.2055944	2022
	Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity.	Jiao B, Ouyang Z, Liu Q, Xu T, Wan M, Ma G, Zhou L, Guo J, Wang J, Tang B, Zhao Z, Shen L.	Gut Microbes	10.1080/19490976.2024.2331434	2024
Genetics	Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy.	Fan G, Cao F, Kuang T, Yi H, Zhao C, Wang L, Peng J, Zhuang Z, Xu T, Luo Y, Xie Y, Li H, Zhang K, Zeng Y, Zhang X, Peng S, Qiu X, Zhou D, Liang H, Yang B, Kang J, Liu Y, Zhang Y.	Gut Microbes	10.1080/19490976.2023.2226925	2023
	Risk and prognostic factors among patients with bacteremia due to Eggerthella lenta.	Venugopal AA, Szpunar S, Johnson LB.	Anaerobe	10.1016/j.anaerobe.2012.05.005	2012
	Clinical characteristics of bloodstream infection by Parvimonas micra: retrospective case series and literature review.	Watanabe T, Hara Y, Yoshimi Y, Fujita Y, Yokoe M, Noguchi Y.	BMC Infect Dis	10.1186/s12879-020-05305-y	2020
Metabolism	The Donor-Dependent and Colon-Region-Dependent Metabolism of (+)-Catechin by Colonic Microbiota in the Simulator of the Human Intestinal Microbial Ecosystem.	Li Q, Van Herreweghen F, De Mey M, Goeminne G, Van de Wiele T.	Molecules	10.3390/molecules27010073	2021
	Dysregulation in the microbiota by HBV and HCV infection induces an altered cytokine profile in the pathobiome of infection.	Padilha MDM, Melo FTV, Laurentino RV, da Silva ANMR, Feitosa RNM.	Braz J Infect Dis	10.1016/j.bjid.2024.104468	2025
Phylogeny	First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study.	Rausch P, Ratjen I, Tittmann L, Enderle J, Wacker EM, Jaeger K, Ruhlemann MC, Franzpotter K, Ellul P, Kruse R, Halfvarson J, Roggenbuck D, Ellinghaus D, Jacobs G, Krawczak M, Schreiber S, Bang C, Lieb W, Franke A.	Gut Microbes	10.1080/19490976.2025.2559119	2025
	Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection.	Herrera G, Arboleda JC, Perez-Jaramillo JE, Patarroyo MA, Ramirez JD, Munoz M.	Microbiol Spectr	10.1128/spectrum.00502-22	2022
	Prevalence of Oral Pathogen Slackia exigua among Clinical Orthodontic and Non-Orthodontic Saliva Samples.	Shen C, Simpson J, Clawson JB, Lam S, Kingsley K.	Microorganisms	10.3390/microorganisms11040867	2023
Genetics	Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.	Li P, Jiang J, Li Y, Lan Y, Yang F, Wang J, Xie Y, Xiong F, Wu J, Liu H, Fan Z.	BMC Genomics	10.1186/s12864-023-09805-4	2023
	Immunoglobulin-coating patterns reveal altered humoral responses to gut bacteria in pediatric cow milk allergies.	Augustine T, Murugesan S, Badri F, Gentilcore G, Grivel JC, Akobeng A, Elawad M, Adeli M, Al Khodor S, van Panhuys N.	J Transl Med	10.1186/s12967-024-05850-z	2024
	Distribution, biosynthesis and therapeutic potential of lignans.	Plaha NS, Awasthi S, Sharma A, Kaushik N.	3 Biotech	10.1007/s13205-022-03318-9	2022
	Specific microbiome patterns and their association with breast cancer: the intestinal microbiota as a potential biomarker and therapeutic strategy.	Amaro-da-Cruz A, Rubio-Tomas T, Alvarez-Mercado AI.	Clin Transl Oncol	10.1007/s12094-024-03554-w	2025
	Bacteremia caused by Eggerthella lenta in an elderly man with a gastrointestinal malignancy: A case report.	Wong D, Aoki F, Rubinstein E.	Can J Infect Dis Med Microbiol	10.1155/2014/802481	2014
	The gut microbiome and metabolome in kidney transplant recipients with normal and moderately decreased kidney function.	Lan Y, Wang D, He J, Yang H, Hou Y, Di W, Wang H, Luo X, Wei L.	Ren Fail	10.1080/0886022x.2023.2228419	2023
	Roles of gut microbiome in epilepsy risk: A Mendelian randomization study.	Zeng Y, Cao S, Yang H.	Front Microbiol	10.3389/fmicb.2023.1115014	2023
	Bacteriophages targeting Enterococcus faecalis enhance the therapeutic efficacy of levodopa in an MPTP-induced Parkinson's disease mouse model with E. faecalis gut colonization.	Hong JP, Shin S, Chung SH, Song MC, Shim JG, Kim Y, Lee B, Yeom M, Park HJ, Jung KH, Hong J, Hahm DH.	Sci Rep	10.1038/s41598-024-77038-w	2024
	Is Piperacillin-Tazobactam an Appropriate Empirical Agent for Hospital-Acquired Sepsis and Community-Acquired Septic Shock of Unknown Origin in Australia?	Gage-Brown A, George C, Maleki J, Singh KP, Muhi S.	Healthcare (Basel)	10.3390/healthcare10050851	2022
	Exclusive Enteral Nutrition Exerts Anti-Inflammatory Effects through Modulating Microbiota, Bile Acid Metabolism, and Immune Activities.	Xiao F, Gao X, Hu H, Le J, Chen Y, Shu X, Liang Z, Xu Y, Wang Y, Zhang T.	Nutrients	10.3390/nu14214463	2022
	A New Perspective on the Health Benefits of Moderate Beer Consumption: Involvement of the Gut Microbiota.	Quesada-Molina M, Munoz-Garach A, Tinahones FJ, Moreno-Indias I.	Metabolites	10.3390/metabo9110272	2019
	Maturation of the oral microbiota during primary teeth eruption: a longitudinal, preliminary study.	Xu H, Tian B, Shi W, Tian J, Wang W, Qin M.	J Oral Microbiol	10.1080/20002297.2022.2051352	2022
Pathogenicity	Association between oral and fecal microbiome dysbiosis and treatment complications in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.	Faraci M, Bonaretti C, Dell'Orso G, Pierri F, Giardino S, Angiero F, Blasi S, Farronato G, Di Marco E, Trevisiol A, Olcese E, Rufino L, Squillario M, Biassoni R.	Sci Rep	10.1038/s41598-024-55690-6	2024
Enzymology	Peritonitis caused by veillonella species and Eggerthella lenta in peritoneal dialysis.	Goupil R, Nadeau-Fredette AC, Tennankore KK, Bargman JM.	Perit Dial Int	10.3747/pdi.2013.00046	2014
Phylogeny	Prediction of delayed graft function by early salivary microbiota following kidney transplantation.	Xiang X, Peng B, Liu K, Wang T, Ding P, Zhu Y, Cheng K, Ming Y, Ming Y.	Appl Microbiol Biotechnol	10.1007/s00253-024-13236-w	2024
Enzymology	Eggerthella lenta bacteremia complicated by spondylodiscitis, psoas abscess, and meningitis.	Gardiner BJ, Korman TM, Junckerstorff RK.	J Clin Microbiol	10.1128/jcm.03158-13	2014
	The Gut Microbiota in Parkinson Disease: Interactions with Drugs and Potential for Therapeutic Applications.	Menozzi E, Schapira AHV.	CNS Drugs	10.1007/s40263-024-01073-4	2024
	Altered gut microbiota-host bile acid metabolism in IBS-D patients with liver depression and spleen deficiency pattern.	Du L, Zhang Z, Zhai L, Xu S, Yang W, Huang C, Lin C, Zhong LLD, Bian Z, Zhao L.	Chin Med	10.1186/s13020-023-00795-9	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
Enzymology	Eggerthella lenta bacteremia in a Crohn's disease patient after ileocecal resection.	Thota VR, Dacha S, Natarajan A, Nerad J.	Future Microbiol	10.2217/fmb.11.31	2011
	Comparing the Clinical Utility of Rapid Diagnostics for Treatment of Bloodstream Infections Using Desirability of Outcome Ranking Approach for the Management of Antibiotic Therapy (DOOR-MAT).	Claeys KC, Hopkins TL, Schlaffer K, Hitchcock S, Jiang Y, Evans S, Johnson JK, Leekha S.	Antimicrob Agents Chemother	10.1128/aac.00441-21	2021
	Differences in Gut Microbiome in Hospitalized Immunocompetent vs. Immunocompromised Children, Including Those With Sickle Cell Disease.	Mohandas S, Soma VL, Tran TDB, Sodergren E, Ambooken T, Goldman DL, Weinstock G, Herold BC.	Front Pediatr	10.3389/fped.2020.583446	2020
Phylogeny	Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome.	De Cesare A, Sala C, Castellani G, Astolfi A, Indio V, Giardini A, Manfreda G.	PLoS One	10.1371/journal.pone.0228338	2020
Pathogenicity	A rare case of non-clostridial infection in a non-diabetic patient.	Darat HN, Kanodia AK, Yong A, Ram B.	BMJ Case Rep	10.1136/bcr-2019-233467	2020
	Complications of percutaneous nephrostomy in a district general hospital.	Turo R, Horsu S, Broome J, Das S, Gulur DM, Pettersson B, Doyle G, Awsare N.	Turk J Urol	10.5152/tud.2018.37336	2018
	Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.	Pidgeon R, Mitchell S, Shamash M, Suleiman L, Dridi L, Maurice CF, Castagner B.	Nat Commun	10.1038/s41467-025-56266-2	2025
	Association between Gut Microbiota and Digestive System Cancers: A Bidirectional Two-Sample Mendelian Randomization Study.	Xie N, Wang Z, Shu Q, Liang X, Wang J, Wu K, Nie Y, Shi Y, Fan D, Wu J.	Nutrients	10.3390/nu15132937	2023
	Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk.	Hussan H, Clinton SK, Grainger EM, Webb M, Wang C, Webb A, Needleman B, Noria S, Zhu J, Choueiry F, Pietrzak M, Bailey MT.	Gut Microbes	10.1080/19490976.2023.2255345	2023
Enzymology	Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease.	Slanzon GS, Ridenhour BJ, Moore DA, Sischo WM, Parrish LM, Trombetta SC, McConnel CS.	PLoS One	10.1371/journal.pone.0262317	2022
Enzymology	Paediatric splenic and rectovesical pouch abscesses caused by Eggerthella lenta.	Kondo S, Okada H, Shimono R, Kusaka T.	BMJ Case Rep	10.1136/bcr-2015-209584	2015
	Snapshot into the Type-2-Diabetes-Associated Microbiome of a Romanian Cohort.	Gradisteanu Pircalabioru G, Chifiriuc MC, Picu A, Petcu LM, Trandafir M, Savu O.	Int J Mol Sci	10.3390/ijms232315023	2022
Pathogenicity	Polyphenols-Gut Microbiota Interrelationship: A Transition to a New Generation of Prebiotics.	Plamada D, Vodnar DC.	Nutrients	10.3390/nu14010137	2021
Pathogenicity	Effects of Iron and Zinc Biofortified Foods on Gut Microbiota In Vivo (Gallus gallus): A Systematic Review.	Juste Contin Gomes M, Stampini Duarte Martino H, Tako E.	Nutrients	10.3390/nu13010189	2021
Metabolism	Intestinal microbiome and digoxin inactivation: meal plan for digoxin users?	Lu L, Wu Y, Zuo L, Luo X, Large PJ.	World J Microbiol Biotechnol	10.1007/s11274-013-1507-x	2014
	Oral Cardiac Drug-Gut Microbiota Interaction in Chronic Heart Failure Patients: An Emerging Association.	Paraskevaidis I, Briasoulis A, Tsougos E.	Int J Mol Sci	10.3390/ijms25031716	2024
	CMV Ileitis: To Treat or Not to Treat? Implications of Initiating Biologic Therapy for Concurrent Crohn's Disease.	Stilwell KT, Estes J, Kurtz MT, Francis JM, Lynch DT, Patel AA.	Case Rep Gastrointest Med	10.1155/2019/4513795	2019
	Exploring Antimycobacterial Potential: Safety Evaluation and Active Compound Isolation from Gymnopilus junonius.	Didloff J, Boukes GJ, Nyambe MN, Beukes DR, Lerata MS, Vilane V, Lee M, Govender S, van de Venter M.	Antibiotics (Basel)	10.3390/antibiotics14020179	2025
	Gut Microbiome and the Role of Metabolites in the Study of Graves' Disease.	Liu H, Liu H, Liu C, Shang M, Wei T, Yin P.	Front Mol Biosci	10.3389/fmolb.2022.841223	2022
	Utility of synovial calprotectin lateral flow test to exclude chronic prosthetic joint infection in periprosthetic fractures: a prospective cohort study.	Lazic I, Burdach A, Pohlig F, von Eisenhart-Rothe R, Suren C.	Sci Rep	10.1038/s41598-022-22892-9	2022
Enzymology	High levels of Bifidobacteria are associated with increased levels of anthocyanin microbial metabolites: a randomized clinical trial.	Boto-Ordonez M, Urpi-Sarda M, Queipo-Ortuno MI, Tulipani S, Tinahones FJ, Andres-Lacueva C.	Food Funct	10.1039/c4fo00029c	2014
	Microbiome Single Cell Atlases Generated with a Commercial Instrument.	Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR.	Adv Sci (Weinh)	10.1002/advs.202409338	2025
Phylogeny	Collinsella aerofaciens as a predictive marker of response to probiotic treatment in non-constipated irritable bowel syndrome.	Gargari G, Mantegazza G, Cremon C, Taverniti V, Valenza A, Barbaro MR, Marasco G, Duncan R, Fiore W, Ferrari R, De Vitis V, Barbara G, Guglielmetti S.	Gut Microbes	10.1080/19490976.2023.2298246	2024
	Gut microbiome health and dysbiosis: A clinical primer.	Bidell MR, Hobbs ALV, Lodise TP.	Pharmacotherapy	10.1002/phar.2731	2022
	Longitudinal exposure to antiseizure medications shape gut-derived microbiome, resistome, and metabolome landscape.	Dop C, Auvin S, Mondot S, Lepage P, Ilhan ZE.	ISME Commun	10.1093/ismeco/ycae123	2024
Genetics	Pharmacogenomic and Pharmacomicrobiomic Aspects of Drugs of Abuse.	Borrego-Ruiz A, Borrego JJ.	Genes (Basel)	10.3390/genes16040403	2025
	Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.	Soltys K, Stuchlikova M, Hlavaty T, Gaalova B, Budis J, Gazdarica J, Krajcovicova A, Zelinkova Z, Szemes T, Kuba D, Drahovska H, Turna J, Stuchlik S.	Sci Rep	10.1038/s41598-020-62811-4	2020
	The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales.	Khomyakova MA, Zavarzina DG, Merkel AY, Klyukina AA, Pikhtereva VA, Gavrilov SN, Slobodkin AI.	Front Microbiol	10.3389/fmicb.2022.1047580	2022
Metabolism	Metabolism of Soy Isoflavones by Intestinal Bacteria: Genome Analysis of an Adlercreutzia Equolifaciens Strain That Does Not Produce Equol.	Vazquez L, Florez AB, Redruello B, Mayo B.	Biomolecules	10.3390/biom10060950	2020
	Disseminated Infection Caused by Eggerthella lenta in a Previously Healthy Young Man: A Case Report.	Salameh A, Klotz SA, Zangeneh TT.	Case Rep Infect Dis	10.1155/2012/517637	2012
	Aortic graft infection with enteric organism after embolization of late type II endoleak.	Li B, Tan KT, MacDonald ME, Byrne J.	J Vasc Surg Cases Innov Tech	10.1016/j.jvscit.2018.10.009	2019
	Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography.	Shuwen H, Yinhang W, Xingming Z, Jing Z, Jinxin L, Wei W, Kefeng D.	Gut Pathog	10.1186/s13099-022-00524-x	2022
Phylogeny	Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.	Shiba T, Komatsu K, Sudo T, Sawafuji R, Saso A, Ueda S, Watanabe T, Nemoto T, Kano C, Nagai T, Ohsugi Y, Katagiri S, Takeuchi Y, Kobayashi H, Iwata T.	Front Cell Infect Microbiol	10.3389/fcimb.2021.723821	2021
	Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission.	Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, Zahra G, Franke A, Ellul P.	Microbiol Spectr	10.1128/spectrum.00616-22	2022
	Structural and functional properties of a plant NRAMP-related aluminum transporter.	Ramanadane K, Liziczai M, Markovic D, Straub MS, Rosalen GT, Udovcic A, Dutzler R, Manatschal C.	Elife	10.7554/elife.85641	2023
	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
Metabolism	Gut bacterial deamination of residual levodopa medication for Parkinson's disease.	van Kessel SP, de Jong HR, Winkel SL, van Leeuwen SS, Nelemans SA, Permentier H, Keshavarzian A, El Aidy S.	BMC Biol	10.1186/s12915-020-00876-3	2020
	In Vitro Activities of Pexiganan and 10 Comparator Antimicrobials against 502 Anaerobic Isolates Recovered from Skin and Skin Structure Infections.	Goldstein EJC, Citron DM, Tyrrell KL, Leoncio ES.	Antimicrob Agents Chemother	10.1128/aac.01401-17	2017
	Small bowel perforation by toothpick.	Lai CMS, Lui TH.	BMJ Case Rep	10.1136/bcr-2018-225258	2018
	A novel pathway of levodopa metabolism by commensal Bifidobacteria.	Cirstea MS, Creus-Cuadros A, Lo C, Yu AC, Serapio-Palacios A, Neilson S, Appel-Cresswell S, Finlay BB.	Sci Rep	10.1038/s41598-023-45953-z	2023
Pathogenicity	DMARDs-Gut Microbiota Feedback: Implications in the Response to Therapy.	Zaragoza-Garcia O, Castro-Alarcon N, Perez-Rubio G, Guzman-Guzman IP.	Biomolecules	10.3390/biom10111479	2020
Enzymology	Eggerthella lenta as a cause of anaerobic spondylodiscitis.	Bok CW, Ng YS.	Singapore Med J		2009
	Sensitivity and specificity of subgingival bacteria in predicting preterm birth- a pilot cohort study.	Hassan KS, El Tantawi MM, Alagl AS, Alnimr AM, Haseeb YA.	Int J Health Sci (Qassim)	10.12816/0049657	2016
	Gut microbiome and cardiovascular disease.	Zhao Y, Wang Z.	Curr Opin Cardiol	10.1097/hco.0000000000000720	2020
	Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis.	Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lahdesmaki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ.	Genome Med	10.1186/s13073-021-00853-7	2021
	Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study.	Moran-Ramos S, Lopez-Contreras BE, Villarruel-Vazquez R, Ocampo-Medina E, Macias-Kauffer L, Martinez-Medina JN, Villamil-Ramirez H, Leon-Mimila P, Del Rio-Navarro BE, Ibarra-Gonzalez I, Vela-Amieva M, Gomez-Perez FJ, Velazquez-Cruz R, Salmeron J, Reyes-Castillo Z, Aguilar-Salinas C, Canizales-Quinteros S.	Gut Microbes	10.1080/19490976.2020.1712985	2020
	Osteoimmunology in periodontitis; a paradigm for Th17/IL-17 inflammatory bone loss.	Ikeuchi T, Moutsopoulos NM.	Bone	10.1016/j.bone.2022.116500	2022
Transcriptome	Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics.	Deng ZL, Pieper DH, Stallmach A, Steube A, Vital M, Reck M, Wagner-Dobler I.	Microbiome	10.1186/s40168-023-01713-9	2023
	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
