Clostridium symbiosum (DSM 934, ATCC 14940, LSU (M. Sebald))

Name: Clostridium symbiosum (DSM 934, ATCC 14940, LSU (M. Sebald))
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2721

Type strain

Strain Designation 2

Culture col. no. DSM 934 ATCC 14940 LSU (M. Sebald) 2 VTT E-981051 4 more

NCBI tax ID(s) 411472 1512

Special Collections DSMZ JCM

History DSMZ <- C. Kaneuchi; ATCC 14940 <- ATCC; ATCC 14940 <- R.E. Reeves; LSU (M. Sebald) (Bacteroides symbiosus) <- J. Shaffer; 2 JCM <-- C. Kaneuchi <-- ATCC 14940 <-- R. E. Reeves ("Bacteroides symbiosus") <-- J. Shaffer 2 (M. Sebald strain LSU).

Links

Clostridium symbiosum 2 is an anaerobe bacterium of the family Clostridiaceae.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 36207

ATCC 14940,DSM 934,JCM 1297,CCRC 14487,CCM 6065,BCRC 14487,VTT E-981051,LMG 28908

@ref 20215

Last LPSN update 2026-05-29 08:25:32

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium symbiosum

Full scientific name Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 (Approved Lists 1980)

Synonyms (1)

"Bacteroides symbiosus"

BacDive ID	Other strains from **Clostridium symbiosum** (10)	Type strain
130933	C. symbiosum SRB539-5-G-R, DSM 29356
150600	C. symbiosum CCUG 41715
152023	C. symbiosum CCUG 45577 B
153376	C. symbiosum CCUG 49377
153644	C. symbiosum CCUG 50474
153779	C. symbiosum CCUG 50960
155139	C. symbiosum CCUG 56568
156494	C. symbiosum CCUG 62167 Q
157675	C. symbiosum LT0011, DSM 108250
158919	C. symbiosum H4_29, DSM 108200

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
472	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Deionized water
472	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
472	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
472	anaerobe
125439	facultative anaerobe	97.932

Spore formation

@ref	Spore formation	Confidence
125439		92.58

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
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	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
472	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Taxonmaps

69479

Global distribution of 16S sequence LC036311 (>99% sequence identity) for [Clostridium] symbiosum subclade from Microbeatlas

Aquatic Samples	3039
Soil Samples	1377
Animal Samples	184529
Plant Samples	554
Total Samples	189499

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
472	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	51765_A02 assembly for [Clostridium] symbiosum NCTC13233	contig	GCA_900461275	1512.13	2814123396	1512	73.51
67770	ASM46648v1 assembly for [Clostridium] symbiosum ATCC 14940	scaffold	GCA_000466485	411472.5	2597490298	411472	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium symbiosum strain ATCC 14940 16S ribosomal RNA gene, partial sequence	M59112	1478	1512
472	Clostridium symbiosum strain DSM 934 16S ribosomal RNA gene, partial sequence	HM245954	845	1512
67770	[Clostridium] symbiosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1297	LC036311	1492	1512
124043	[Clostridium] symbiosum strain VTT E-981051 16S ribosomal RNA gene, partial sequence.	KU321267	1466	1512

GC content

@ref	GC-content (mol%)	Method
472	46.1
67770	46.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: 51765_A02 assembly for [Clostridium] symbiosum NCTC13233
NCBI: GCA_900461275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.93	no
125439	gram_stain	BacteriaNetⓘ	variable	52.88	no
125439	motility	BacteriaNetⓘ	yes	85.61	no
125439	spore_formation	BacteriaNetⓘ	yes	92.58	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium symbiosum ATCC 14940
PATRIC: 411472.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	63.19	no
125438	anaerobic	anaerobicⓘ	yes	89.94	yes
125438	spore-forming	spore-formingⓘ	yes	70.56	no
125438	aerobic	aerobicⓘ	no	94.86	yes
125438	thermophilic	thermophileⓘ	no	92.98	yes
125438	flagellated	motile2+ⓘ	yes	70.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
Metabolism	Molecular and Low-Resolution Structural Characterization of the Na⁺-Translocating Glutaconyl-CoA Decarboxylase From Clostridium symbiosum.	Vitt S, Prinz S, Hellwig N, Morgner N, Ermler U, Buckel W.	Front Microbiol	10.3389/fmicb.2020.00480	2020
	Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.	Minot SS, Li N, Srinivasan H, Ayers JL, Yu M, Koester ST, Stangis MM, Dominitz JA, Halberg RB, Grady WM, Dey N.	Sci Rep	10.1038/s41598-024-70702-1	2024
Pathogenicity	Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk.	Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS.	STAR Protoc	10.1016/j.xpro.2021.100607	2021
	Maternal diet and gut microbiome composition modulate early-life immune development.	Grant ET, Boudaud M, Muller A, Muller A, Macpherson AJ, Desai MS.	EMBO Mol Med	10.15252/emmm.202217241	2023
	Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction.	Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N.	Cell Rep	10.1016/j.celrep.2022.111093	2022
	Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host.	Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC.	Cell Host Microbe	10.1016/j.chom.2024.03.001	2024
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
Metabolism	Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.	Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.06.007	2017
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
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
	A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.	Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC.	Cell	10.1016/j.cell.2016.10.043	2016
Enzymology	Isolation and characterization of two new homoacetogenic hydrogen-utilizing bacteria from the human intestinal tract that are closely related to Clostridium coccoides.	Kamlage B, Gruhl B, Blaut M.	Appl Environ Microbiol	10.1128/aem.63.5.1732-1738.1997	1997
	A toolbox for genetic manipulation in intestinal Clostridium symbiosum.	Yang P, Tian J, Zhang L, Zhang H, Yang G, Ren Y, Fang J, Gu Y, Jiang W.	Synth Syst Biotechnol	10.1016/j.synbio.2023.12.005	2024
	Identification of FtfL as a novel target of berberine in intestinal bacteria.	Yan J, Fang C, Yang G, Li J, Liu Y, Zhang L, Yang P, Fang J, Gu Y, Zhang Y, Jiang W.	BMC Biol	10.1186/s12915-023-01778-w	2023
	Characterizing the mucin-degrading capacity of the human gut microbiota.	Glover JS, Ticer TD, Engevik MA.	Sci Rep	10.1038/s41598-022-11819-z	2022
Metabolism	Determination of Butyrate Synthesis Capacity in Gut Microbiota: Quantification of but Gene Abundance by qPCR in Fecal Samples.	Daskova N, Heczkova M, Modos I, Videnska P, Splichalova P, Pelantova H, Kuzma M, Gojda J, Cahova M.	Biomolecules	10.3390/biom11091303	2021
Metabolism	Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.	Sharma M, Pudlo N, Jarva MA, Kaur A, John A, Burchill L, Lingford JP, Epa R, Abayakoon P, Scott NE, Turkenburg JP, Davies GJ, Martens EC, Goddard-Borger ED, Williams SJ.	J Biol Chem	10.1016/j.jbc.2025.108320	2025
	Lipid complexation reduces rice starch digestibility and boosts short-chain fatty acid production via gut microbiota.	Shen Y, An Z, Huyan Z, Shu X, Wu D, Zhang N, Pellegrini N, Rubert J.	NPJ Sci Food	10.1038/s41538-023-00230-1	2023