Enzymology	Isolation of catechin-converting human intestinal bacteria.	Kutschera M, Engst W, Blaut M, Braune A.	J Appl Microbiol	10.1111/j.1365-2672.2011.05025.x	2011
Metabolism	Fucose ameliorates the proinflammatory property of Fusobacterium nucleatum in colitis via altering its metabolism.	Duan C, Hou L, Deng X, Wu J, Qian W, Han C, Hou X.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1190602	2023
Metabolism	Therapeutic Potential of Metabolites from Lactobacillus rhamnosus and Mare's Milk in the Treatment of Dysbiosis.	Kozhakhmetov S, Babenko D, Kozhakhmetova S, Tuyakova A, Nurgaziyev M, Nurgozhina A, Muhanbetganov N, Chulenbayeva L, Sergazy S, Gulyayev A, Aljofan M, Kushugulova A.	Biomed Res Int	10.1155/2022/3851478	2022
	Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.	White MG, Damania A, Alshenaifi J, Sahasrabhojane P, Peacock O, Losh J, Wong MC, Lutter-Berkova Z, Chang GJ, Futreal A, Wargo JA, Ajami NJ, Kopetz S, You YN.	Ann Surg	10.1097/sla.0000000000006015	2023
	A decade of insight: bibliometric analysis of gut microbiota's role in osteoporosis (2014-2024).	Luo ZQ, Huang YJ, Chen ZH, Lu CY, Zhou B, Gong XH, Shen Z, Wang T.	Front Med (Lausanne)	10.3389/fmed.2024.1409534	2024
	Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis.	Ellis JL, Wang M, Fu X, Fields CJ, Donovan SM, Booth SL.	Curr Dev Nutr	10.1093/cdn/nzac019	2022
Metabolism	Colonic microflora and plasma metabolite-based comparative analysis of unilateral ureteral obstruction-induced chronic kidney disease after treatment with the Chinese medicine FuZhengHuaYuJiangZhuTongLuo and AST-120.	Chen Z, Wu S, Huang L, Li J, Li X, Zeng Y, Chen Z, Chen M.	Heliyon	10.1016/j.heliyon.2024.e24987	2024
	Nutrition, hydration and supplementation considerations for mountaineers in high-altitude conditions: a narrative review.	Karpecka-Galka E, Fraczek B.	Front Sports Act Living	10.3389/fspor.2024.1435494	2024
	Emerging Targets and Treatments for Sarcopenia: A Narrative Review.	Cacciatore S, Calvani R, Esposito I, Massaro C, Gava G, Picca A, Tosato M, Marzetti E, Landi F.	Nutrients	10.3390/nu16193271	2024
	Chronic Ulcers and Malnutrition in an African Patient.	Singer TG, Bray MA, Chan A, Ikeda S, Walters B, Fuller MY, Falco C.	Pediatrics	10.1542/peds.2020-1717	2020
	Phytochemicals From Vicia faba Beans as Ligands of the Aryl Hydrocarbon Receptor to Regulate Autoimmune Diseases.	Mendez-Lopez LF, Sosa de Leon D, Lopez-Cabanillas Lomeli M, Gonzalez-Martinez BE, Vazquez-Rodriguez JA.	Front Nutr	10.3389/fnut.2022.790440	2022
Phylogeny	Machine learning-causal inference based on multi-omics data reveals the association of altered gut bacteria and bile acid metabolism with neonatal jaundice.	Chen W, Zhang P, Zhang X, Xiao T, Zeng J, Guo K, Qiu H, Cheng G, Wang Z, Zhou W, Zeng S, Wang M.	Gut Microbes	10.1080/19490976.2024.2388805	2024
	A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110.	Droste J, Kulisch M, Wolf T, Schaffert L, Schneiker-Bekel S, Puhler A, Kalinowski J.	Appl Microbiol Biotechnol	10.1007/s00253-020-10923-2	2020
	NNAN: Nearest Neighbor Attention Network to Predict Drug-Microbe Associations.	Zhu B, Xu Y, Zhao P, Yiu SM, Yu H, Shi JY.	Front Microbiol	10.3389/fmicb.2022.846915	2022
	Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome.	Kawano Y, Edwards M, Huang Y, Bilate AM, Araujo LP, Tanoue T, Atarashi K, Ladinsky MS, Reiner SL, Wang HH, Mucida D, Honda K, Ivanov II.	Cell	10.1016/j.cell.2022.08.005	2022
Enzymology	[Bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents - Special references to bacteria isolated between April 2011 and March 2012].	Shinagawa N, Taniguchi M, Hirata K, Furuhata T, Mizuguchi T, Osanai H, Yanai Y, Hata F, Kihara C, Sasaki K, Oono K, Nakamura M, Shibuya H, Hasegawa I, Kimura M, Watabe K, Hoshikawa T, Oshima H, Aikawa N, Sasaki J, Suzuki M, Sekine K, Abe S, Takeyama H, Wakasugi T, Mashita K, Tanaka M, Mizuno A, Ishikawa M, Iwai A, Saito T, Muramoto M, Kubo S, Lee S, Fukuhara K, Kobayashi Y, Yamaue H, Hirono S, Takesue Y, Fujiwara T, Shinoura S, Kimura H, Iwagaki H, Tokunaga N, Sueda T, Hiyama E, Murakami Y, Ohge H, Uemura K, Tsumura H, Kanehiro T, Takeuchi H, Tanakaya K, Iwasaki M.	Jpn J Antibiot		2014
	Interplay Between Drug-Induced Liver Injury and Gut Microbiota: A Comprehensive Overview.	Li G, Hou Y, Zhang C, Zhou X, Bao F, Yang Y, Chen L, Yu D.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2024.05.003	2024
Pathogenicity	CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.	Zhang AN, Gaston JM, Cardenas P, Zhao S, Gu X, Alm EJ.	Cell Genom	10.1016/j.xgen.2024.100725	2025
	A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe: Implications for Future Studies.	Zhou DT, Mudhluli TE, Hall LJ, Manasa J, Munyati S.	Pediatric Health Med Ther	10.2147/phmt.s414766	2023
Metabolism	Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.	Bess EN, Bisanz JE, Yarza F, Bustion A, Rich BE, Li X, Kitamura S, Waligurski E, Ang QY, Alba DL, Spanogiannopoulos P, Nayfach S, Koliwad SK, Wolan DW, Franke AA, Turnbaugh PJ.	Nat Microbiol	10.1038/s41564-019-0596-1	2020
	Identification of the Microbial Transformation Products of Secoisolariciresinol Using an Untargeted Metabolomics Approach and Evaluation of the Osteogenic Activities of the Metabolites.	Yu WX, Tang HH, Ye JJ, Xiao HH, Lam CY, Shum TF, Sun ZK, Li YZ, Zang XY, Du WC, Zhang JP, Kong TH, Zhou LP, Chiou JC, Kung CF, Mok KW, Hu J, Wong MS.	Molecules	10.3390/molecules28155742	2023
	Multiple Pyogenic Liver Abscesses Caused by Eggerthella lenta Treated with Ertapenem: A Case Report.	Elias RM, Khoo SY, Pupaibool J, Nienaber JH, Cummins NW.	Case Rep Med	10.1155/2012/718130	2012
Genetics	Integration analysis of tumor metagenome and peripheral immunity data of diffuse large-B cell lymphoma.	Zhang Y, Han S, Xiao X, Zheng L, Chen Y, Zhang Z, Gao X, Zhou S, Yu K, Huang L, Fu J, Hong Y, Jiang J, Qian W, Yang H, Shen J.	Front Immunol	10.3389/fimmu.2023.1146861	2023
Enzymology	[Bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents--special references to bacteria isolated between April 2010 and March 2011].	Shinagawa N, Taniguchi M, Hirata K, Furuhata T, Fukuhara K, Mizugucwi T, Osanai H, Yanai Y, Hata F, Kihara C, Sasaki K, Oono K, Nakamura M, Shibuya H, Hasegawa I, Kimura M, Watabe K, Kobayashi Y, Yamaue H, Hirono S, Takesue Y, Fujiwara T, Shinoura S, Kimura H, Hoshikawa T, Oshima H, Aikawa N, Sasaki J, Suzuki M, Sekine K, Abe S, Takeyama H, Wakasugi T, Mashita K, Tanaka M, Mizuno A, Ishikawa M, Iwai A, Saito T, Muramoto M, Kubo S, Lee S, Fukuhara K, Iwagaki H, Tokunaga N, Sueda T, Hiyama E, Murakami Y, Ohge H, Uemura K, Tsumura H, Kanehiro T, Takeuchi H, Tanakaya K, Iwasaki M.	Jpn J Antibiot		2014
	Role of the intestinal microbiota and diet in the onset and progression of colorectal and breast cancers and the interconnection between both types of tumours	Ruiz-Saavedra S, Zapico A, Gonzalez S, Salazar N, de los Reyes-Gavilan C.	Microbiome Res Rep		2023
	Identification of a novel gut microbiota signature associated with colorectal cancer in Thai population.	Iadsee N, Chuaypen N, Techawiwattanaboon T, Jinato T, Patcharatrakul T, Malakorn S, Petchlorlian A, Praditpornsilpa K, Patarakul K.	Sci Rep	10.1038/s41598-023-33794-9	2023
	Lactobacillus Intestinalis Primes Epithelial Cells to Suppress Colitis-Related Th17 Response by Host-Microbe Retinoic Acid Biosynthesis.	Wang QW, Jia DJ, He JM, Sun Y, Qian Y, Ge QW, Qi YD, Wang QY, Hu YY, Wang L, Fang YF, He HQ, Luo M, Feng LJ, Si JM, Song ZF, Wang LJ, Chen SJ.	Adv Sci (Weinh)	10.1002/advs.202303457	2023
	Dysbiosis signatures of gut microbiota and the progression of type 2 diabetes: a machine learning approach in a Mexican cohort.	Neri-Rosario D, Martinez-Lopez YE, Esquivel-Hernandez DA, Sanchez-Castaneda JP, Padron-Manrique C, Vazquez-Jimenez A, Giron-Villalobos D, Resendis-Antonio O.	Front Endocrinol (Lausanne)	10.3389/fendo.2023.1170459	2023
	Altered gut microbiota composition in children and their caregivers infected with the SARS-CoV-2 Omicron variant.	Wang YZ, Zhou JG, Lu YM, Hu H, Xiao FF, Ge T, Wang X, Zheng L, Yu LH, Le J, Yu H, Yu GJ, Xia Q, Zhang T, Zhou WH.	World J Pediatr	10.1007/s12519-022-00659-6	2023
	The Implication of the Gut Microbiome in Heart Failure.	Lupu VV, Adam Raileanu A, Mihai CM, Morariu ID, Lupu A, Starcea IM, Frasinariu OE, Mocanu A, Dragan F, Fotea S.	Cells	10.3390/cells12081158	2023
	Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).	Peters BA, Qi Q, Usyk M, Daviglus ML, Cai J, Franceschini N, Lash JP, Gellman MD, Yu B, Boerwinkle E, Knight R, Burk RD, Kaplan RC.	Gut Microbes	10.1080/19490976.2023.2186685	2023
Metabolism	Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism.	Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP.	Science	10.1126/science.aau6323	2019
Pathogenicity	Characterizing the Effects of Calcium and Prebiotic Fiber on Human Gut Microbiota Composition and Function Using a Randomized Crossover Design-A Feasibility Study.	Yoon LS, Michels KB.	Nutrients	10.3390/nu13061937	2021
Genetics	Characterization and Spatial Mapping of the Human Gut Metasecretome.	Velez-Cortes F, Wang H.	mSystems	10.1128/msystems.00717-22	2022
Pathogenicity	Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.	Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.	Sci Rep	10.1038/s41598-024-53784-9	2024
Metabolism	Bacterial species involved in the conversion of dietary flavonoids in the human gut.	Braune A, Blaut M.	Gut Microbes	10.1080/19490976.2016.1158395	2016
Metabolism	Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease.	Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K, Tasian GE.	J Am Soc Nephrol	10.1681/asn.2019101131	2020
	Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents.	Klure DM, Dearing MD.	FEMS Microbiol Ecol	10.1093/femsec/fiad127	2023
Enzymology	Effects of intestinal microbiota on pharmacokinetics of cyclosporine a in rats.	Zhou J, Zhang R, Guo P, Li P, Huang X, Wei Y, Yang C, Zhou J, Yang T, Liu Y, Shi S.	Front Microbiol	10.3389/fmicb.2022.1032290	2022
	Accelerometer-based physical activity is associated with the gut microbiota in 8416 individuals in SCAPIS.	Baldanzi G, Sayols-Baixeras S, Ekblom-Bak E, Ekblom O, Dekkers KF, Hammar U, Nguyen D, Ahmad S, Ericson U, Arvidsson D, Borjesson M, Johanson PJ, Smith JG, Bergstrom G, Lind L, Engstrom G, Arnlov J, Kennedy B, Orho-Melander M, Fall T.	EBioMedicine	10.1016/j.ebiom.2024.104989	2024
	Influence of Bifidobacterium breve on the Glycaemic Control, Lipid Profile and Microbiome of Type 2 Diabetic Subjects: A Preliminary Randomized Clinical Trial.	Chaiyasut C, Sivamaruthi BS, Lailerd N, Sirilun S, Thangaleela S, Khongtan S, Bharathi M, Kesika P, Saelee M, Choeisoongnern T, Fukngoen P, Peerajan S, Sittiprapaporn P.	Pharmaceuticals (Basel)	10.3390/ph16050695	2023
	Gut microbiota composition and frailty in elderly patients with Chronic Kidney Disease.	Margiotta E, Miragoli F, Callegari ML, Vettoretti S, Caldiroli L, Meneghini M, Zanoni F, Messa P.	PLoS One	10.1371/journal.pone.0228530	2020
Metabolism	Identification of Human Gut Microbiome Associated with Enterolignan Production.	Sawane K, Hosomi K, Park J, Ookoshi K, Nanri H, Nakagata T, Chen YA, Mohsen A, Kawashima H, Mizuguchi K, Miyachi M, Kunisawa J.	Microorganisms	10.3390/microorganisms10112169	2022
Pathogenicity	An exploration of alginate oligosaccharides modulating intestinal inflammatory networks via gut microbiota.	Zhang Z, Wang X, Li F.	Front Microbiol	10.3389/fmicb.2023.1072151	2023
	Microbially Produced Imidazole Propionate Is Associated With Heart Failure and Mortality.	Molinaro A, Nemet I, Bel Lassen P, Chakaroun R, Nielsen T, Aron-Wisnewsky J, Bergh PO, Li L, Henricsson M, Kober L, Isnard R, Helft G, Stumvoll M, Pedersen O, Smith JG, Tang WHW, Clement K, Hazen SL, Backhed F, MetaCardis Consortium.	JACC Heart Fail	10.1016/j.jchf.2023.03.008	2023
Pathogenicity	Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.	Lindner S, Miltiadous O, Ramos RJF, Paredes J, Kousa AI, Dai A, Fei T, Lauder E, Frame J, Waters NR, Sadeghi K, Armijo GK, Ghale R, Victor K, Gipson B, Monette S, Russo MV, Nguyen CL, Slingerland J, Taur Y, Markey KA, Andrlova H, Giralt S, Perales MA, Reddy P, Peled JU, Smith M, Cross JR, Burgos da Silva M, Campbell C, van den Brink MRM.	Nat Microbiol	10.1038/s41564-024-01617-w	2024
	Characterization of the Interindividual Variability Associated with the Microbial Metabolism of (-)-Epicatechin.	Lessard-Lord J, Roussel C, Guay V, Desjardins Y.	J Agric Food Chem	10.1021/acs.jafc.3c05491	2023
Pathogenicity	Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers.	Queipo-Ortuno MI, Boto-Ordonez M, Murri M, Gomez-Zumaquero JM, Clemente-Postigo M, Estruch R, Cardona Diaz F, Andres-Lacueva C, Tinahones FJ.	Am J Clin Nutr	10.3945/ajcn.111.027847	2012
	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
	The microbial-derived bile acid lithocholate and its epimers inhibit Clostridioides difficile growth and pathogenicity while sparing members of the gut microbiota.	Kisthardt SC, Thanissery R, Pike CM, Foley MH, Theriot CM.	J Bacteriol	10.1128/jb.00180-23	2023
	Menopause is associated with postprandial metabolism, metabolic health and lifestyle: The ZOE PREDICT study.	Bermingham KM, Linenberg I, Hall WL, Kade K, Franks PW, Davies R, Wolf J, Hadjigeorgiou G, Asnicar F, Segata N, Manson JE, Newson LR, Delahanty LM, Ordovas JM, Chan AT, Spector TD, Valdes AM, Berry SE.	EBioMedicine	10.1016/j.ebiom.2022.104303	2022
Phylogeny	Profiling of Bile Microbiome Identifies District Microbial Population between Choledocholithiasis and Cholangiocarcinoma Patients.	Dangtakot R, Intuyod K, Ahooja A, Wongwiwatchai J, Hanpanich P, Lulitanond A, Chamgramol Y, Pinlaor S, Pinlaor P.	Asian Pac J Cancer Prev	10.31557/apjcp.2021.22.1.233	2021
	Characteristics of Gut Microbiota in Patients With Clear Cell Renal Cell Carcinoma.	Chen Y, Ma J, Dong Y, Yang Z, Zhao N, Liu Q, Zhai W, Zheng J.	Front Microbiol	10.3389/fmicb.2022.913718	2022
Metabolism	A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols.	Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP.	Elife	10.7554/elife.50845	2020
Metabolism	Lignan transformation by gut bacteria lowers tumor burden in a gnotobiotic rat model of breast cancer.	Mabrok HB, Klopfleisch R, Ghanem KZ, Clavel T, Blaut M, Loh G.	Carcinogenesis	10.1093/carcin/bgr256	2012
Metabolism	Bacterial conversion of secoisolariciresinol and anhydrosecoisolariciresinol.	Struijs K, Vincken JP, Gruppen H.	J Appl Microbiol	10.1111/j.1365-2672.2009.04209.x	2009
	Gut microbial metabolism of bile acids modifies the effect of Mediterranean diet interventions on cardiometabolic risk in a randomized controlled trial.	Gao P, Rinott E, Dong D, Mei Z, Wang F, Liu Y, Kamer O, Yaskolka Meir A, Tuohy KM, Bluher M, Stumvoll M, Stampfer MJ, Shai I, Wang DD.	Gut Microbes	10.1080/19490976.2024.2426610	2024
	Exploring the Involvement of Gut Microbiota in Cancer Therapy-Induced Cardiotoxicity.	Kunika, Frey N, Rangrez AY.	Int J Mol Sci	10.3390/ijms24087261	2023
	Alteration of Skin Microbiome in CKD Patients Is Associated With Pruritus and Renal Function.	Tian Y, Gu C, Yan F, Gu Y, Feng Y, Chen J, Sheng J, Hu L, Jiang P, Guo W, Feng N.	Front Cell Infect Microbiol	10.3389/fcimb.2022.923581	2022
	Strain diversity in the microbiome: Lessons from Bacteroides fragilis.	Carrow HC, Batachari LE, Chu H.	PLoS Pathog	10.1371/journal.ppat.1009056	2020
	Frailty and Age-Associated Assessments Associated with Chronic Kidney Disease and Transplantation Outcomes.	Fulinara CP, Huynh A, Goldwater D, Abdalla B, Schaenman J.	J Transplant	10.1155/2023/1510259	2023
	Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management.	Villa F, Marchandin H, Lavigne J-P, Schuldiner S, Cellier N, Sotto A, Loubet P.	Clin Microbiol Rev	10.1128/cmr.00143-23	2024
Genetics	Making Millennial Medicine More Meta.	Turnbaugh PJ.	mSystems	10.1128/msystems.00154-17	2018
	Diet-microbiota associations in gastrointestinal research: a systematic review.	Duncanson K, Williams G, Hoedt EC, Collins CE, Keely S, Talley NJ.	Gut Microbes	10.1080/19490976.2024.2350785	2024
	Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis.	Huang L, Liu B, Liu Z, Feng W, Liu M, Wang Y, Peng D, Fu X, Zhu H, Cui Z, Xie L, Ma Y.	Front Cell Infect Microbiol	10.3389/fcimb.2021.788836	2021
	Helicobacter pylori infection altered gastric microbiota in patients with chronic gastritis.	Hua Z, Xu L, Zhu J, Xiao L, Lu B, Wu J, Wu Z, Zhou Q, Zhang J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1221433	2023
	A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases.	Liu X, Tang S, Zhong H, Tong X, Jie Z, Ding Q, Wang D, Guo R, Xiao L, Xu X, Yang H, Wang J, Zong Y, Liu W, Liu X, Zhang Y, Brix S, Kristiansen K, Hou Y, Jia H, Zhang T.	Cell Discov	10.1038/s41421-020-00239-w	2021
Pathogenicity	Antimicrobial Susceptibility Patterns of Anaerobic Bacterial Clinical Isolates From 2014 to 2016, Including Recently Named or Renamed Species.	Byun JH, Kim M, Lee Y, Lee K, Chong Y.	Ann Lab Med	10.3343/alm.2019.39.2.190	2019
Enzymology	Effect of Gut Microbiota on the Pharmacokinetics of Nifedipine in Spontaneously Hypertensive Rats.	Zhou R, Yang H, Zhu P, Liu Y, Zhang Y, Zhang W, Zhou H, Li X, Li Q.	Pharmaceutics	10.3390/pharmaceutics15082085	2023
	Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes.	Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K, Mayer EA.	Microbiome	10.1186/s40168-022-01450-5	2023
	Abnormal proliferation of gut mycobiota contributes to the aggravation of Type 2 diabetes.	Bao L, Zhang Y, Zhang G, Jiang D, Yan D.	Commun Biol	10.1038/s42003-023-04591-x	2023
	Compliance with Nutritional Recommendations and Gut Microbiota Profile in Galician Overweight/Obese and Normal-Weight Individuals.	Sinisterra-Loaiza L, Alonso-Lovera P, Cardelle-Cobas A, Miranda JM, Vazquez BI, Cepeda A.	Nutrients	10.3390/nu15153418	2023
Genetics	Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo (Gallus gallus).	Dias DM, Kolba N, Binyamin D, Ziv O, Regini Nutti M, Martino HSD, Glahn RP, Koren O, Tako E.	Nutrients	10.3390/nu10121970	2018
Genetics	The Depletion of Carbohydrate Metabolic Genes in the Gut Microbiome Contributes to the Transition From Central Obesity to Type 2 Diabetes.	Jia R, Huang M, Qian L, Yan X, Lv Q, Ye H, Ye L, Wu X, Chen W, Chen Y, Jia Y, Huang Y, Wu H.	Front Endocrinol (Lausanne)	10.3389/fendo.2021.747646	2021
	Periodontal status and the incidence of selected bacterial pathogens in periodontal pockets and vascular walls in patients with atherosclerosis and abdominal aortic aneurysms.	Kregielczak A, Dorocka-Bobkowska B, Slomski R, Oszkinis G, Krasinski Z.	PLoS One	10.1371/journal.pone.0270177	2022
Enzymology	Polymicrobial bloodstream infection with Eggerthella lenta and Desulfovibrio desulfuricans.	Liderot K, Larsson M, Borang S, Ozenci V.	J Clin Microbiol	10.1128/jcm.02481-09	2010
Pathogenicity	Impact of Variations in Test Method Parameters on In Vitro Activity of Surotomycin against Clostridium difficile and Surotomycin Quality Control Limits for Broth Microdilution and Agar Dilution Susceptibility Testing.	Traczewski MM, Deane J, Sahm D, Brown SD, Chesnel L.	J Clin Microbiol	10.1128/jcm.02881-15	2016
	Gut Microbiota Modulation through Akkermansia spp. Supplementation Increases CAR T-cell Potency.	Marcos-Kovandzic L, Avagliano M, Ben Khelil M, Srikanthan J, Abdallah R, Petrocelli V, Rengassamy J, Alfaro A, Bied M, Fidelle M, Ferrere G, Daillere R, Arbab A, Amine-Hneineh R, Pages A, Dartigues P, Ly P, Simon S, Durand S, Gottschlich A, Ginhoux F, Bleriot C, Liu P, Zhao L, Creusot L, Rolhion N, Derosa L, Kroemer G, Menger L, Kobold S, Castilla-Llorente C, Sokol H, Casola S, Pasolli E, Zitvogel L, Bigenwald C.	Cancer Discov	10.1158/2159-8290.cd-24-1230	2025
	Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data.	Chen H, Ou R, Tang N, Su W, Yang R, Yu X, Zhang G, Jiao J, Zhou X.	J Transl Med	10.1186/s12967-023-03953-7	2023
	Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.	Lindell AE, Zimmermann-Kogadeeva M, Patil KR.	Nat Rev Microbiol	10.1038/s41579-022-00681-5	2022
	Adjuvant Injections Altered the Ileal and Fecal Microbiota Differently with Changes in Immunoglobulin Isotypes and Antimycobacterial Antibody Responses.	Khadka S, Omura S, Sato F, Tsunoda I.	Int J Mol Sci	10.3390/ijms24032818	2023
Genetics	Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.	Hacker D, Siebert K, Smith BJ, Kohler N, Riva A, Mahapatra A, Heimes H, Nie J, Metwaly A, Holz H, Manz Q, De Zen F, Heetmeyer J, Socas K, Le Thi G, Meng C, Kleigrewe K, Pauling JK, Neuhaus K, List M, Pollard KS, Schwerd T, Haller D.	Cell Host Microbe	10.1016/j.chom.2024.10.001	2024
Metabolism	Heterogeneity in gut microbiota drive polyphenol metabolism that influences alpha-synuclein misfolding and toxicity.	Ho L, Zhao D, Ono K, Ruan K, Mogno I, Tsuji M, Carry E, Brathwaite J, Sims S, Frolinger T, Westfall S, Mazzola P, Wu Q, Hao K, Lloyd TE, Simon JE, Faith J, Pasinetti GM.	J Nutr Biochem	10.1016/j.jnutbio.2018.10.019	2019
	Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation.	Mokrani M, Charradi K, Limam F, Aouani E, Urdaci MC.	Gut Pathog	10.1186/s13099-022-00505-0	2022
Enzymology	Clinical and microbiological characteristics of Eggerthella lenta bacteremia.	Gardiner BJ, Tai AY, Kotsanas D, Francis MJ, Roberts SA, Ballard SA, Junckerstorff RK, Korman TM.	J Clin Microbiol	10.1128/jcm.02926-14	2015
Metabolism	Bacterial transformation of dietary lignans in gnotobiotic rats.	Woting A, Clavel T, Loh G, Blaut M.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2010.00863.x	2010
	Key bacterial taxa determine longitudinal dynamics of aromatic amino acid catabolism in infants' gut.	Laursen MF, Sinha AK, Sinha AK, Pedersen M, Roager HM.	Gut Microbes	10.1080/19490976.2023.2221426	2023
Metabolism	Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics.	Haiser HJ, Seim KL, Balskus EP, Turnbaugh PJ.	Gut Microbes	10.4161/gmic.27915	2014
Enzymology	Reconstruction of Acinetobacter johnsonii ICE_NC genome using hybrid de novo genome assemblies and identification of the 12alpha-hydroxysteroid dehydrogenase gene.	Favale N, Costa S, Scapoli C, Carrieri A, Sabbioni S, Tamburini E, Benazzo A, Bernacchia G.	J Appl Microbiol	10.1111/jam.15657	2022
Metabolism	Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta.	Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ.	Science	10.1126/science.1235872	2013
	Interactions between the gut microbiota and immune cell dynamics: novel insights into the gut-bone axis	You Y, Xiang T, Yang C, Xiao S, Tang Y, Luo G, Ling Z, Luo F, Chen Y.	Gut microbes		2025
	Dysbiosis in Children With Neurological Impairment and Long-Term Enteral Nutrition.	Panelli S, Calcaterra V, Verduci E, Comandatore F, Pelizzo G, Borghi E, Bandi C, Zuccotti G.	Front Nutr	10.3389/fnut.2022.895046	2022
Pathogenicity	The Effect of Gut Microbiota-Targeted Interventions on Neuroinflammation and Motor Function in Parkinson's Disease Animal Models-A Systematic Review.	Panaitescu PS, Razniceanu V, Mocrei-Rebrean SM, Neculicioiu VS, Dragos HM, Costache C, Filip GA.	Curr Issues Mol Biol	10.3390/cimb46050244	2024
	Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.	Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, Poissant J.	Nat Commun	10.1038/s41467-024-49963-x	2024
Phylogeny	A prebiotic intervention study in children with autism spectrum disorders (ASDs).	Grimaldi R, Gibson GR, Gibson GR, Vulevic J, Giallourou N, Castro-Mejia JL, Hansen LH, Leigh Gibson E, Nielsen DS, Costabile A.	Microbiome	10.1186/s40168-018-0523-3	2018
Enzymology	Clinical and microbiological characteristics of bacteremia caused by Eggerthella, Paraeggerthella, and Eubacterium species at a university hospital in Taiwan from 2001 to 2010.	Lee MR, Huang YT, Liao CH, Chuang TY, Wang WJ, Lee SW, Lee LN, Hsueh PR.	J Clin Microbiol	10.1128/jcm.00548-12	2012
	Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.	Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN.	Cell Host Microbe	10.1016/j.chom.2021.06.019	2021
Metabolism	Microbiota-derived imidazole propionate inhibits type 2 diabetic skin wound healing by targeting SPNS2-mediated S1P transport.	Zheng S, Wang H, Han J, Dai X, Lv Y, Sun T, Liu H.	iScience	10.1016/j.isci.2023.108092	2023
	Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.	Dahal RH, Kim S, Kim YK, Kim ES, Kim J.	Front Microbiol	10.3389/fmicb.2023.1174832	2023
Metabolism	Gut Microbiota as a Source of Uremic Toxins.	Popkov VA, Zharikova AA, Demchenko EA, Andrianova NV, Zorov DB, Plotnikov EY.	Int J Mol Sci	10.3390/ijms23010483	2022
	Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures.	Haddad G, Bellali S, Takakura T, Fontanini A, Ominami Y, Bou Khalil J, Raoult D.	Microorganisms	10.3390/microorganisms9061170	2021
Genetics	OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes.	Chetal K, Janga SC.	Biomed Res Int	10.1155/2015/318217	2015
Metabolism	INTEDE: interactome of drug-metabolizing enzymes.	Yin J, Li F, Zhou Y, Mou M, Lu Y, Chen K, Xue J, Luo Y, Fu J, He X, Gao J, Zeng S, Yu L, Zhu F.	Nucleic Acids Res	10.1093/nar/gkaa755	2021
	A cross-sectional study identifying disparities in serum metabolic profiles among hypertensive patients with ISH, IDH and SDH subtypes.	Shen Y, Wang P, Yang X, Chen M, Dong Y, Li J.	Front Cardiovasc Med	10.3389/fcvm.2023.1102754	2023
	Altered Gut Microbiota as a Potential Risk Factor for Coronary Artery Disease in Diabetes: A Two-Sample Bi-Directional Mendelian Randomization Study.	Zeng Z, Qiu J, Chen Y, Liang D, Wei F, Fu Y, Zhang J, Wei X, Zhang X, Tao J, Lin L, Zheng J.	Int J Med Sci	10.7150/ijms.92131	2024
Pathogenicity	Immunometabolic Analysis of Mobiluncus mulieris and Eggerthella sp. Reveals Novel Insights Into Their Pathogenic Contributions to the Hallmarks of Bacterial Vaginosis.	McKenzie R, Maarsingh JD, Laniewski P, Herbst-Kralovetz MM.	Front Cell Infect Microbiol	10.3389/fcimb.2021.759697	2021
	Stage-specific roles of microbial dysbiosis and metabolic disorders in rheumatoid arthritis.	Cheng M, Zhao Y, Cui Y, Zhong C, Zha Y, Li S, Cao G, Li M, Zhang L, Ning K, Han J.	Ann Rheum Dis	10.1136/ard-2022-222871	2022
	The relationship between fecal bile acids and microbiome community structure in pediatric Crohn's disease.	Connors J, Dunn KA, Allott J, Bandsma R, Rashid M, Otley AR, Bielawski JP, Van Limbergen J.	ISME J	10.1038/s41396-019-0560-3	2020
	Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children.	Bonham KS, Fahur Bottino G, McCann SH, Beauchemin J, Weisse E, Barry F, Cano Lorente R, RESONANCE Consortium, Huttenhower C, Bruchhage M, D'Sa V, Deoni S, Klepac-Ceraj V.	Sci Adv	10.1126/sciadv.adi0497	2023
	Impact of the microbiota on solid organ transplant rejection.	Sepulveda M, Pirozzolo I, Alegre ML.	Curr Opin Organ Transplant	10.1097/mot.0000000000000702	2019
	Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease.	Hoskinson C, Dai DLY, Del Bel KL, Becker AB, Moraes TJ, Mandhane PJ, Finlay BB, Simons E, Kozyrskyj AL, Azad MB, Subbarao P, Petersen C, Turvey SE.	Nat Commun	10.1038/s41467-023-40336-4	2023
	"Sentinel or accomplice": gut microbiota and microglia crosstalk in disorders of gut-brain interaction.	Zheng H, Zhang C, Zhang J, Duan L.	Protein Cell	10.1093/procel/pwad020	2023
Enzymology	Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.	Vernocchi P, Del Chierico F, Russo A, Majo F, Rossitto M, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paci P, Ercolini D, Marini F, Fiscarelli EV, Dallapiccola B, Lucidi V, Miccheli A, Putignani L.	PLoS One	10.1371/journal.pone.0208171	2018
	Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.	Liu X, Wu J, Tang J, Xu Z, Zhou B, Liu Y, Hu F, Zhang G, Cheng R, Xia X, Chen Y, Wu H, Wang D, Yue J, Dong B, Fu J, Yu H, Dong B.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13313	2023
	Implementing a multidisciplinary care bundle to reduce colon surgical site infections.	Park CM, Ha TS, Lee WY, Chung DR, Park YA, Choi JR, Jeong NY.	Ann Surg Treat Res	10.4174/astr.2020.99.5.285	2020
Metabolism	Completion of the gut microbial epi-bile acid pathway.	Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM.	Gut Microbes	10.1080/19490976.2021.1907271	2021
	Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.	Gao W, Gao X, Zhu L, Gao S, Sun R, Feng Z, Wu D, Liu Z, Zhu R, Jiao N.	Gut Microbes	10.1080/19490976.2023.2245562	2023
	Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile.	Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Im H, Vivas EI, Simcox J, Venturelli OS.	Cell Host Microbe	10.1016/j.chom.2024.12.001	2025
Enzymology	The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome.	Enright EF, Gahan CG, Joyce SA, Griffin BT.	Yale J Biol Med		2016
	Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.	Maeda Y, Motooka D, Kawasaki T, Oki H, Noda Y, Adachi Y, Niitsu T, Okamoto S, Tanaka K, Fukushima K, Amiya S, Hara R, Oguro-Igashira E, Matsuki T, Hirata H, Takeda Y, Kida H, Kumanogoh A, Nakamura S, Takeda K.	BMC Infect Dis	10.1186/s12879-022-07358-7	2022
Pathogenicity	Microbiota, IgA and Multiple Sclerosis.	Boussamet L, Rajoka MSR, Berthelot L.	Microorganisms	10.3390/microorganisms10030617	2022
Pathogenicity	Association of Sarcopenia and Gut Microbiota Composition in Older Patients with Advanced Chronic Kidney Disease, Investigation of the Interactions with Uremic Toxins, Inflammation and Oxidative Stress.	Margiotta E, Caldiroli L, Callegari ML, Miragoli F, Zanoni F, Armelloni S, Rizzo V, Messa P, Vettoretti S.	Toxins (Basel)	10.3390/toxins13070472	2021
Metabolism	Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis.	Probstel AK, Zhou X, Baumann R, Wischnewski S, Kutza M, Rojas OL, Sellrie K, Bischof A, Kim K, Ramesh A, Dandekar R, Greenfield AL, Schubert RD, Bisanz JE, Vistnes S, Khaleghi K, Landefeld J, Kirkish G, Liesche-Starnecker F, Ramaglia V, Singh S, Tran EB, Barba P, Zorn K, Oechtering J, Forsberg K, Shiow LR, Henry RG, Graves J, Cree BAC, Hauser SL, Kuhle J, Gelfand JM, Andersen PM, Schlegel J, Turnbaugh PJ, Seeberger PH, Gommerman JL, Wilson MR, Schirmer L, Baranzini SE.	Sci Immunol	10.1126/sciimmunol.abc7191	2020
Metabolism	Biotransformation of C-glucosylisoflavone puerarin to estrogenic (3S)-equol in co-culture of two human intestinal bacteria.	Jin JS, Nishihata T, Kakiuchi N, Hattori M.	Biol Pharm Bull	10.1248/bpb.31.1621	2008
Pathogenicity	Comparative in vitro activities of SMT19969, a new antimicrobial agent, against Clostridium difficile and 350 gram-positive and gram-negative aerobic and anaerobic intestinal flora isolates.	Goldstein EJ, Citron DM, Tyrrell KL, Merriam CV.	Antimicrob Agents Chemother	10.1128/aac.01136-13	2013
Phylogeny	Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.	Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N.	Microbiome	10.1186/s40168-017-0396-x	2018
	Factors Explaining Interpersonal Variation in Plasma Enterolactone Concentrations in Humans.	Halldin E, Eriksen AK, Brunius C, da Silva AB, Bronze M, Hanhineva K, Aura AM, Landberg R.	Mol Nutr Food Res	10.1002/mnfr.201801159	2019
	Current Updates on the Role of Microbiome in Endometriosis: A Narrative Review.	Ser HL, Au Yong SJ, Shafiee MN, Mokhtar NM, Ali RAR.	Microorganisms	10.3390/microorganisms11020360	2023
	Towards geospatially-resolved public-health surveillance via wastewater sequencing.	Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Lucaci AG, Solle NS, Kumar N, Shukla B, Vidovic D, Currall B, Williams SL, Schurer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Wain Hirschberg J, Proszynski J, Al Ghalith G, Can Kurt K, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, Mason CE.	Nat Commun	10.1038/s41467-024-52427-x	2024
Metabolism	Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice.	Belik J, Shifrin Y, Arning E, Bottiglieri T, Pan J, Daigneault MC, Allen-Vercoe E.	Sci Rep	10.1038/srep39854	2017
	The Impact of Long-Term Macrolide Exposure on the Gut Microbiome and Its Implications for Metabolic Control.	Choo JM, Martin AM, Taylor SL, Sun E, Mobegi FM, Kanno T, Richard A, Burr LD, Lingman S, Martin M, Keating DJ, Mason AJ, Rogers GB.	Microbiol Spectr	10.1128/spectrum.00831-23	2023
	Toward an improved definition of a healthy microbiome for healthy aging.	Ghosh TS, Shanahan F, O'Toole PW.	Nat Aging	10.1038/s43587-022-00306-9	2022
	Tutorial: Microbiome studies in drug metabolism.	Dodd D, Cann I.	Clin Transl Sci	10.1111/cts.13416	2022