Enzymology	Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.	Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2022.11.015	2023
Phylogeny	Imaging the in vivo growth patterns of bacteria in human gut Microbiota.	Lin L, Song J, Li J, Zuo X, Wei H, Yang C, Wang W.	Gut Microbes	10.1080/19490976.2021.1960134	2021
Phylogeny	Predictable modulation of cancer treatment outcomes by the gut microbiota.	Heshiki Y, Vazquez-Uribe R, Li J, Ni Y, Quainoo S, Imamovic L, Li J, Sorensen M, Chow BKC, Weiss GJ, Xu A, Sommer MOA, Panagiotou G.	Microbiome	10.1186/s40168-020-00811-2	2020
	Deep-learning-enabled antibiotic discovery through molecular de-extinction.	Wan F, Torres MDT, Peng J, de la Fuente-Nunez C.	Nat Biomed Eng	10.1038/s41551-024-01201-x	2024
Metabolism	Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis.	Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE.	Cell Host Microbe	10.1016/j.chom.2020.01.010	2020
Metabolism	Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B.	Liu QQ, Li CM, Fu LN, Wang HL, Tan J, Wang YQ, Sun DF, Gao QY, Chen YX, Fang JY.	Gut Microbes	10.1080/19490976.2020.1788900	2020
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
Enzymology	Techniques for controlling variability in gram staining of obligate anaerobes.	Johnson MJ, Thatcher E, Cox ME.	J Clin Microbiol	10.1128/jcm.33.3.755-758.1995	1995
Phylogeny	Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China.	Chen R, Feng Y, Wang X, Yang J, Zhang X, Lu X, Zong Z.	Sci Rep	10.1038/srep43555	2017
	Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.	Jernberg C, Sullivan A, Edlund C, Jansson JK.	Appl Environ Microbiol	10.1128/aem.71.1.501-506.2005	2005
Metabolism	An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases.	Kress D, Brugel D, Schall I, Linder D, Buckel W, Essen LO.	J Biol Chem	10.1074/jbc.m109.037762	2009
	Proteomic indicators of oxidation and hydration state in colorectal cancer.	Dick JM.	PeerJ	10.7717/peerj.2238	2016
Phylogeny	High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.	Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N.	Nucleic Acids Res	10.1093/nar/gkt1070	2013
Metabolism	Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome.	McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI.	PLoS Biol	10.1371/journal.pbio.1001637	2013
Phylogeny	Phylogenetic analysis of the bacterial communities in marine sediments.	Gray JP, Herwig RP.	Appl Environ Microbiol	10.1128/aem.62.11.4049-4059.1996	1996
	Gut butyrate-producers confer post-infarction cardiac protection.	Chen HC, Liu YW, Chang KC, Wu YW, Chen YM, Chao YK, You MY, Lundy DJ, Lin CJ, Hsieh ML, Cheng YC, Prajnamitra RP, Lin PJ, Ruan SC, Chen DH, Shih ESC, Chen KW, Chang SS, Chang CMC, Puntney R, Moy AW, Cheng YY, Chien HY, Lee JJ, Wu DC, Hwang MJ, Coonen J, Hacker TA, Yen CE, Rey FE, Kamp TJ, Hsieh PCH.	Nat Commun	10.1038/s41467-023-43167-5	2023
	Lactococcus lactis and Bifidobacterium longum attenuate Clostridioides difficile- or Clostridium symbiosum-induced colitis and depression/anxiety-like behavior in male mice.	Joo MK, Ma X, Shin JW, Shin YJ, Kim DH.	Microbes Infect	10.1016/j.micinf.2025.105560	2025
	Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.	Li J, Popovich PG, Kigerl KA, McTigue DM, Schwab J, Barnes S, Yarar-Fisher C.	Top Spinal Cord Inj Rehabil	10.46292/sci24-00061	2025
Metabolism	Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria.	Zhou Z, Jiang A, Jiang X, Hatzios SK.	Cell Host Microbe	10.1016/j.chom.2025.07.008	2025
	Integrated Microbiota-Bile Acid Analysis as Potential NonInvasive Biomarkers for Ulcerative Colitis Staging Diagnose.	He T, Wang Y, Zhao L, Che Y, Zhang L, Zeng Y, Shen H, Hao H, Cao L.	FASEB J	10.1096/fj.202501078r	2025
Metabolism	BCAA-producing Clostridium symbiosum promotes colorectal tumorigenesis through the modulation of host cholesterol metabolism.	Ren YM, Zhuang ZY, Xie YH, Yang PJ, Xia TX, Xie YL, Liu ZH, Kang ZR, Leng XX, Lu SY, Zhang L, Chen JX, Xu J, Zhao EH, Wang Z, Wang M, Cui Y, Tan J, Liu Q, Jiang WH, Xiong H, Hong J, Chen YX, Chen HY, Fang JY.	Cell Host Microbe	10.1016/j.chom.2024.07.012	2024