	Succinate-producing microbiota drives tuft cell hyperplasia to protect against Clostridioides difficile.	Kellogg TD, Ceglia S, Mortzfeld BM, Tanna TM, Zeamer AL, Mancini MR, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi A, Bucci V.	J Exp Med	10.1084/jem.20232055	2025
	Infant gut microbiota and environment associate with juvenile idiopathic arthritis many years prior to disease onset, especially in genetically vulnerable children.	Kindgren E, Ahrens AP, Triplett EW, Ludvigsson J.	EBioMedicine	10.1016/j.ebiom.2023.104654	2023
	Comparative study of different liquid diets for dairy calves and the impact on performance and the bacterial community during diarrhea.	Coelho MG, Virginio Junior GF, Tomaluski CR, de Toledo AF, Reis ME, Donde SC, Mendes LW, Coutinho LL, Bittar CMM.	Sci Rep	10.1038/s41598-022-17613-1	2022
	Breast Cancer Survivors and Healthy Women: Could Gut Microbiota Make a Difference?-"BiotaCancerSurvivors": A Case-Control Study.	Caleca T, Ribeiro P, Vitorino M, Menezes M, Sampaio-Alves M, Mendes AD, Vicente R, Negreiros I, Faria A, Costa DA.	Cancers (Basel)	10.3390/cancers15030594	2023
	Effects of Alternative Administration Programs of a Synbiotic Supplement on Broiler Performance, Foot Pad Dermatitis, Caecal Microbiota, and Blood Metabolites.	Brugaletta G, De Cesare A, Zampiga M, Laghi L, Oliveri C, Zhu C, Manfreda G, Syed B, Valenzuela L, Sirri F.	Animals (Basel)	10.3390/ani10030522	2020
	A grape seed and bilberry extract reduces blood pressure in individuals at risk of developing type 2 diabetes: the PRECISE study, a double-blind placebo-controlled cross-over intervention study.	Grohmann T, Walker AW, Russell WR, Hoggard N, Zhang X, Horgan G, de Roos B.	Front Nutr	10.3389/fnut.2023.1139880	2023
	Butterflies in the gut: the interplay between intestinal microbiota and stress.	Lai TT, Liou CW, Tsai YH, Lin YY, Wu WL.	J Biomed Sci	10.1186/s12929-023-00984-6	2023
	Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa.	Leon LM, Park AE, Borges AL, Zhang JY, Bondy-Denomy J.	Nucleic Acids Res	10.1093/nar/gkab006	2021
Pathogenicity	The Effects of High-Salt Gastric Intake on the Composition of the Intestinal Microbiota in Wistar Rats.	Dong Z, Liu Y, Pan H, Wang H, Wang X, Xu X, Xiao K, Liu M, Xu Z, Li L, Zhang Y.	Med Sci Monit	10.12659/msm.922160	2020
Pathogenicity	Children and adolescents with attention deficit hyperactivity disorder and autism spectrum disorder share distinct microbiota compositions.	Bundgaard-Nielsen C, Lauritsen MB, Knudsen JK, Rold LS, Larsen MH, Hindersson P, Villadsen AB, Leutscher PDC, Hagstrom S, Nyegaard M, Sorensen S.	Gut Microbes	10.1080/19490976.2023.2211923	2023
Phylogeny	DNA-DNA relatedness and phylogenetic positions of Slackia exigua, Slackia heliotrinireducens, Eggerthella lenta, and other related bacteria.	Nakazawa F, Hoshino E.	Oral Microbiol Immunol	10.1111/j.1399-302x.2004.00162.x	2004
	Plant-Derived Nutraceuticals in Mental Health and Brain Function: Mechanisms of Action and Therapeutic Potential.	Borrego-Ruiz A, Borrego JJ.	Int J Mol Sci	10.3390/ijms26188849	2025
Genetics	The gut microbiome is a significant risk factor for future chronic lung disease.	Liu Y, Teo SM, Meric G, Tang HHF, Zhu Q, Sanders JG, Vazquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M.	J Allergy Clin Immunol	10.1016/j.jaci.2022.12.810	2023
Pathogenicity	Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids.	Qian X, Yanagi K, Kane AV, Alden N, Lei M, Snydman DR, Vickers RJ, Lee K, Thorpe CM.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00046.2020	2020
Enzymology	Targeted Synthesis and Characterization of a Gene Cluster Encoding NAD(P)H-Dependent 3alpha-, 3beta-, and 12alpha-Hydroxysteroid Dehydrogenases from Eggerthella CAG:298, a Gut Metagenomic Sequence.	Mythen SM, Devendran S, Mendez-Garcia C, Cann I, Ridlon JM.	Appl Environ Microbiol	10.1128/aem.02475-17	2018
	Modulation of gut microbiota with Ayurveda diet and lifestyle: A review on its possible way to treat type 2 diabetes.	Chauhan A, Semwal DK, Semwal RB, Joshi SK, Adhana RK, Goswami MS.	Ayu	10.4103/ayu.ayu_7_20	2022
	Methyl halide transferase-based gas reporters for quantification of filamentous bacteria in microdroplet emulsions.	Song X, Kong SJ, Seo S, Prabhakar RG, Shamoo Y.	Appl Environ Microbiol	10.1128/aem.00764-23	2023
	The gut microbiome in microscopic polyangiitis with kidney involvement: common and unique alterations, clinical association and values for disease diagnosis and outcome prediction.	Yu B, Jin L, Chen Z, Nie W, Chen L, Ma Y, Chen H, Wu Y, Ma Y, Chen J, Han F.	Ann Transl Med	10.21037/atm-21-1315	2021
	Gut microbiota and the prevalence and incidence of renal stones.	Kim HN, Kim JH, Chang Y, Yang D, Joo KJ, Cho YS, Park HJ, Kim HL, Ryu S.	Sci Rep	10.1038/s41598-022-07796-y	2022
Phylogeny	Key Technologies for Progressing Discovery of Microbiome-Based Medicines.	Young RB, Marcelino VR, Chonwerawong M, Gulliver EL, Forster SC.	Front Microbiol	10.3389/fmicb.2021.685935	2021
Enzymology	First report of Gordonibacter pamelaeae bacteremia.	Woo PC, Teng JL, Lam KK, Tse CW, Leung KW, Leung AW, Lau SK, Yuen KY.	J Clin Microbiol	10.1128/jcm.01459-09	2010
Pathogenicity	Antioxidant, Anti-Inflammatory, Anti-Menopausal, and Anti-Cancer Effects of Lignans and Their Metabolites.	Jang WY, Kim MY, Cho JY.	Int J Mol Sci	10.3390/ijms232415482	2022
	Electroacupuncture modulates the intestinal microecology to improve intestinal motility in spinal cord injury rats.	Cheng J, Li W, Wang Y, Cao Q, Ni Y, Zhang W, Guo J, Chen B, Zang Y, Zhu Y.	Microb Biotechnol	10.1111/1751-7915.13968	2022
Pathogenicity	Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly.	Ivey KL, Chan AT, Izard J, Cassidy A, Rogers GB, Rimm EB.	mBio	10.1128/mbio.01205-19	2019
	Weighted Gene Co-Expression Network Analysis Identifies a Functional Guild and Metabolite Cluster Mediating the Relationship between Mucosal Inflammation and Adherence to the Mediterranean Diet in Ulcerative Colitis.	Strauss JC, Haskey N, Ramay HR, Ghosh TS, Taylor LM, Yousuf M, Ohland C, McCoy KD, Ingram RJM, Ghosh S, Panaccione R, Raman M.	Int J Mol Sci	10.3390/ijms24087323	2023
	Beyond Metabolism: The Complex Interplay Between Dietary Phytoestrogens, Gut Bacteria, and Cells of Nervous and Immune Systems.	Cady N, Peterson SR, Freedman SN, Mangalam AK.	Front Neurol	10.3389/fneur.2020.00150	2020
Metabolism	Complex influences of gut microbiome metabolism on various drug responses.	Chae S, Kim DJ, Cho JY.	Transl Clin Pharmacol	10.12793/tcp.2020.28.e3	2020
	Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders.	Proffitt C, Bidkhori G, Lee S, Tebani A, Mardinoglu A, Uhlen M, Moyes DL, Shoaie S.	iScience	10.1016/j.isci.2022.104513	2022
	The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery.	Louca P, Meijnikman AS, Nogal A, Asnicar F, Attaye I, Vijay A, Kouraki A, Visconti A, Wong K, Berry SE, Leeming ER, Mompeo O, Tettamanzi F, Baleanu AF, Falchi M, Hadjigeorgiou G, Wolf J, Acherman YIZ, Van de Laar AW, Gerdes VEA, Michelotti GA, Franks PW, Segata N, Mangino M, Spector TD, Bulsiewicz WJ, Nieuwdorp M, Valdes AM, Menni C.	Cell Rep Med	10.1016/j.xcrm.2023.100993	2023
	A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.	Han W, Ye Y.	Pac Symp Biocomput	10.1142/9789813279827_0022	2019
Genetics	Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.	Rampelli S, Soverini M, D'Amico F, Barone M, Tavella T, Monti D, Capri M, Astolfi A, Brigidi P, Biagi E, Franceschi C, Turroni S, Candela M.	mSystems	10.1128/msystems.00124-20	2020
Pathogenicity	[Bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents--special references to bacteria isolated between April 2009 and March 2010].	Shinagawa N, Osanai H, Hirata K, Furuhata T, Mizukuchi T, Yanai Y, Hata F, Taniguchi M, Sasaki K, Someya T, Sasaki K, Oono K, Mizuno I, Shamoto T, Fukui T, Tokita S, Nakamura M, Mashita K, Shibuya H, Tanaka M, Hasegawa I, Kimura M, Oshima H, Maeda H, Ishikawa S, Mukaiya M, Kihara C, Mizuno A, Watabe K, Iwai A, Saito T, Hoshikawa T, Kimura H, Moori N, Sumita N, Jae-Hoon Y, Kubo S, Lee S, Aikawa N, Sekine K, Abe S, Oomura T, Takeyama H, Wakasugi T, Kobayashi Y, Tsuji T, Yamaue H, Ozawa S, Takesue Y, Fujiwara T, Tsumura H, Kimura H, Yokoyama T, Iwagaki H, Takeuchi H, Tanakaya K, Sueda T, Hiyama E, Murakami Y, Ohge H, Uemura K, Yasunami Y, Sasaki T.	Jpn J Antibiot		2011
	Implication of Gut Microbiota in Cardiovascular Diseases.	Zhou W, Cheng Y, Zhu P, Nasser MI, Nasser MI, Zhang X, Zhao M.	Oxid Med Cell Longev	10.1155/2020/5394096	2020
Metabolism	Impact of outdoor nature-related activities on gut microbiota, fecal serotonin, and perceived stress in preschool children: the Play&Grow randomized controlled trial.	Sobko T, Liang S, Cheng WHG, Tun HM.	Sci Rep	10.1038/s41598-020-78642-2	2020
	Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.	Fix J, Chandrashekhar K, Perez J, Bucardo F, Hudgens MG, Yuan L, Twitchell E, Azcarate-Peril MA, Vilchez S, Becker-Dreps S.	Am J Trop Med Hyg	10.4269/ajtmh.19-0355	2020
	Clostridium scindens: history and current outlook for a keystone species in the mammalian gut involved in bile acid and steroid metabolism.	Daniel SL, Ridlon JM.	FEMS Microbiol Rev	10.1093/femsre/fuaf016	2025
	Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease.	Zhang P, Wang X, Li S, Cao X, Zou J, Fang Y, Shi Y, Xiang F, Shen B, Li Y, Fang B, Zhang Y, Guo R, Lv Q, Zhang L, Lu Y, Wang Y, Yu J, Xie Y, Wang R, Chen X, Yu J, Zhang Z, He J, Zhan J, Lv W, Nie Y, Cai J, Xu X, Hu J, Zhang Q, Gao T, Jiang X, Tan X, Xue N, Wang Y, Ren Y, Wang L, Zhang H, Ning Y, Chen J, Zhang L, Jin S, Ren F, Ehrlich SD, Zhao L, Ding X.	Genome Biol	10.1186/s13059-023-03056-y	2023
	Antimicrobial Stewardship Opportunities in Patients with Bacteremia Not Identified by BioFire FilmArray.	Ny P, Ozaki A, Pallares J, Nieberg P, Wong-Beringer A.	J Clin Microbiol	10.1128/jcm.01941-18	2019
	An Inductive Logistic Matrix Factorization Model for Predicting Drug-Metabolite Association With Vicus Regularization.	Ma Y, Liu L, Chen Q, Ma Y.	Front Microbiol	10.3389/fmicb.2021.650366	2021
	Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations.	Kleigrewe K, Haack M, Baudin M, Menabreaz T, Crovadore J, Masri M, Beyrer M, Andlauer W, Lefort F, Dawid C, Bruck TB, Bruck WM.	Int J Mol Sci	10.3390/ijms231810473	2022
Metabolism	Colonic Bacteria-Transformed Catechin Metabolite Response to Cytokine Production by Human Peripheral Blood Mononuclear Cells.	Krishnamoorthy R, Adisa AR, Periasamy VS, Athinarayanan J, Pandurangan SB, Alshatwi AA.	Biomolecules	10.3390/biom9120830	2019
	Dual Regulation Mechanism of Obesity: DNA Methylation and Intestinal Flora.	Ren Y, Huang P, Zhang L, Tang YF, Luo SL, She Z, Peng H, Chen YQ, Luo JW, Duan WX, Liu LJ, Liu LQ.	Biomedicines	10.3390/biomedicines12081633	2024
	A Novel Trimethylamine Oxide-Induced Model Implicates Gut Microbiota-Related Mechanisms in Frailty.	Chen SY, Rong XY, Sun XY, Zou YR, Zhao C, Wang HJ.	Front Cell Infect Microbiol	10.3389/fcimb.2022.803082	2022
Genetics	Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.	Serrano-Gomez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, Machiels K, Guarner F, Vermeire S, Manichanh C.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.11.037	2021
	Cultivation of gastrointestinal microbiota in a new growth system revealed dysbiosis and metabolic disruptions in carcinoma-bearing rats.	Pena-Ocana BA, Hoshiko Y, Silva-Flores M, Maeda T, Perez-Torres I, Garcia-Contreras R, Gutierrez-Sarmiento W, Hernandez-Esquivel L, Marin-Hernandez A, Sanchez-Thomas R, Saavedra E, Rodriguez-Zavala JS, Jasso-Chavez R.	Front Microbiol	10.3389/fmicb.2022.949272	2022
Pathogenicity	Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry.	McCann SE, Hullar MAJ, Tritchler DL, Cortes-Gomez E, Yao S, Davis W, O'Connor T, Erwin D, Thompson LU, Yan L, Lampe JW.	Nutrients	10.3390/nu13030919	2021
Phylogeny	Gut Microbial Characteristics of Adult Patients With Epilepsy.	Dong L, Zheng Q, Cheng Y, Zhou M, Wang M, Xu J, Xu Z, Wu G, Yu Y, Ye L, Feng Z.	Front Neurosci	10.3389/fnins.2022.803538	2022
	Benefits of Fermented Papaya in Human Health.	Leitao M, Ribeiro T, Garcia PA, Barreiros L, Correia P.	Foods	10.3390/foods11040563	2022
	A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes.	Radwan S, Gilfillan D, Eklund B, Radwan HM, El Menofy NG, Lee J, Kapuscinski M, Abdo Z.	PLoS One	10.1371/journal.pone.0238764	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
	Zinc Deficiency During Pregnancy Leads to Altered Microbiome and Elevated Inflammatory Markers in Mice.	Sauer AK, Grabrucker AM.	Front Neurosci	10.3389/fnins.2019.01295	2019
	Factors driving the inter-individual variability in the metabolism and bioavailability of (poly)phenolic metabolites: A systematic review of human studies	Favari C, Rinaldi de Alvarenga J, Sanchez-Martinez L, Tosi N, Mignogna C, Cremonini E, Manach C, Bresciani L, Del Rio D, Mena P.	Redox Biol		2024
	Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori.	Gudra D, Silamikelis I, Pjalkovskis J, Danenberga I, Pupola D, Skenders G, Ustinova M, Megnis K, Leja M, Vangravs R, Fridmanis D.	PLoS One	10.1371/journal.pone.0289879	2023
Metabolism	Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside.	Clavel T, Henderson G, Engst W, Dore J, Blaut M.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2005.00057.x	2006
	Kombuchas from Green and Black Tea Modulate the Gut Microbiota and Improve the Intestinal Health of Wistar Rats Fed a High-Fat High-Fructose Diet.	Costa MAC, Dias Moreira LP, Duarte VDS, Cardoso RR, Sao Jose VPB, Silva BPD, Grancieri M, Corich V, Giacomini A, Bressan J, Martino HSD, Barros FAR.	Nutrients	10.3390/nu14245234	2022
	Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.	Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR.	Front Microbiol	10.3389/fmicb.2018.03220	2018
Phylogeny	Anaerobic, non-sporulating, Gram-positive bacilli bacteraemia characterized by 16S rRNA gene sequencing.	Lau SK, Woo PC, Fung AM, Chan KM, Woo GK, Yuen KY.	J Med Microbiol	10.1099/jmm.0.45803-0	2004
Pathogenicity	[Bacteria isolated from surgical infections and their susceptibilities to antimicrobial agents --special references to bacteria isolated between April 2008 and March 2009].	Shinagawa N, Hasegawa M, Hirata K, Furuhata T, Mizukuchi T, Osanai H, Yanai Y, Hata F, Sasaki K, Someya T, Harada K, Oono K, Tokita S, Nakamura M, Shibuya H, Hasegawa I, Kimura M, Oshima H, Maeda H, Mukaiya M, Kihara C, Kosho W, Hoshikawa T, Kimura H, Ushijima Y, Yae-Hoon Y, Aikawa N, Abe S, Yura J, Takeyama H, Wakasugi T, Taniguchi M, Mizuno I, Fukui T, Mashita K, Ishikawa S, Mizuno A, Moori N, Sumita N, Kubo S, Lee S, Oomura T, Kobayashi Y, Tsuji T, Yamaue H, Kawai M, Takesue Y, Tanaka N, Kimura H, Iwagaki H, Sueda T, Hiyama E, Murakami Y, Ooge H, Uemura K, Tsumura H, Yokoyama T, Takeuchi H, Tanakaya K, Yasunami Y, Ryu S.	Jpn J Antibiot		2010
Metabolism	Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans.	Clavel T, Borrmann D, Braune A, Dore J, Blaut M.	Anaerobe	10.1016/j.anaerobe.2005.11.002	2006
Metabolism	Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine.	Chen J, Wang Q, Wang A, Lin Z.	Front Cell Infect Microbiol	10.3389/fcimb.2019.00470	2019
Phylogeny	Application of rrs gene sequencing to elucidate the clinical significance of Eggerthela lenta infection.	Landais C, Doudier B, Imbert G, Fenollar F, Brouqui P.	J Clin Microbiol	10.1128/jcm.01805-06	2007
	Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.	Wyatt NJ, Watson H, Anderson CA, Kennedy NA, Raine T, Ahmad T, Allerton D, Bardgett M, Clark E, Clewes D, Cotobal Martin C, Doona M, Doyle JA, Frith K, Hancock HC, Hart AL, Hildreth V, Irving PM, Iqbal S, Kennedy C, King A, Lawrence S, Lees CW, Lees R, Letchford L, Liddle T, Lindsay JO, Maier RH, Mansfield JC, Marchesi JR, McGregor N, McIntyre RE, Ostermayer J, Osunnuyi T, Powell N, Prescott NJ, Satsangi J, Sharma S, Shrestha T, Speight A, Strickland M, Wason JM, Whelan K, Wood R, Young GR, Zhang X, Parkes M, Stewart CJ, Jostins-Dean L, Lamb CA.	BMJ Open	10.1136/bmjopen-2023-073639	2024
Genetics	A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota.	Zhang XX, Lv QB, Yan QL, Zhang Y, Guo RC, Meng JX, Ma H, Qin SY, Zhu QH, Li CQ, Liu R, Liu G, Li SH, Sun DB, Ni HB.	Microbiol Spectr	10.1128/spectrum.02211-22	2022
	Interactions between Gut Microbiota and Polyphenols: New Insights into the Treatment of Fatigue.	Luo C, Wei X, Song J, Xu X, Huang H, Fan S, Zhang D, Han L, Lin J.	Molecules	10.3390/molecules27217377	2022
	Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective.	Valles-Colomer M, Menni C, Berry SE, Valdes AM, Spector TD, Segata N.	Nat Med	10.1038/s41591-023-02260-4	2023
Pathogenicity	FuZhengHuaYuJiangZhuTongLuoFang Prescription Modulates Gut Microbiota and Gut-Derived Metabolites in UUO Rats.	Chen Z, Wu S, Zeng Y, Chen Z, Li X, Li J, He L, Chen M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.837205	2022
	Fermented Papaya Preparation Restores Age-Related Reductions in Peripheral Blood Mononuclear Cell Cytolytic Activity in Tube-Fed Patients.	Fujita Y, Tsuno H, Nakayama J.	PLoS One	10.1371/journal.pone.0169240	2017
	Insights in the Complex DegU, DegS, and Spo0A Regulation System of Paenibacillus polymyxa by CRISPR-Cas9-Based Targeted Point Mutations.	Meliawati M, May T, Eckerlin J, Heinrich D, Herold A, Schmid J.	Appl Environ Microbiol	10.1128/aem.00164-22	2022
	Polyphenols-Gut-Heart: An Impactful Relationship to Improve Cardiovascular Diseases.	Bianchi F, Cappella A, Gagliano N, Sfondrini L, Stacchiotti A.	Antioxidants (Basel)	10.3390/antiox11091700	2022
	Sex-specific relationships of the infant microbiome and early-childhood behavioral outcomes.	Laue HE, Karagas MR, Coker MO, Bellinger DC, Baker ER, Korrick SA, Madan JC.	Pediatr Res	10.1038/s41390-021-01785-z	2022
	Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins.	Mesnage R, Bowyer RCE, El Balkhi S, Saint-Marcoux F, Gardere A, Ducarmon QR, Geelen AR, Zwittink RD, Tsoukalas D, Sarandi E, Paramera EI, Spector T, Steves CJ, Antoniou MN.	Environ Health	10.1186/s12940-022-00860-0	2022
	Relationship between gut microbiota and rheumatoid arthritis: A bibliometric analysis.	Dong Y, Yao J, Deng Q, Li X, He Y, Ren X, Zheng Y, Song R, Zhong X, Ma J, Shan D, Lv F, Wang X, Yuan R, She G.	Front Immunol	10.3389/fimmu.2023.1131933	2023
Genetics	Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature.	Yadav M, Pandey R, Chauhan NS.	Front Microbiol	10.3389/fmicb.2020.588545	2020
	mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.	Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G.	Nat Methods	10.1038/s41592-023-02125-1	2024
	Thiostrepton alleviates experimental colitis by promoting RORgammat ubiquitination and modulating dysbiosis.	Luo Y, Liu C, Luo Y, Zhang X, Li J, Hu C, Yang S.	Cell Mol Immunol	10.1038/s41423-023-01085-y	2023
	The heart-gut axis: new target for atherosclerosis and congestive heart failure therapy.	Forkosh E, Ilan Y.	Open Heart	10.1136/openhrt-2018-000993	2019
	Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome.	Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB.	BMC Microbiol	10.1186/s12866-022-02495-0	2022
	Plasma quercetin metabolites are affected by intestinal microbiota of human microbiota-associated mice fed with a quercetin-containing diet.	Tamura M, Nakagawa H, Hori S, Suzuki T, Hirayama K.	J Clin Biochem Nutr	10.3164/jcbn.19-45	2019
	Effects of Rare Microbiome Taxa Filtering on Statistical Analysis.	Cao Q, Sun X, Rajesh K, Chalasani N, Gelow K, Katz B, Shah VH, Sanyal AJ, Smirnova E.	Front Microbiol	10.3389/fmicb.2020.607325	2020
Metabolism	Structural and biochemical characterization of 20beta-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32.	Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM.	J Biol Chem	10.1074/jbc.ra119.009390	2019
	Therapeutics for neurodegenerative diseases by targeting the gut microbiome: from bench to bedside.	Ma YY, Li X, Yu JT, Wang YJ.	Transl Neurodegener	10.1186/s40035-024-00404-1	2024
	Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps.	Avelar-Barragan J, DeDecker L, Lu ZN, Coppedge B, Karnes WE, Whiteson KL.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00328-6	2022
Phylogeny	Signatures of early frailty in the gut microbiota.	Jackson MA, Jeffery IB, Jeffery IB, Beaumont M, Bell JT, Clark AG, Ley RE, O'Toole PW, Spector TD, Steves CJ.	Genome Med	10.1186/s13073-016-0262-7	2016
Phylogeny	Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement.	Brereton NJB, Pitre FE, Gonzalez E.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.040	2021
	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
	A systematic review of microbiome changes and impact of probiotic supplementation in children and adolescents with neuropsychiatric disorders.	Ligezka AN, Sonmez AI, Corral-Frias MP, Golebiowski R, Lynch B, Croarkin PE, Romanowicz M.	Prog Neuropsychopharmacol Biol Psychiatry	10.1016/j.pnpbp.2020.110187	2021
Phylogeny	Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair.	Sharda M, Badrinarayanan A, Seshasayee ASN.	Genome Biol Evol	10.1093/gbe/evaa223	2020
Pathogenicity	Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment.	Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, Andre F, Pasolli E, Delaloge S, Zitvogel L.	Cell Death Differ	10.1038/s41418-021-00784-1	2021
	Gut microbiota and metabolic health among overweight and obese individuals.	Kim MH, Yun KE, Kim J, Park E, Chang Y, Ryu S, Kim HL, Kim HN.	Sci Rep	10.1038/s41598-020-76474-8	2020
Metabolism	Diversification of host bile acids by members of the gut microbiota.	Winston JA, Theriot CM.	Gut Microbes	10.1080/19490976.2019.1674124	2020
	Non-antibiotics disrupt colonization resistance against enteropathogens.	Griesshammer A, de la Cuesta-Zuluaga J, Muller P, Gekeler C, Homolak J, Chang H, Schmitt K, Planker C, Schmidtchen V, Gallage S, Bohn E, Nguyen TH, Hetzer J, Heikenwalder M, Huang KC, Zahir T, Maier L.	Nature	10.1038/s41586-025-09217-2	2025
	Microbial and immunological responses relative to high-altitude exposure in mountaineers.	Kleessen B, Schroedl W, Stueck M, Richter A, Rieck O, Krueger M.	Med Sci Sports Exerc	10.1249/01.mss.0000174888.22930.e0	2005
	Intra- and Inter-individual Differences in the Human Intestinal Microbial Conversion of (-)-Epicatechin and Bioactivity of Its Major Colonic Metabolite 5-(3',4'-Dihydroxy-Phenyl)-gamma-Valerolactone in Regulating Nrf2-Mediated Gene Expression.	Liu C, Boeren S, Rietjens IMCM.	Front Nutr	10.3389/fnut.2022.910785	2022
	Genetic variants in cellular transport do not affect mesalamine response in ulcerative colitis.	Moran CJ, Huang H, Rivas M, Kaplan JL, Daly MJ, Winter HS.	PLoS One	10.1371/journal.pone.0192806	2018
	Gut Microbiota Features in Young Children With Autism Spectrum Disorders.	Coretti L, Paparo L, Riccio MP, Amato F, Cuomo M, Natale A, Borrelli L, Corrado G, Comegna M, Buommino E, Castaldo G, Bravaccio C, Chiariotti L, Berni Canani R, Lembo F.	Front Microbiol	10.3389/fmicb.2018.03146	2018
Metabolism	Droplet-based microfluidic platform for high-throughput screening of Streptomyces.	Tu R, Zhang Y, Hua E, Bai L, Huang H, Yun K, Wang M.	Commun Biol	10.1038/s42003-021-02186-y	2021
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
Enzymology	Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.	Kageyama A, Benno Y.	Microbiol Immunol	10.1111/j.1348-0421.2001.tb02624.x	2001
Genetics	Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation.	Bordugo A, Salvetti E, Rodella G, Piazza M, Dianin A, Amoruso A, Piacentini G, Pane M, Torriani S, Vitulo N, Felis GE.	Microorganisms	10.3390/microorganisms9122599	2021
Enzymology	Fungemia due to Lachancea fermentati: a case report.	Leuck AM, Rothenberger MK, Green JS.	BMC Infect Dis	10.1186/1471-2334-14-250	2014
	Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers.	Zhu Q, Hou Q, Huang S, Ou Q, Huo D, Vazquez-Baeza Y, Cen C, Cantu V, Estaki M, Chang H, Belda-Ferre P, Kim HC, Chen K, Knight R, Zhang J.	ISME J	10.1038/s41396-021-01016-7	2021
Pathogenicity	Gut microbiome-mediated mechanisms in aging-related diseases: are probiotics ready for prime time?	Ren J, Li H, Zeng G, Pang B, Wang Q, Wei J.	Front Pharmacol	10.3389/fphar.2023.1178596	2023
	Clinical manifestation of macrolide antibiotic toxicity in CKD and dialysis patients.	Ma TK, Chow KM, Choy AS, Kwan BC, Szeto CC, Li PK.	Clin Kidney J	10.1093/ckj/sfu098	2014
	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
	Effects of a high-gamma-polyglutamic acid-containing natto diet on liver lipids and cecal microbiota of adult female mice.	Tamura M, Watanabe J, Hori S, Inose A, Kubo Y, Noguchi T, Nishikawa T, Ikezawa M, Araki R, Kobori M.	Biosci Microbiota Food Health	10.12938/bmfh.2020-061	2021
Genetics	Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome.	Yang Z, Fu H, Su H, Cai X, Wang Y, Hong Y, Hu J, Xie Z, Wang X.	Front Microbiol	10.3389/fmicb.2022.1017147	2022
	Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men.	Li J, Li Y, Ivey KL, Wang DD, Wilkinson JE, Franke A, Lee KH, Chan A, Huttenhower C, Hu FB, Rimm EB, Sun Q.	Gut	10.1136/gutjnl-2020-322473	2022
	Nutraceuticals and Herbal Food Supplements for Weight Loss: Is There a Prebiotic Role in the Mechanism of Action?	Bertuccioli A, Cardinali M, Biagi M, Moricoli S, Morganti I, Zonzini GB, Rigillo G.	Microorganisms	10.3390/microorganisms9122427	2021
	Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease.	Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC.	Cell Host Microbe	10.1016/j.chom.2020.12.003	2021
	Repairing gut barrier by traditional Chinese medicine: roles of gut microbiota.	Zhou Y, Zhang D, Cheng H, Wu J, Liu J, Feng W, Peng C.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1389925	2024
	Next-Generation Probiotics as Novel Therapeutics for Improving Human Health: Current Trends and Future Perspectives.	Abouelela ME, Helmy YA.	Microorganisms	10.3390/microorganisms12030430	2024
Genetics	Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture.	Reddel S, Del Chierico F, Quagliariello A, Giancristoforo S, Vernocchi P, Russo A, Fiocchi A, Rossi P, Putignani L, El Hachem M.	Sci Rep	10.1038/s41598-019-41149-6	2019
Pathogenicity	Effects of Anthocyanin on Intestinal Health: A Systematic Review.	Verediano TA, Stampini Duarte Martino H, Dias Paes MC, Tako E.	Nutrients	10.3390/nu13041331	2021
	Gut microbiota-derived ursodeoxycholic acid alleviates low birth weight-induced colonic inflammation by enhancing M2 macrophage polarization.	Pi Y, Wu Y, Zhang X, Lu D, Han D, Zhao J, Zheng X, Zhang S, Ye H, Lian S, Bai Y, Wang Z, Tao S, Ni D, Zou X, Jia W, Zhang G, Li D, Wang J.	Microbiome	10.1186/s40168-022-01458-x	2023
Metabolism	A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota.	Sharma AK, Jaiswal SK, Chaudhary N, Sharma VK.	Sci Rep	10.1038/s41598-017-10203-6	2017
	Beneficial metabolic transformations and prebiotic potential of hemp bran and its alcalase hydrolysate, after colonic fermentation in a gut model.	Nissen L, Casciano F, Babini E, Gianotti A.	Sci Rep	10.1038/s41598-023-27726-w	2023
Metabolism	The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.	Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.	Gut Microbes	10.1080/19490976.2020.1854008	2021
	Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life.	Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D, Weinberg A.	mBio	10.1128/mbio.01229-22	2022
Enzymology	Multiple bacteria in aortic aneurysms.	Marques da Silva R, Lingaas PS, Geiran O, Tronstad L, Olsen I.	J Vasc Surg	10.1016/s0741-5214(03)00926-1	2003
	Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial.	Chong CYL, Vatanen T, Alexander T, Bloomfield FH, O'Sullivan JM.	Front Cell Infect Microbiol	10.3389/fcimb.2021.595323	2021
Pathogenicity	Advancing functional and translational microbiome research using meta-omics approaches.	Zhang X, Li L, Butcher J, Stintzi A, Figeys D.	Microbiome	10.1186/s40168-019-0767-6	2019
	Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.	Manara S, Selma-Royo M, Huang KD, Asnicar F, Armanini F, Blanco-Miguez A, Cumbo F, Golzato D, Manghi P, Pinto F, Valles-Colomer M, Amoroso L, Corrias MV, Ponzoni M, Raffaeta R, Cabrera-Rubio R, Olcina M, Pasolli E, Collado MC, Segata N.	Curr Biol	10.1016/j.cub.2023.04.011	2023
	Stewed Rhubarb Decoction Ameliorates Adenine-Induced Chronic Renal Failure in Mice by Regulating Gut Microbiota Dysbiosis.	Wang R, Hu B, Ye C, Zhang Z, Yin M, Cao Q, Ba Y, Liu H.	Front Pharmacol	10.3389/fphar.2022.842720	2022
	Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients.	Wang H, Ong E, Kao JY, Sun D, He Y.	Front Microbiol	10.3389/fmicb.2021.633732	2021
Phylogeny	The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.	Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ, Dewhirst FE, Paster BJ, Tzellas N, Coleman B.	Int J Syst Bacteriol	10.1099/00207713-49-2-595	1999
Genetics	Consistency across multi-omics layers in a drug-perturbed gut microbial community.	Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Muller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P.	Mol Syst Biol	10.15252/msb.202311525	2023
	Changes in intestinal microbiota in postmenopausal oestrogen receptor-positive breast cancer patients treated with (neo)adjuvant chemotherapy.	Aarnoutse R, Ziemons J, Hillege LE, de Vos-Geelen J, de Boer M, Bisschop SMP, Vriens BEPJ, Vincent J, van de Wouw AJ, Le GN, Venema K, Rensen SS, Penders J, Smidt ML.	NPJ Breast Cancer	10.1038/s41523-022-00455-5	2022
Genetics	Finegoldia magna Isolated from Orthopedic Joint Implant-Associated Infections.	Soderquist B, Bjorklund S, Hellmark B, Jensen A, Bruggemann H.	J Clin Microbiol	10.1128/jcm.00866-17	2017
Pathogenicity	Gut microbiome in chronic rheumatic and inflammatory bowel diseases: Similarities and differences.	Salem F, Kindt N, Marchesi JR, Netter P, Lopez A, Kokten T, Danese S, Jouzeau JY, Peyrin-Biroulet L, Moulin D.	United European Gastroenterol J	10.1177/2050640619867555	2019
	Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin A from Ellagic Acid.	Selma MV, Beltran D, Luna MC, Romo-Vaquero M, Garcia-Villalba R, Mira A, Espin JC, Tomas-Barberan FA.	Front Microbiol	10.3389/fmicb.2017.01521	2017
	Gut microbiome sheds light on the development and treatment of abdominal aortic aneurysm.	Ling X, Jie W, Qin X, Zhang S, Shi K, Li T, Guo J.	Front Cardiovasc Med	10.3389/fcvm.2022.1063683	2022
Metabolism	Quantitative systems pharmacology and the personalized drug-microbiota-diet axis.	Thiele I, Clancy CM, Heinken A, Fleming RMT.	Curr Opin Syst Biol	10.1016/j.coisb.2017.06.001	2017
Pathogenicity	Insight into Polyphenol and Gut Microbiota Crosstalk: Are Their Metabolites the Key to Understand Protective Effects against Metabolic Disorders?	Koudoufio M, Desjardins Y, Feldman F, Spahis S, Delvin E, Levy E.	Antioxidants (Basel)	10.3390/antiox9100982	2020
	Hippuric Acid Promotes Renal Fibrosis by Disrupting Redox Homeostasis via Facilitation of NRF2-KEAP1-CUL3 Interactions in Chronic Kidney Disease.	Sun B, Wang X, Liu X, Wang L, Ren F, Wang X, Leng X.	Antioxidants (Basel)	10.3390/antiox9090783	2020
	The Influence of Polyphenols on Atherosclerosis Development.	Ziolkiewicz A, Kasprzak-Drozd K, Rusinek R, Markut-Miotla E, Oniszczuk A.	Int J Mol Sci	10.3390/ijms24087146	2023
	Control points for design of taxonomic composition in synthetic human gut communities.	Connors BM, Thompson J, Ertmer S, Clark RL, Pfleger BF, Venturelli OS.	Cell Syst	10.1016/j.cels.2023.11.007	2023
	Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.	Thomas AM, Fidelle M, Routy B, Kroemer G, Wargo JA, Segata N, Zitvogel L.	Nat Rev Clin Oncol	10.1038/s41571-023-00785-8	2023
	Diosmetin has therapeutic efficacy in colitis regulating gut microbiota, inflammation, and oxidative stress via the circ-Sirt1/Sirt1 axis.	Li HL, Wei YY, Li XH, Zhang SS, Zhang RT, Li JH, Ma BW, Shao SB, Lv ZW, Ruan H, Zhou HG, Yang C.	Acta Pharmacol Sin	10.1038/s41401-021-00726-0	2022
	Tuftsin-Phosphorylcholine Maintains Normal Gut Microbiota in Collagen Induced Arthritic Mice.	Ben-Amram H, Bashi T, Werbner N, Neuman H, Fridkin M, Blank M, Shoenfeld Y, Koren O.	Front Microbiol	10.3389/fmicb.2017.01222	2017
Pathogenicity	Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer.	Hamamah S, Lobiuc A, Covasa M.	Int J Mol Sci	10.3390/ijms25169026	2024