	Bacteremia Caused by Clostridium symbiosum in University Clinical Hospital Mostar: A Case Report.	Martinovic Rizikalo D, Jakovac S, Petrovic T, Kljakic M, Misetic A, Coric R.	Cureus	10.7759/cureus.71974	2024
	Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.	Zhang Y, Luo J, Chen K, Li N, Luo C, Di S, Qin J, Zhang F, Chen H, Dai M.	J Transl Med	10.1186/s12967-025-06676-z	2025
Pathogenicity	Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets.	Haque S, Bantun F, Jalal NA, Faidah H, Babalghith AO, Alobaidy MA, Aldairi AF, Ahmad F.	Gut Pathog	10.1186/s13099-025-00712-5	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
	The Gut Microbiota-Metabolic Axis: Emerging Insights from Human and Experimental Studies on Type 2 Diabetes Mellitus-A Narrative Review.	Alqahtani MS.	Medicina (Kaunas)	10.3390/medicina61112017	2025
Metabolism	Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.	Kuo TH, Wu PH, Liu PY, Chuang YS, Tai CJ, Kuo MC, Chiu YW, Lin YT.	Int J Mol Sci	10.3390/ijms262110463	2025
	Clostridium Symbiosum Sepsis Diagnosed Using Next-Generation Sequencing in a 2 Year Old Child: A Case Report.	Pan Y, Fan Q.	Fetal Pediatr Pathol	10.1080/15513815.2022.2158696	2023
	Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines.	Finazzi M, Bovio F, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Microorganisms	10.3390/microorganisms13010192	2025
	EzSEA: an interactive web interface for enzyme sequence evolution analysis.	Jiang AK, Zhao J, Jiang X.	Bioinform Adv	10.1093/bioadv/vbaf118	2025
	Pylephlebitis: A Rare but Redoubtable Complication of Intra-Abdominal Infections-A Series of 15 Cases.	Benea SN, Deaconu T, Florea D, Moroti R, Oprica G, Nae A, Patrascu RE, Militaru E, Gedik H, Savulescu-Fiedler I.	Life (Basel)	10.3390/life15101525	2025
	Cross-cohort microbiome-wide study reveals consistent alterations in the gut bacteriome, but not the gut mycobiome, in patients with hypertension.	Gao Y, Wang D, Lu T, Liu K, Li S, Kang J, Sha S, Xing G, Cheng L, Fan S, Yang W, Yan Q, Ding Y, Xu D.	mSystems	10.1128/msystems.00657-25	2025
Genetics	Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.	Fan KC, Lin CC, Chiu YL, Koh SH, Liu YC, Chuang YF.	Alzheimers Res Ther	10.1186/s13195-025-01769-9	2025
	Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.	Liu W, Lau HCH, Ding X, Yin X, Wu WKK, Wong SH, Sung JJY, Zhang T, Yu J.	Imeta	10.1002/imt2.70008	2025
	Enhanced glucose homeostasis via Clostridium symbiosum-mediated glucagon-like peptide 1 inhibition of hepatic gluconeogenesis in mid-intestinal bypass surgery.	Luo X, Tao F, Tan C, Xu CY, Zheng ZH, Pang Q, He XA, Cao JQ, Duan JY.	World J Gastroenterol	10.3748/wjg.v29.i39.5471	2023
Genetics	Influence of the Gut Microbiota on Acute Ischemic Stroke Functional Outcomes at Three Months.	Lledos M, Prats-Sanchez L, Muino E, Cullell N, Llucia-Carol L, Carcel-Marquez J, Gallego-Fabrega C, Martin-Campos JM, Marin R, Aguilera-Simon A, Guasch-Jimenez M, Ezcurra-Diaz G, Camps-Renom P, Del Mar Freijo M, Marti-Fabregas J, Fernandez-Cadenas I.	Eur J Neurol	10.1111/ene.70265	2025
	Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.	Mayer MH, Woldemariam S, Gisinger C, Dorner TE.	Int J Environ Res Public Health	10.3390/ijerph21091246	2024
	BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen.	Hall B, Levy S, Dufault-Thompson K, Arp G, Zhong A, Ndjite GM, Weiss A, Braccia D, Jenkins C, Grant MR, Abeysinghe S, Yang Y, Jermain MD, Wu CH, Ma B, Jiang X.	Nat Microbiol	10.1038/s41564-023-01549-x	2024
	Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.	Minabou Ndjite G, Jiang AK, Ravel CT, Grant MR, Jiang X, Hall B.	Commun Biol	10.1038/s42003-025-08391-3	2025
	Members of Lachnospiraceae produce valerate and caproate in response to short-chain fatty acids.	Fitzgerald BG, Govind M, Firth IJ, Herold L, Froment J, Vancuren SJ, Allen-Vercoe E, Kimber MS, Sorbara MT.	Microbiome	10.1186/s40168-025-02220-9	2025