	The gut microbiota and its interactions with cardiovascular disease.	Xu H, Wang X, Feng W, Liu Q, Zhou S, Liu Q, Cai L.	Microb Biotechnol	10.1111/1751-7915.13524	2020
	Antidiabetic Function of Lactobacillus fermentum MF423-Fermented Rice Bran and Its Effect on Gut Microbiota Structure in Type 2 Diabetic Mice.	Ai X, Wu C, Yin T, Zhur O, Liu C, Yan X, Yi C, Liu D, Xiao L, Li W, Xie B, He H.	Front Microbiol	10.3389/fmicb.2021.682290	2021
Metabolism	Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.	Mallory EK, Acharya A, Rensi SE, Turnbaugh PJ, Bright RA, Altman RB.	Pac Symp Biocomput	10.1142/9789813235533_0006	2018
	Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study.	Al Bataineh MT, Dash NR, Bel Lassen P, Banimfreg BH, Nada AM, Belda E, Clement K.	Sci Rep	10.1038/s41598-020-66598-2	2020
Phylogeny	Does entry to center-based childcare affect gut microbial colonization in young infants?	Hermes GDA, Eckermann HA, de Vos WM, de Weerth C.	Sci Rep	10.1038/s41598-020-66404-z	2020
Pathogenicity	Early-life gut dysbiosis linked to juvenile mortality in ostriches.	Videvall E, Song SJ, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK.	Microbiome	10.1186/s40168-020-00925-7	2020
Metabolism	Gut microbiota determines the fate of dietary fiber-targeted interventions in host health.	Wang W, Fan Z, Yan Q, Pan T, Luo J, Wei Y, Li B, Fang Z, Lu W.	Gut Microbes	10.1080/19490976.2024.2416915	2024
	From Tumor Cells to Endothelium and Gut Microbiome: A Complex Interaction Favoring the Metastasis Cascade.	Abdel Sater AH, Bouferraa Y, Amhaz G, Haibe Y, Lakkiss AE, Shamseddine A.	Front Oncol	10.3389/fonc.2022.804983	2022
Pathogenicity	Quinones are growth factors for the human gut microbiota.	Fenn K, Strandwitz P, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K.	Microbiome	10.1186/s40168-017-0380-5	2017
Phylogeny	Genotypic diversity of anaerobic isolates from bloodstream infections.	Simmon KE, Mirrett S, Reller LB, Petti CA.	J Clin Microbiol	10.1128/jcm.02469-07	2008
	Dysbiosis of human gut microbiome in young-onset colorectal cancer.	Yang Y, Du L, Shi D, Kong C, Liu J, Liu G, Li X, Ma Y.	Nat Commun	10.1038/s41467-021-27112-y	2021
Genetics	A metagenome-wide association study of gut microbiome and visceral fat accumulation.	Nie X, Chen J, Ma X, Ni Y, Shen Y, Yu H, Panagiotou G, Bao Y.	Comput Struct Biotechnol J	10.1016/j.csbj.2020.09.026	2020
Metabolism	Metagenomic analysis of bile salt biotransformation in the human gut microbiome.	Das P, Marcisauskas S, Ji B, Nielsen J.	BMC Genomics	10.1186/s12864-019-5899-3	2019
Pathogenicity	Fourth Belgian multicentre survey of antibiotic susceptibility of anaerobic bacteria.	Wybo I, Van den Bossche D, Soetens O, Vekens E, Vandoorslaer K, Claeys G, Glupczynski Y, Ieven M, Melin P, Nonhoff C, Rodriguez-Villalobos H, Verhaegen J, Pierard D.	J Antimicrob Chemother	10.1093/jac/dkt344	2014
	Resveratrol affects in vitro rumen fermentation, methane production and prokaryotic community composition in a time- and diet-specific manner.	Ma T, Wu W, Tu Y, Zhang N, Diao Q.	Microb Biotechnol	10.1111/1751-7915.13566	2020
Pathogenicity	The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.	Lv Y, Zhao X, Guo W, Gao Y, Yang S, Li Z, Wang G.	J Diabetes Res	10.1155/2018/1890978	2018
Enzymology	Cystathionine beta-Synthase (CBS) Domain-containing Pyrophosphatase as a Target for Diadenosine Polyphosphates in Bacteria.	Anashkin VA, Salminen A, Tuominen HK, Orlov VN, Lahti R, Baykov AA.	J Biol Chem	10.1074/jbc.m115.680272	2015
Pathogenicity	Adjunctive Probiotics Alleviates Asthmatic Symptoms via Modulating the Gut Microbiome and Serum Metabolome.	Liu A, Ma T, Xu N, Jin H, Zhao F, Kwok LY, Zhang H, Zhang S, Sun Z.	Microbiol Spectr	10.1128/spectrum.00859-21	2021
	Engineering probiotics as living diagnostics and therapeutics for improving human health.	Zhou Z, Chen X, Sheng H, Shen X, Sun X, Yan Y, Wang J, Yuan Q.	Microb Cell Fact	10.1186/s12934-020-01318-z	2020
Pathogenicity	The Gut-Brain Axis: Two Ways Signaling in Parkinson's Disease.	Dogra N, Mani RJ, Katare DP.	Cell Mol Neurobiol	10.1007/s10571-021-01066-7	2022
	Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.	Warner BB, Rosa BA, Ndao IM, Tarr PI, Miller JP, England SK, Luby JL, Rogers CE, Hall-Moore C, Bryant RE, Wang JD, Linneman LA, Smyser TA, Smyser CD, Barch DM, Miller GE, Chen E, Martin J, Mitreva M.	Nat Commun	10.1038/s41467-023-41421-4	2023
	Changes of saliva microbiota in the onset and after the treatment of diabetes in patients with periodontitis.	Yang Y, Liu S, Wang Y, Wang Z, Ding W, Sun X, He K, Feng Q, Zhang X.	Aging (Albany NY)	10.18632/aging.103399	2020
Phylogeny	Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers.	Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L, Makivuokko H, Kajander K, Palva A.	BMC Gastroenterol	10.1186/1471-230x-9-95	2009
	Role of the gut microbiome in three major psychiatric disorders.	Borkent J, Ioannou M, Laman JD, Haarman BCM, Sommer IEC, Sommer IEC.	Psychol Med	10.1017/s0033291722000897	2022
Metabolism	A Novel Heme Transporter from the Energy Coupling Factor Family Is Vital for Group A Streptococcus Colonization and Infections.	Chatterjee N, Cook LCC, Lyles KV, Nguyen HAT, Devlin DJ, Thomas LS, Eichenbaum Z.	J Bacteriol	10.1128/jb.00205-20	2020
	The intestinal and biliary microbiome in autoimmune liver disease-current evidence and concepts.	Liwinski T, Heinemann M, Schramm C.	Semin Immunopathol	10.1007/s00281-022-00936-6	2022
Metabolism	Effect of a Flaxseed Lignan Intervention on Circulating Bile Acids in a Placebo-Controlled Randomized, Crossover Trial.	Navarro SL, Levy L, Curtis KR, Elkon I, Kahsai OJ, Ammar HS, Randolph TW, Hong NN, Carnevale Neto F, Raftery D, Chapkin RS, Lampe JW, Hullar MAJ.	Nutrients	10.3390/nu12061837	2020
	Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.	Clooney AG, Eckenberger J, Laserna-Mendieta E, Sexton KA, Bernstein MT, Vagianos K, Sargent M, Ryan FJ, Moran C, Sheehan D, Sleator RD, Targownik LE, Bernstein CN, Shanahan F, Claesson MJ.	Gut	10.1136/gutjnl-2020-321106	2021
Metabolism	5-(3',4'-Dihydroxyphenyl-gamma-valerolactone), a Major Microbial Metabolite of Proanthocyanidin, Attenuates THP-1 Monocyte-Endothelial Adhesion.	Lee CC, Kim JH, Kim JS, Oh YS, Han SM, Park JHY, Lee KW, Lee CY.	Int J Mol Sci	10.3390/ijms18071363	2017
Pathogenicity	The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2.	Sarkar A, Harty S, Moeller AH, Klein SL, Erdman SE, Friston KJ, Carmody RN.	Trends Mol Med	10.1016/j.molmed.2021.09.009	2021
Phylogeny	Diet-induced alterations of host cholesterol metabolism are likely to affect the gut microbiota composition in hamsters.	Martinez I, Perdicaro DJ, Brown AW, Hammons S, Carden TJ, Carr TP, Eskridge KM, Walter J.	Appl Environ Microbiol	10.1128/aem.03046-12	2013
Pathogenicity	Comparative in vitro activities of LFF571 against Clostridium difficile and 630 other intestinal strains of aerobic and anaerobic bacteria.	Citron DM, Tyrrell KL, Merriam CV, Goldstein EJ.	Antimicrob Agents Chemother	10.1128/aac.06305-11	2012
Phylogeny	Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study.	Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z, Jiang Q.	BMC Microbiol	10.1186/s12866-018-1232-6	2018
	Gut-Brain Axis: Role of Gut Microbiota on Neurological Disorders and How Probiotics/Prebiotics Beneficially Modulate Microbial and Immune Pathways to Improve Brain Functions.	Suganya K, Koo BS.	Int J Mol Sci	10.3390/ijms21207551	2020
	2017 NIH-wide workshop report on "The Human Microbiome: Emerging Themes at the Horizon of the 21st Century".	2017 NIH-wide microbiome workshop writing team.	Microbiome	10.1186/s40168-019-0627-4	2019
	Enteric Phageome Alterations in Patients With Type 2 Diabetes.	Chen Q, Ma X, Li C, Shen Y, Zhu W, Zhang Y, Guo X, Zhou J, Liu C.	Front Cell Infect Microbiol	10.3389/fcimb.2020.575084	2020
Pathogenicity	B Cells and Microbiota in Autoimmunity.	Botia-Sanchez M, Alarcon-Riquelme ME, Galicia G.	Int J Mol Sci	10.3390/ijms22094846	2021
Enzymology	Bacteriology of histopathologically defined appendicitis in children.	Rautio M, Saxen H, Siitonen A, Nikku R, Jousimies-Somer H.	Pediatr Infect Dis J	10.1097/00006454-200011000-00010	2000
	Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.	Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2019.06.013	2019
	Gut microbiome - A potential mediator of pathogenesis in heart failure and its comorbidities: State-of-the-art review.	Mamic P, Chaikijurajai T, Tang WHW.	J Mol Cell Cardiol	10.1016/j.yjmcc.2020.12.001	2021
	Combined berberine and probiotic treatment as an effective regimen for improving postprandial hyperlipidemia in type 2 diabetes patients: a double blinded placebo controlled randomized study.	Wang S, Ren H, Zhong H, Zhao X, Li C, Ma J, Gu X, Xue Y, Huang S, Yang J, Chen L, Chen G, Qu S, Liang J, Qin L, Huang Q, Peng Y, Li Q, Wang X, Zou Y, Shi Z, Li X, Li T, Yang H, Lai S, Xu G, Li J, Zhang Y, Gu Y, Wang W.	Gut Microbes	10.1080/19490976.2021.2003176	2022
	Exploring the multifactorial aspects of Gut Microbiome in Parkinson's Disease.	Pavan S, Prabhu AN, Prasad Gorthi S, Das B, Mutreja A, Shetty V, Ramamurthy T, Ballal M.	Folia Microbiol (Praha)	10.1007/s12223-022-00977-2	2022
Metabolism	Interindividual Differences in Human Intestinal Microbial Conversion of (-)-Epicatechin to Bioactive Phenolic Compounds.	Liu C, Vervoort J, Beekmann K, Baccaro M, Kamelia L, Wesseling S, Rietjens IMCM.	J Agric Food Chem	10.1021/acs.jafc.0c05890	2020
	Mammalian gut metabolomes mirror microbiome composition and host phylogeny.	Gregor R, Probst M, Eyal S, Aksenov A, Sasson G, Horovitz I, Dorrestein PC, Meijler MM, Mizrahi I.	ISME J	10.1038/s41396-021-01152-0	2022
	Drivers and determinants of strain dynamics following fecal microbiota transplantation.	Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P.	Nat Med	10.1038/s41591-022-01913-0	2022
Pathogenicity	Hypertension Is Associated With Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population.	Silveira-Nunes G, Durso DF, Jr LRAO, Cunha EHM, Maioli TU, Vieira AT, Speziali E, Correa-Oliveira R, Martins-Filho OA, Teixeira-Carvalho A, Franceschi C, Rampelli S, Turroni S, Brigidi P, Faria AMC.	Front Pharmacol	10.3389/fphar.2020.00258	2020
	The secret social lives of African crested rats, Lophiomys imhausi.	Weinstein SB, Malanga KN, Agwanda B, Maldonado JE, Dearing MD.	J Mammal	10.1093/jmammal/gyaa127	2020
	Metabotypes of flavan-3-ol colonic metabolites after cranberry intake: elucidation and statistical approaches.	Mena P, Favari C, Acharjee A, Chernbumroong S, Bresciani L, Curti C, Brighenti F, Heiss C, Rodriguez-Mateos A, Del Rio D.	Eur J Nutr	10.1007/s00394-021-02692-z	2022
Phylogeny	Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans.	Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C, Rotimi CN.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00063	2020
Pathogenicity	Effects of beta-lactam antibiotics and fluoroquinolones on human gut microbiota in relation to Clostridium difficile associated diarrhea.	Knecht H, Neulinger SC, Heinsen FA, Knecht C, Schilhabel A, Schmitz RA, Zimmermann A, dos Santos VM, Ferrer M, Rosenstiel PC, Schreiber S, Friedrichs AK, Ott SJ.	PLoS One	10.1371/journal.pone.0089417	2014
	Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate.	Chu L, Luo X, Zhu T, Cao Y, Zhang L, Deng Z, Gao J.	Nat Commun	10.1038/s41467-022-29188-6	2022
	Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease.	Peterson CT, Sharma V, Uchitel S, Denniston K, Chopra D, Mills PJ, Peterson SN.	J Altern Complement Med	10.1089/acm.2017.0422	2018
	The Role of the Microbiome on the Pathogenesis and Treatment of Colorectal Cancer.	Yu I, Wu R, Tokumaru Y, Terracina KP, Takabe K.	Cancers (Basel)	10.3390/cancers14225685	2022
	The changing epidemiology of VanB Enterococcus faecium in Poland.	Sadowy E, Gawryszewska I, Kuch A, Zabicka D, Hryniewicz W.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-018-3209-7	2018
Pathogenicity	In vitro activities of a new des-fluoro(6) quinolone, garenoxacin, against clinical anaerobic bacteria.	Liebetrau A, Rodloff AC, Behra-Miellet J, Dubreuil L.	Antimicrob Agents Chemother	10.1128/aac.47.11.3667-3671.2003	2003
Metabolism	Exosomes derived from human placental mesenchymal stem cells ameliorate myocardial infarction via anti-inflammation and restoring gut dysbiosis.	Yang L, Wang T, Zhang X, Zhang H, Yan N, Zhang G, Yan R, Li Y, Yu J, He J, Jia S, Wang H.	BMC Cardiovasc Disord	10.1186/s12872-022-02508-w	2022
	The Potential Role of Phytonutrients Flavonoids Influencing Gut Microbiota in the Prophylaxis and Treatment of Inflammatory Bowel Disease.	Wang L, Gao M, Kang G, Huang H.	Front Nutr	10.3389/fnut.2021.798038	2021
Pathogenicity	Convergent and Divergent Age Patterning of Gut Microbiota Diversity in Humans and Nonhuman Primates.	Sang J, Zhuang D, Zhang T, Wu Q, Yu J, Zhang Z.	mSystems	10.1128/msystems.01512-21	2022
	Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis.	Lee MJ, Park YM, Kim B, Tae IH, Kim NE, Pranata M, Kim T, Won S, Kang NJ, Lee YK, Lee DW, Nam MH, Hong SJ, Kim BS.	Gut Microbes	10.1080/19490976.2022.2068366	2022
	Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.	van Dijkhuizen EHP, Del Chierico F, Malattia C, Russo A, Pires Marafon D, Ter Haar NM, Magni-Manzoni S, Vastert SJ, Dallapiccola B, Prakken B, Martini A, De Benedetti F, Putignani L, Model Driven Paediatric European Digital Repository Consortium.	Arthritis Rheumatol	10.1002/art.40827	2019
	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	OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement.	Battenberg K, Lee EK, Chiu JC, Berry AM, Potter D.	BMC Bioinformatics	10.1186/s12859-017-1726-5	2017
	New Avenues for Parkinson's Disease Therapeutics: Disease-Modifying Strategies Based on the Gut Microbiota.	Lorente-Picon M, Laguna A.	Biomolecules	10.3390/biom11030433	2021
Metabolism	Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.	Haran JP, Bhattarai SK, Foley SE, Dutta P, Ward DV, Bucci V, McCormick BA.	mBio	10.1128/mbio.00632-19	2019
	Crosstalk between Gut Microbiota and Host Immunity: Impact on Inflammation and Immunotherapy.	Campbell C, Kandalgaonkar MR, Golonka RM, Yeoh BS, Vijay-Kumar M, Saha P.	Biomedicines	10.3390/biomedicines11020294	2023
Metabolism	Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters.	Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, Chihara N, Tomita A, Sato W, Kim SW, Morita H, Hattori M, Yamamura T.	PLoS One	10.1371/journal.pone.0137429	2015
	An untargeted fecal and urine metabolomics analysis of the interplay between the gut microbiome, diet and human metabolism in Indian and Chinese adults.	Jain A, Li XH, Chen WN.	Sci Rep	10.1038/s41598-019-45640-y	2019
Enzymology	Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles.	Altun O, Almuhayawi M, Ullberg M, Ozenci V.	J Clin Microbiol	10.1128/jcm.01835-13	2013
Metabolism	An atypical phosphodiesterase capable of degrading haloalkyl phosphate diesters from Sphingobium sp. strain TCM1.	Abe K, Mukai N, Morooka Y, Makino T, Oshima K, Takahashi S, Kera Y.	Sci Rep	10.1038/s41598-017-03142-9	2017
	Molecular characterization of vanB elements in naturally occurring gut anaerobes.	Ballard SA, Pertile KK, Lim M, Johnson PD, Grayson ML.	Antimicrob Agents Chemother	10.1128/aac.49.5.1688-1694.2005	2005
	Bile Acid-Related Regulation of Mucosal Inflammation and Intestinal Motility: From Pathogenesis to Therapeutic Application in IBD and Microscopic Colitis.	Di Vincenzo F, Puca P, Lopetuso LR, Petito V, Masi L, Bartocci B, Murgiano M, De Felice M, Petronio L, Gasbarrini A, Scaldaferri F.	Nutrients	10.3390/nu14132664	2022
Metabolism	Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts.	Garcia-Bayona L, Coyne MJ, Hantman N, Montero-Llopis P, Von SS, Ito T, Malamy MH, Basler M, Barquera B, Comstock LE.	Proc Natl Acad Sci U S A	10.1073/pnas.2009556117	2020
	Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts.	Luo G, Li B, Yang C, Wang Y, Bian X, Li W, Liu F, Huo G.	Front Microbiol	10.3389/fmicb.2019.00712	2019
	Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis.	Colquhoun C, Duncan M, Grant G.	Diseases	10.3390/diseases8020013	2020
	Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants.	Kim AH, Armah G, Dennis F, Wang L, Rodgers R, Droit L, Baldridge MT, Handley SA, Harris VC.	Cell Host Microbe	10.1016/j.chom.2021.12.002	2022
	DNA sequence repeats identify numerous Type I restriction-modification systems that are potential epigenetic regulators controlling phase-variable regulons; phasevarions.	Atack JM, Guo C, Yang L, Zhou Y, Jennings MP.	FASEB J	10.1096/fj.201901536rr	2020
	Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.	Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK, Baranzini SE.	Proc Natl Acad Sci U S A	10.1073/pnas.1711235114	2017
Phylogeny	Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.	Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M, Lipkin WI.	Microbiome	10.1186/s40168-017-0261-y	2017
Metabolism	Biogeography of microbial bile acid transformations along the murine gut.	Marion S, Desharnais L, Studer N, Dong Y, Notter MD, Poudel S, Menin L, Janowczyk A, Hettich RL, Hapfelmeier S, Bernier-Latmani R.	J Lipid Res	10.1194/jlr.ra120001021	2020
Metabolism	Subclinical atherosclerosis is linked to small intestinal bacterial overgrowth via vitamin K2-dependent mechanisms.	Ponziani FR, Pompili M, Di Stasio E, Zocco MA, Gasbarrini A, Gasbarrini A, Flore R.	World J Gastroenterol	10.3748/wjg.v23.i7.1241	2017
Pathogenicity	Triclosan and prescription antibiotic exposures and enterolactone production in adults.	Adgent MA, Rogan WJ.	Environ Res	10.1016/j.envres.2015.06.017	2015
	Gut Microbiome of Patients With Breast Cancer in Vietnam.	Nguyen SM, Tran HTT, Long J, Shrubsole MJ, Cai H, Yang Y, Nguyen LM, Nguyen GH, Nguyen CV, Ta TV, Wu J, Cai Q, Zheng W, Tran TV, Shu XO.	JCO Glob Oncol	10.1200/go.23.00234	2024
Metabolism	Commensal Gut Bacteria Convert the Immunosuppressant Tacrolimus to Less Potent Metabolites.	Guo Y, Crnkovic CM, Won KJ, Yang X, Lee JR, Orjala J, Lee H, Jeong H.	Drug Metab Dispos	10.1124/dmd.118.084772	2019
	Human gut microbiome: Therapeutic opportunities for metabolic syndrome-Hype or hope?	Horvath A, Zukauskaite K, Hazia O, Balazs I, Stadlbauer V.	Endocrinol Diabetes Metab	10.1002/edm2.436	2024
	Negative interactions determine Clostridioides difficile growth in synthetic human gut communities.	Hromada S, Qian Y, Jacobson TB, Clark RL, Watson L, Safdar N, Amador-Noguez D, Venturelli OS.	Mol Syst Biol	10.15252/msb.202110355	2021
	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	Antibiotics may increase triazine herbicide exposure risk via disturbing gut microbiota.	Zhan J, Liang Y, Liu D, Ma X, Li P, Liu C, Liu X, Wang P, Zhou Z.	Microbiome	10.1186/s40168-018-0602-5	2018
Pathogenicity	The impact of Bacillus subtilis DSM 32315 on the pathology, performance, and intestinal microbiome of broiler chickens in a necrotic enteritis challenge.	Whelan RA, Doranalli K, Rinttila T, Vienola K, Jurgens G, Apajalahti J.	Poult Sci	10.3382/ps/pey500	2019
Metabolism	Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease.	Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ, Arnold M, Kastenmuller G, Griffiths WJ, Thiele I, Alzheimer's Disease Metabolomics Consortium, Kaddurah-Daouk R, Price ND.	Cell Rep Med	10.1016/j.xcrm.2020.100138	2020
	Planktonic and Sessile Artificial Colonic Microbiota Harbor Distinct Composition and Reestablish Differently upon Frozen and Freeze-Dried Long-Term Storage.	Bircher L, Schwab C, Geirnaert A, Greppi A, Lacroix C.	mSystems	10.1128/msystems.00521-19	2020
Pathogenicity	Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review.	Yang Q, Liang Q, Balakrishnan B, Belobrajdic DP, Feng QJ, Zhang W.	Nutrients	10.3390/nu12020381	2020
	A P4 Medicine Perspective of Gut Microbiota and Prediabetes: Systems Analysis and Personalized Intervention.	Huang Q, Fang Q, Hu Z.	J Transl Int Med	10.2478/jtim-2020-0020	2020
	Long-term safety of certolizumab pegol in plaque psoriasis: pooled analysis over 3 years from three phase III, randomized, placebo-controlled studies.	Blauvelt A, Paul C, van de Kerkhof P, Warren RB, Gottlieb AB, Langley RG, Brock F, Arendt C, Boehnlein M, Lebwohl M, Reich K.	Br J Dermatol	10.1111/bjd.19314	2021
	Time-, Sex-, and Dose-Dependent Alterations of the Gut Microbiota by Consumption of Dietary Daikenchuto (TU-100).	Miyoshi J, Nobutani K, Musch MW, Ringus DL, Hubert NA, Yamamoto M, Kase Y, Nishiyama M, Chang EB.	Evid Based Complement Alternat Med	10.1155/2018/7415975	2018
Enzymology	Cystathionine beta-synthase (CBS) domains confer multiple forms of Mg2+-dependent cooperativity to family II pyrophosphatases.	Salminen A, Anashkin VA, Lahti M, Tuominen HK, Lahti R, Baykov AA.	J Biol Chem	10.1074/jbc.m114.589473	2014
Pathogenicity	Dysbiosis of the gut microbiota in disease.	Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ.	Microb Ecol Health Dis	10.3402/mehd.v26.26191	2015
Phylogeny	The role of the gut microbiome in the association between habitual anthocyanin intake and visceral abdominal fat in population-level analysis.	Jennings A, Koch M, Jensen MK, Bang C, Kassubek J, Muller HP, Nothlings U, Franke A, Lieb W, Cassidy A.	Am J Clin Nutr	10.1093/ajcn/nqz299	2020
	Human Microbiota and Breast Cancer-Is There Any Relevant Link?-A Literature Review and New Horizons Toward Personalised Medicine.	Alpuim Costa D, Nobre JG, Batista MV, Ribeiro C, Calle C, Cortes A, Marhold M, Negreiros I, Borralho P, Brito M, Cortes J, Braga SA, Costa L.	Front Microbiol	10.3389/fmicb.2021.584332	2021
Genetics	Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium.	Mu A, Carter GP, Li L, Isles NS, Vrbanac AF, Morton JT, Jarmusch AK, De Souza DP, Narayana VK, Kanojia K, Nijagal B, McConville MJ, Knight R, Howden BP, Stinear TP.	mSystems	10.1128/msystems.00452-20	2020
Genetics	Metatranscriptome of human faecal microbial communities in a cohort of adult men.	Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C.	Nat Microbiol	10.1038/s41564-017-0084-4	2018
Metabolism	Use of Shotgun Metagenomics and Metabolomics to Evaluate the Impact of Glyphosate or Roundup MON 52276 on the Gut Microbiota and Serum Metabolome of Sprague-Dawley Rats.	Mesnage R, Teixeira M, Mandrioli D, Falcioni L, Ducarmon QR, Zwittink RD, Mazzacuva F, Caldwell A, Halket J, Amiel C, Panoff JM, Belpoggi F, Antoniou MN.	Environ Health Perspect	10.1289/ehp6990	2021
	Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation.	Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR, Prendergast AJ.	Sci Transl Med	10.1126/scitranslmed.aav0537	2019
	Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.	Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.04.010	2017
	'RA and the microbiome: do host genetic factors provide the link?	Wells PM, Williams FMK, Matey-Hernandez ML, Menni C, Steves CJ.	J Autoimmun	10.1016/j.jaut.2019.02.004	2019
Metabolism	Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire.	Zhang C, Bjorkman A, Cai K, Liu G, Wang C, Li Y, Xia H, Sun L, Kristiansen K, Wang J, Han J, Hammarstrom L, Pan-Hammarstrom Q.	Front Immunol	10.3389/fimmu.2018.00908	2018
	Strains of the Propionibacterium acnes type III lineage are associated with the skin condition progressive macular hypomelanosis.	Barnard E, Liu J, Yankova E, Cavalcanti SM, Magalhaes M, Li H, Patrick S, McDowell A.	Sci Rep	10.1038/srep31968	2016
Pathogenicity	The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.	Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterstrom CK, Allander T, Andersson B, Borenstein E, Dahlin M, Prast-Nielsen S.	NPJ Biofilms Microbiomes	10.1038/s41522-018-0073-2	2019
	Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota.	Shimizu H, Benno Y.	Microbiol Immunol	10.1111/1348-0421.12332	2015
	Gestational Diabetes Mellitus Is Associated with Reduced Dynamics of Gut Microbiota during the First Half of Pregnancy.	Zheng W, Xu Q, Huang W, Yan Q, Chen Y, Zhang L, Tian Z, Liu T, Yuan X, Liu C, Luo J, Guo C, Song W, Zhang L, Liang X, Qin H, Li G.	mSystems	10.1128/msystems.00109-20	2020
Metabolism	A microbial transporter of the dietary antioxidant ergothioneine.	Dumitrescu DG, Gordon EM, Kovalyova Y, Seminara AB, Duncan-Lowey B, Forster ER, Zhou W, Booth CJ, Shen A, Kranzusch PJ, Hatzios SK.	Cell	10.1016/j.cell.2022.10.008	2022
Metabolism	Short-chain ketone production by engineered polyketide synthases in Streptomyces albus.	Yuzawa S, Mirsiaghi M, Jocic R, Fujii T, Masson F, Benites VT, Baidoo EEK, Sundstrom E, Tanjore D, Pray TR, George A, Davis RW, Gladden JM, Simmons BA, Katz L, Keasling JD.	Nat Commun	10.1038/s41467-018-07040-0	2018
Pathogenicity	Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.	Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2018.09.009	2018
	Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.	Ianiro G, Puncochar M, Karcher N, Porcari S, Armanini F, Asnicar F, Beghini F, Blanco-Miguez A, Cumbo F, Manghi P, Pinto F, Pinto F, Masucci L, Quaranta G, De Giorgi S, Sciume GD, Bibbo S, Del Chierico F, Putignani L, Sanguinetti M, Gasbarrini A, Valles-Colomer M, Cammarota G, Segata N.	Nat Med	10.1038/s41591-022-01964-3	2022
	From obesity through gut microbiota to cardiovascular diseases: a dangerous journey.	Marzullo P, Di Renzo L, Pugliese G, De Siena M, Barrea L, Muscogiuri G, Colao A, Savastano S, Obesity Programs of nutrition, Education, Research and Assessment (OPERA) Group.	Int J Obes Suppl	10.1038/s41367-020-0017-1	2020
	Biological Aging and the Human Gut Microbiota.	Maffei VJ, Kim S, Blanchard E, Luo M, Jazwinski SM, Taylor CM, Welsh DA.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glx042	2017
Enzymology	Identification and characterization of a 20beta-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058.	Devendran S, Mendez-Garcia C, Ridlon JM.	J Lipid Res	10.1194/jlr.m074914	2017
	Anaerobes and bacterial vaginosis in pregnancy: virulence factors contributing to vaginal colonisation.	Africa CW, Nel J, Stemmet M.	Int J Environ Res Public Health	10.3390/ijerph110706979	2014
Genetics	Re-evaluation of Diadenosine Tetraphosphate (Ap4A) From a Stress Metabolite to Bona Fide Secondary Messenger.	Ferguson F, McLennan AG, Urbaniak MD, Jones NJ, Copeland NA.	Front Mol Biosci	10.3389/fmolb.2020.606807	2020
Phylogeny	Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria.	Lee EH, Degener JE, Welling GW, Veloo AC.	J Clin Microbiol	10.1128/jcm.02166-10	2011
	Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.	Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, Gonzalez A, Midtvedt T, Eggesbo M.	Microbiome	10.1186/s40168-019-0645-2	2019
Enzymology	Succinivibrionaceae is dominant family in fecal microbiota of Behçet's Syndrome patients with uveitis.	Tecer D, Gogus F, Kalkanci A, Erdogan M, Hasanreisoglu M, Ergin C, Karakan T, Kozan R, Coban S, Diker KS.	PLoS One	10.1371/journal.pone.0241691	2020
Metabolism	Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics.	Carmody RN, Turnbaugh PJ.	J Clin Invest	10.1172/jci72335	2014
Enzymology	Local bacteria affect the efficacy of chemotherapeutic drugs.	Lehouritis P, Cummins J, Stanton M, Murphy CT, McCarthy FO, Reid G, Urbaniak C, Byrne WL, Tangney M.	Sci Rep	10.1038/srep14554	2015
Metabolism	Enterolignan-producing phenotypes are associated with increased gut microbial diversity and altered composition in premenopausal women in the United States.	Hullar MA, Lancaster SM, Li F, Tseng E, Beer K, Atkinson C, Wahala K, Copeland WK, Randolph TW, Newton KM, Lampe JW.	Cancer Epidemiol Biomarkers Prev	10.1158/1055-9965.epi-14-0262	2015
Enzymology	Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating.	Cuiv PO, Smith WJ, Pottenger S, Burman S, Shanahan ER, Morrison M.	Sci Rep	10.1038/srep13282	2015
Enzymology	Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces.	Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R.	Appl Environ Microbiol	10.1128/aem.70.12.7220-7228.2004	2004
	Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics.	Hromada S, Venturelli OS.	PLoS Biol	10.1371/journal.pbio.3002100	2023
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
	Microbiota-Dependent Involvement of Th17 Cells in Murine Models of Inflammatory Arthritis.	Evans-Marin H, Rogier R, Koralov SB, Manasson J, Roeleveld D, van der Kraan PM, Scher JU, Koenders MI, Abdollahi-Roodsaz S.	Arthritis Rheumatol	10.1002/art.40657	2018
	Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia.	Liu F, Ling Z, Xiao Y, Yang Q, Wang B, Zheng L, Jiang P, Li L, Wang W.	Front Physiol	10.3389/fphys.2017.00126	2017
	A microbial signature for Crohn's disease.	Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, Vermeire S, Sokol H, Guarner F, Manichanh C.	Gut	10.1136/gutjnl-2016-313235	2017
	Helicobacter pylori antibiotic eradication coupled with a chemically defined diet in INS-GAS mice triggers dysbiosis and vitamin K deficiency resulting in gastric hemorrhage.	Quinn L, Sheh A, Ellis JL, Smith DE, Booth SL, Fu X, Muthupalani S, Ge Z, Puglisi DA, Wang TC, Gonda TA, Holcombe H, Fox JG.	Gut Microbes	10.1080/19490976.2019.1710092	2020
Pathogenicity	Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.	Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE, Hanson MR.	Microbiome	10.1186/s40168-016-0171-4	2016
	Alteration of the intestinal microbiome characterizes preclinical inflammatory arthritis in mice and its modulation attenuates established arthritis.	Rogier R, Evans-Marin H, Manasson J, van der Kraan PM, Walgreen B, Helsen MM, van den Bersselaar LA, van de Loo FA, van Lent PL, Abramson SB, van den Berg WB, Koenders MI, Scher JU, Abdollahi-Roodsaz S.	Sci Rep	10.1038/s41598-017-15802-x	2017
Enzymology	Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency.	Jacobs JP, Lin L, Goudarzi M, Ruegger P, McGovern DP, Fornace AJ, Borneman J, Xia L, Braun J.	Gut Microbes	10.1080/19490976.2016.1257469	2017
Metabolism	16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.	Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.	PLoS One	10.1371/journal.pone.0213869	2019
Phylogeny	High mortality associated with Catabacter hongkongensis bacteremia.	Lau SK, Fan RY, Lo HW, Ng RH, Wong SS, Li IW, Wu AK, Ng KH, Tseung S, Lee RA, Fung KS, Que TL, Yuen KY, Woo PC.	J Clin Microbiol	10.1128/jcm.00128-12	2012
	Transfer of vancomycin resistance transposon Tn1549 from Clostridium symbiosum to Enterococcus spp. in the gut of gnotobiotic mice.	Launay A, Ballard SA, Johnson PD, Grayson ML, Lambert T.	Antimicrob Agents Chemother	10.1128/aac.50.3.1054-1062.2006	2006
	Multivariate Analysis of Fecal Metabolites from Children with Autism Spectrum Disorder and Gastrointestinal Symptoms before and after Microbiota Transfer Therapy.	Qureshi F, Adams J, Hanagan K, Kang DW, Krajmalnik-Brown R, Hahn J.	J Pers Med	10.3390/jpm10040152	2020
	Gut Microbiota, Blood Metabolites, and Spleen Immunity in Broiler Chickens Fed Berry Pomaces and Phenolic-Enriched Extractives.	Das Q, Islam MR, Lepp D, Tang J, Yin X, Mats L, Liu H, Ross K, Kennes YM, Yacini H, Warriner K, Marcone MF, Diarra MS.	Front Vet Sci	10.3389/fvets.2020.00150	2020
Metabolism	Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.	Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar S, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A.	Nat Microbiol	10.1038/s41564-021-00917-9	2021
Pathogenicity	First comprehensive evaluation of the M.I.C. evaluator device compared to Etest and CLSI reference dilution methods for antimicrobial susceptibility testing of clinical strains of anaerobes and other fastidious bacterial species.	Rennie RP, Turnbull L, Brosnikoff C, Cloke J.	J Clin Microbiol	10.1128/jcm.05397-11	2012
Metabolism	Ammonia production by human faecal bacteria, and the enumeration, isolation and characterization of bacteria capable of growth on peptides and amino acids.	Richardson AJ, McKain N, Wallace RJ.	BMC Microbiol	10.1186/1471-2180-13-6	2013
Pathogenicity	Drug-gut microbiota interactions: implications for neuropharmacology.	Walsh J, Griffin BT, Clarke G, Hyland NP.	Br J Pharmacol	10.1111/bph.14366	2018
Metabolism	Design of synthetic human gut microbiome assembly and butyrate production.	Clark RL, Connors BM, Stevenson DM, Hromada SE, Hamilton JJ, Amador-Noguez D, Venturelli OS.	Nat Commun	10.1038/s41467-021-22938-y	2021
Phylogeny	Accurate genome relative abundance estimation for closely related species in a metagenomic sample.	Sohn MB, An L, Pookhao N, Li Q.	BMC Bioinformatics	10.1186/1471-2105-15-242	2014
Metabolism	l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans.	Koeth RA, Lam-Galvez BR, Kirsop J, Wang Z, Levison BS, Gu X, Copeland MF, Bartlett D, Cody DB, Dai HJ, Culley MK, Li XS, Fu X, Wu Y, Li L, DiDonato JA, Tang WHW, Garcia-Garcia JC, Hazen SL.	J Clin Invest	10.1172/jci94601	2019
	Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches.	Duenas M, Cueva C, Munoz-Gonzalez I, Jimenez-Giron A, Sanchez-Patan F, Santos-Buelga C, Moreno-Arribas MV, Bartolome B.	Antioxidants (Basel)	10.3390/antiox4010001	2015
Metabolism	Understanding the apothecaries within: the necessity of a systematic approach for defining the chemical output of the human microbiome.	Beebe K, Sampey B, Watkins SM, Milburn M, Eckhart AD.	Clin Transl Sci	10.1111/cts.12131	2014
Genetics	The gut microbiome in atherosclerotic cardiovascular disease.	Jie Z, Xia H, Zhong SL, Feng Q, Li S, Liang S, Zhong H, Liu Z, Gao Y, Zhao H, Zhang D, Su Z, Fang Z, Lan Z, Li J, Xiao L, Li J, Li R, Li X, Li F, Ren H, Huang Y, Peng Y, Li G, Wen B, Dong B, Chen JY, Geng QS, Zhang ZW, Yang H, Wang J, Wang J, Zhang X, Madsen L, Brix S, Ning G, Xu X, Liu X, Hou Y, Jia H, He K, Kristiansen K.	Nat Commun	10.1038/s41467-017-00900-1	2017
Metabolism	RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice.	Fu ZD, Selwyn FP, Cui JY, Klaassen CD.	Drug Metab Dispos	10.1124/dmd.117.077313	2017
	Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome.	Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J, Spector TD, Jia H.	Cell Syst	10.1016/j.cels.2016.10.004	2016
Metabolism	Chemical transformation of xenobiotics by the human gut microbiota.	Koppel N, Maini Rekdal V, Balskus EP.	Science	10.1126/science.aag2770	2017
	RNA-Seq Quantification of Hepatic Drug Processing Genes in Germ-Free Mice.	Selwyn FP, Cui JY, Klaassen CD.	Drug Metab Dispos	10.1124/dmd.115.063545	2015
	Development of a microarray-based tool to characterize vaginal bacterial fluctuations and application to a novel antibiotic treatment for bacterial vaginosis.	Cruciani F, Biagi E, Severgnini M, Consolandi C, Calanni F, Donders G, Brigidi P, Vitali B.	Antimicrob Agents Chemother	10.1128/aac.00225-15	2015
Genetics	Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication.	Suzuki S, Yamada T.	PeerJ	10.7717/peerj.8722	2020
Phylogeny	Cooking shapes the structure and function of the gut microbiome.	Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ.	Nat Microbiol	10.1038/s41564-019-0569-4	2019
	Metagenomic profiling of known and unknown microbes with microbeGPS.	Lindner MS, Renard BY.	PLoS One	10.1371/journal.pone.0117711	2015
Pathogenicity	Antibacterial activity of eravacycline (TP-434), a novel fluorocycline, against hospital and community pathogens.	Sutcliffe JA, O'Brien W, Fyfe C, Grossman TH.	Antimicrob Agents Chemother	10.1128/aac.01288-13	2013
Enzymology	A roadmap for metagenomic enzyme discovery.	Robinson SL, Piel J, Sunagawa S.	Nat Prod Rep	10.1039/d1np00006c	2021
	The Gut Microbiota in Multiple Sclerosis: An Overview of Clinical Trials.	Schepici G, Silvestro S, Bramanti P, Mazzon E.	Cell Transplant	10.1177/0963689719873890	2019
Metabolism	Ruminal Prevotella spp. may play an important role in the conversion of plant lignans into human health beneficial antioxidants.	Schogor AL, Huws SA, Santos GT, Scollan ND, Hauck BD, Winters AL, Kim EJ, Petit HV.	PLoS One	10.1371/journal.pone.0087949	2014
Metabolism	In vitro and in vivo characterization of Clostridium scindens bile acid transformations.	Marion S, Studer N, Desharnais L, Menin L, Escrig S, Meibom A, Hapfelmeier S, Bernier-Latmani R.	Gut Microbes	10.1080/19490976.2018.1549420	2019
	An insight into gut microbiota and its functionalities.	Adak A, Khan MR.	Cell Mol Life Sci	10.1007/s00018-018-2943-4	2019
	Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease.	Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, Degnan PH, Hu J, Peter I, Zhang W, Ruggiero E, Cho JH, Goodman AL, Flavell RA.	Cell	10.1016/j.cell.2014.08.006	2014
Phylogeny	High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray.	Paliy O, Kenche H, Abernathy F, Michail S.	Appl Environ Microbiol	10.1128/aem.02764-08	2009
	Alignment-free visualization of metagenomic data by nonlinear dimension reduction.	Laczny CC, Pinel N, Vlassis N, Wilmes P.	Sci Rep	10.1038/srep04516	2014
Metabolism	Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters.	Lecomte V, Kaakoush NO, Maloney CA, Raipuria M, Huinao KD, Mitchell HM, Morris MJ.	PLoS One	10.1371/journal.pone.0126931	2015
Metabolism	A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont.	Liou CS, Sirk SJ, Diaz CAC, Klein AP, Fischer CR, Higginbottom SK, Erez A, Donia MS, Sonnenburg JL, Sattely ES.	Cell	10.1016/j.cell.2020.01.023	2020
	The Association Between Intestinal Bacteria and Allergic Diseases-Cause or Consequence?	Han P, Gu JQ, Li LS, Wang XY, Wang HT, Wang Y, Chang C, Sun JL.	Front Cell Infect Microbiol	10.3389/fcimb.2021.650893	2021
Metabolism	Mapping human microbiome drug metabolism by gut bacteria and their genes.	Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL.	Nature	10.1038/s41586-019-1291-3	2019
Phylogeny	Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria.	Kawase T, Saito A, Sato T, Kanai R, Fujii T, Nikaidou N, Miyashita K, Watanabe T.	Appl Environ Microbiol	10.1128/aem.70.2.1135-1144.2004	2004
Metabolism	Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans.	Clavel T, Henderson G, Alpert CA, Philippe C, Rigottier-Gois L, Dore J, Blaut M.	Appl Environ Microbiol	10.1128/aem.71.10.6077-6085.2005	2005
Pathogenicity	Microbiota and Colorectal Cancer: From Gut to Bedside.	Silva M, Brunner V, Tschurtschenthaler M.	Front Pharmacol	10.3389/fphar.2021.760280	2021
	High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter.	Ray S, Berry SP, Wilson EA, Zhang CH, Shekhar M, Singharoy A, Gaudet R.	Elife	10.7554/elife.84006	2023
Metabolism	Targeting gut microbiota for precision medicine: Focusing on the efficacy and toxicity of drugs.	Feng W, Liu J, Ao H, Yue S, Peng C.	Theranostics	10.7150/thno.47289	2020
Pathogenicity	In vitro susceptibility testing of Dientamoeba fragilis.	Nagata N, Marriott D, Harkness J, Ellis JT, Stark D.	Antimicrob Agents Chemother	10.1128/aac.05125-11	2012
Genetics	Experimental design and quantitative analysis of microbial community multiomics.	Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C.	Genome Biol	10.1186/s13059-017-1359-z	2017
Metabolism	The variable subdomain of Escherichia coli SecA functions to regulate SecA ATPase activity and ADP release.	Das S, Grady LM, Michtavy J, Zhou Y, Cohan FM, Hingorani MM, Oliver DB.	J Bacteriol	10.1128/jb.00039-12	2012
Enzymology	Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation.	Reck M, Tomasch J, Deng Z, Jarek M, Husemann P, Wagner-Dobler I, COMBACTE Consortium.	BMC Genomics	10.1186/s12864-015-1694-y	2015
Pathogenicity	Personalized Mapping of Drug Metabolism by the Human Gut Microbiome.	Javdan B, Lopez JG, Chankhamjon P, Lee YJ, Hull R, Wu Q, Wang X, Chatterjee S, Donia MS.	Cell	10.1016/j.cell.2020.05.001	2020
	Changes in human fecal microbiota due to chemotherapy analyzed by TaqMan-PCR, 454 sequencing and PCR-DGGE fingerprinting.	Zwielehner J, Lassl C, Hippe B, Pointner A, Switzeny OJ, Remely M, Kitzweger E, Ruckser R, Haslberger AG.	PLoS One	10.1371/journal.pone.0028654	2011
Metabolism	Colonization-induced host-gut microbial metabolic interaction.	Claus SP, Ellero SL, Berger B, Krause L, Bruttin A, Molina J, Paris A, Want EJ, de Waziers I, Cloarec O, Richards SE, Wang Y, Dumas ME, Ross A, Rezzi S, Kochhar S, Van Bladeren P, Lindon JC, Holmes E, Nicholson JK.	mBio	10.1128/mbio.00271-10	2011
Metabolism	Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas.	Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, Barre A, Avenaud P, Jacob D, Couloux A, Barbe V, de Daruvar A, Blanchard A, Bebear C.	PLoS Genet	10.1371/journal.pgen.1000677	2009
Enzymology	Comparison of the BD GeneOhm VanR assay to culture for identification of vancomycin-resistant enterococci in rectal and stool specimens.	Stamper PD, Cai M, Lema C, Eskey K, Carroll KC.	J Clin Microbiol	10.1128/jcm.01458-07	2007
Phylogeny	The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young.	Bian G, Gloor GB, Gong A, Jia C, Zhang W, Hu J, Zhang H, Zhang Y, Zhou Z, Zhang J, Burton JP, Reid G, Xiao Y, Zeng Q, Yang K, Li J.	mSphere	10.1128/msphere.00327-17	2017
Enzymology	Diet rapidly and reproducibly alters the human gut microbiome.	David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ.	Nature	10.1038/nature12820	2014
Metabolism	Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness.	Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV.	Nature	10.1038/nature13823	2014
	The gut microbiota and host health: a new clinical frontier.	Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A.	Gut	10.1136/gutjnl-2015-309990	2016
Metabolism	First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.	Muller B, Sun L, Schnurer A.	Microbiologyopen	10.1002/mbo3.50	2013
Metabolism	Characterization of the serpin-encoding gene of Bifidobacterium breve 210B.	Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02938-09	2010
	Systems biology of host-microbe metabolomics.	Heinken A, Thiele I.	Wiley Interdiscip Rev Syst Biol Med	10.1002/wsbm.1301	2015
	Impact of Gut Microbiota Composition on Onset and Progression of Chronic Non-Communicable Diseases.	Noce A, Marrone G, Di Daniele F, Ottaviani E, Wilson Jones G, Bernini R, Romani A, Rovella V.	Nutrients	10.3390/nu11051073	2019
Metabolism	Oxalate-degrading activity in Bifidobacterium animalis subsp. lactis: impact of acidic conditions on the transcriptional levels of the oxalyl coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes.	Turroni S, Bendazzoli C, Dipalo SC, Candela M, Vitali B, Gotti R, Brigidi P.	Appl Environ Microbiol	10.1128/aem.00844-10	2010
Phylogeny	Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.	Schwiertz A, Le Blay G, Blaut M.	Appl Environ Microbiol	10.1128/aem.66.1.375-382.2000	2000
Metabolism	Bidirectional interactions between indomethacin and the murine intestinal microbiota.	Liang X, Bittinger K, Li X, Abernethy DR, Bushman FD, FitzGerald GA.	Elife	10.7554/elife.08973	2015
	The first 1000 cultured species of the human gastrointestinal microbiota.	Rajilic-Stojanovic M, de Vos WM.	FEMS Microbiol Rev	10.1111/1574-6976.12075	2014
	Mediterranean Diet: Prevention of Colorectal Cancer.	Donovan MG, Selmin OI, Doetschman TC, Romagnolo DF.	Front Nutr	10.3389/fnut.2017.00059	2017
Phylogeny	Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited.	Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Moller K.	Appl Environ Microbiol	10.1128/aem.68.2.673-690.2002	2002
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Pathogenicity	The Gut Microbiota Links Dietary Polyphenols With Management of Psychiatric Mood Disorders.	Westfall S, Pasinetti GM.	Front Neurosci	10.3389/fnins.2019.01196	2019
	Bidirectional Interactions between Green Tea (GT) Polyphenols and Human Gut Bacteria.	Choi SR, Lee H, Singh D, Singh D, Cho D, Chung JO, Roh JH, Kim WG, Lee CH.	J Microbiol Biotechnol	10.4014/jmb.2306.06014	2023
Phylogeny	Eggerthella timonensis sp. nov, a new species isolated from the stool sample of a pygmy female.	Bilen M, Fonkou MDM, Tomei E, Armstrong N, Bittar F, Lagier JC, Daoud Z, Fournier PE, Raoult D, Cadoret F	Microbiologyopen	10.1002/mbo3.575	2018
Metabolism	Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243(T).	Harris SC, Devendran S, Mendez-Garcia C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JM	Gut Microbes	10.1080/19490976.2018.1458180	2018
Metabolism	Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme.	Kumar K, Jaiswal SK, Dhoke GV, Srivastava GN, Sharma AK, Sharma VK	J Cell Biochem	10.1002/jcb.26638	2018
Metabolism	Bioconversion of (-)-epicatechin, (+)-epicatechin, (-)-catechin, and (+)-catechin by (-)-epigallocatechin-metabolizing bacteria.	Takagaki A, Nanjo F	Biol Pharm Bull	10.1248/bpb.b14-00813	2015
Phylogeny	Isolation and characterization of rat intestinal bacteria involved in biotransformation of (-)-epigallocatechin.	Takagaki A, Kato Y, Nanjo F	Arch Microbiol	10.1007/s00203-014-1006-y	2014
Phylogeny	Isolation and characterization of novel S-equol-producing bacteria from brines of stinky tofu, a traditional fermented soy food in Taiwan.	Abiru Y, Ueno T, Uchiyama S	Int J Food Sci Nutr	10.3109/09637486.2013.816936	2013
Genetics	Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).	Saunders E, Pukall R, Abt B, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C	Stand Genomic Sci	10.4056/sigs.33592	2009
Cultivation	Production of antagonistic substance by Eikenella corrodens isolated from the oral cavity of human beings with and without periodontal disease.	Apolonio AC, Carvalho MA, Ribas RN, Sousa-Gaia LG, Santos KV, Lana MA, Nicoli JR, Farias LM	J Appl Microbiol	10.1111/j.1365-2672.2006.03211.x	2007
Phylogeny	Production of equol from daidzein by gram-positive rod-shaped bacterium isolated from rat intestine.	Minamida K, Tanaka M, Abe A, Sone T, Tomita F, Hara H, Asano K	J Biosci Bioeng	10.1263/jbb.102.247	2006
Phylogeny	Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov.	Kageyama A, Benno Y, Nakase T	Int J Syst Bacteriol	10.1099/00207713-49-4-1725	1999
Metabolism	Experimental root canal infections in conventional and germ-free mice.	Sobrinho AP, Barros MH, Nicoli JR, Carvalho MA, Farias LM, Bambirra EA, Bahia MG, Vieira EC	J Endod	10.1016/S0099-2399(98)80021-6	1998
Metabolism	Reduction of digoxin to 20R-dihydrodigoxin by cultures of Eubacterium lentum.	Robertson LW, Chandrasekaran A, Reuning RH, Hui J, Rawal BD	Appl Environ Microbiol	10.1128/aem.51.6.1300-1303.1986	1986
Metabolism	Bile salt 3 alpha- and 12 alpha-hydroxysteroid dehydrogenases from Eubacterium lentum and related organisms.	MacDonald IA, Jellett JF, Mahony DE, Holdeman LV	Appl Environ Microbiol	10.1128/aem.37.5.992-1000.1979	1979
Pathogenicity	Immuno-electron microscopic localization of a choriogonadotropin-like antigen in cancer-associated bacteria.	Slifkin M, Pardo M, Pouchet-Melvin GR, Acevedo HF	Oncology	10.1159/000225343	1979
Stress	Eggerthella lenta DSM 2243 Alleviates Bile Acid Stress Response in Clostridium ramosum and Anaerostipes caccae by Transformation of Bile Acids.	Pedersen KJ, Haange SB, Zizalova K, Viehof A, Clavel T, Lenicek M, Engelmann B, Wick LY, Schaap FG, Jehmlich N, Rolle-Kampczyk U, von Bergen M	Microorganisms	10.3390/microorganisms10102025	2022
Phylogeny	Umbribacter vaginalis gen. nov., sp. nov.: novel bacterium isolated from the human vagina.	Srinivasan S, Strenk SM, Beamer MA, Fiedler TL, Proll S, Acevedo-Oquendo GR, Bonura GM, Nagana Gowda GA, Raftery D, Hillier SL, Fredricks DN.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006931	2025
Genetics	Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut.	Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD, Tall ML, Michelle C, Yasir M, Ibraheem Azhar E, Bibi F, Bittar F, Jiman-Fatani AA, Daoud Z, Cadoret F, Fournier PE, Edouard S.	Microbiologyopen	10.1002/mbo3.758	2019
Genetics	Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.	Padmanabhan R, Dubourg G, Jean-Christophe lagier, Nguyen TT, Couderc C, Rossi-Tamisier M, Caputo A, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.5399696	2014
	Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.	Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O'Toole PW, Fardeau ML, Ollivier B, Brugere JF.	Microorganisms	10.3390/microorganisms11112794	2023
Phylogeny	Catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from Hong Kong and Canada.	Lau SK, McNabb A, Woo GK, Hoang L, Fung AM, Chung LM, Woo PC, Yuen KY.	J Clin Microbiol	10.1128/jcm.01831-06	2007
Phylogeny	Actinomyces cardiffensis sp. nov. from human clinical sources.	Hall V, Collins MD, Hutson R, Falsen E, Duerden BI.	J Clin Microbiol	10.1128/jcm.40.9.3427-3431.2002	2002
Phylogeny	Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut.	Elsawi Z, Togo AH, Beye M, Dubourg G, Andrieu C, Armsrtong N, Richez M, di Pinto F, Bittar F, Labas N, Fournier PE, Raoult D, Khelaifia S	Microbiologyopen	10.1002/mbo3.458	2017