	Nutraceutical supplement slim reshaped colon histomorphology and reduces Mucispirillum schaedleri in obese mice.	Freitas JA, Nehmi Filho V, Santamarina AB, Murata GM, Franco LAM, Fonseca JV, Martins RC, Souza GA, Benicio G, Sabbag IM, de Souza EA, Otoch JP, Pessoa AFM.	Front Microbiol	10.3389/fmicb.2025.1494994	2025
	Hormonal Contraceptives and the Gut Microbiome in Female Athletes: Implications for Health, Performance, and Exercise-Related Physiological Adjustments	Pierudzka W, Slawatycki J, Klemenska P, Warczak K, Wasilewska P, Horwat P, Gorski J.	Cureus
	Changes of antibiotic resistance genes and gut microbiota after the ingestion of goat milk.	Liu Y, Zhang F.	J Dairy Sci	10.3168/jds.2021-21325	2022
	Prebiotic, probiotic, and postbiotic properties of fermented corn starch and their application in type 2 diabetes management.	Gumenku L, Erukainure OL, Islam MS, Olaniran AO.	World J Diabetes	10.4239/wjd.v16.i8.107775	2025
	Lactoferrin-osteopontin complexes: insights into intestinal organoid bioavailability and gut microbiota modulation.	Ceroni C, Dayon L, Van den Abbeele P, Roch A, Dervaux J, Ernest M, Sirugue P, Baudot A, Kraus MR, Brandenberg N, O'Regan J, Goulding D, Mashinchian O.	Commun Biol	10.1038/s42003-025-08460-7	2025
Phylogeny	Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods.	Korobeinikova AV, Zlobovskaya OA, Sheptulina AF, Ashniev GA, Bobrova MM, Yafarova AA, Akasheva DU, Kabieva SS, Bakoev SY, Zagaynova AV, Lukashina MV, Abramov IA, Pokrovskaya MS, Doludin YV, Tolkacheva LR, Kurnosov AS, Zyatenkova EV, Lavrenova EA, Efimova IA, Glazunova EV, Kiselev AR, Shipulin GA, Kontsevaya AV, Keskinov AA, Yudin VS, Makarov VV, Drapkina OM, Yudin SM.	Int J Mol Sci	10.3390/ijms242015272	2023
	Causal relationship among immune cells, basal cell carcinoma, and gut microbiome: a two-sample Mendelian randomization analysis and mediation analysis.	Li H, Chen L.	Discov Oncol	10.1007/s12672-025-03378-2	2025
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
Phylogeny	Isolation and identification of aerobic and anaerobic bacteria from the feces of wild Korean water deer (Hydropotes inermis argyropus).	Islam MA, Kim S, Islam MS, Islam O, Park S, Taili I, Jeong DH, Na KJ.	J Vet Sci	10.4142/jvs.24236	2024
	Role of gut microbiome in colorectal cancer: a comprehensive umbrella review protocol	Seneviwickrama M, Gunasekera K, Gamage K, Gonapaladeniya M, Ranasinghe S.	BMJ Open		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
Pathogenicity	Interactions between toll-like receptors signaling pathway and gut microbiota in host homeostasis.	Chen L, Zhang L, Hua H, Liu L, Mao Y, Wang R.	Immun Inflamm Dis	10.1002/iid3.1356	2024
	Th17 cells sense microbiome to promote depressive-like behaviors.	Medina-Rodriguez EM, Watson J, Reyes J, Trivedi M, Beurel E.	Microbiome	10.1186/s40168-022-01428-3	2023
Genetics	Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.	Park S, Zhang T, Kang S.	Int J Mol Sci	10.3390/ijms24119533	2023
Metabolism	Gut microbiota-mediated modulation of host amino acid availability and metabolism.	Han Z, Zhao L, Hu Q, Hung I, Liu C, Liu S, Mei X, Zeng X, Bin P, Wang J.	Gut Microbes	10.1080/19490976.2025.2552345	2025
	Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.	Wong MK, Armstrong E, Heirali AA, Schneeberger PHH, Chen H, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	mBio	10.1128/mbio.01904-25	2025
	A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information	Silva-Andrade C, Hernandez S, Saa P, Perez-Rueda E, Garrido D, Martin A.	PeerJ		2025
	Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.	Zhu M, Wang Q, Yang Y, Liu X, Zhang J, Li G, Liu W, Xiang X, Chen J.	Nutr J	10.1186/s12937-025-01116-6	2025
Genetics	Characteristics of the gut virome in patients with premalignant colorectal adenoma.	Zhang P, Tuo X, Jiang J, Zhang Y, Zhao J, Deng C, Zhao G, Cheng Y, Song L, Yang Y, Guo R, Zhang H, Zhao H, Ma S, Li L, Shi H.	J Transl Med	10.1186/s12967-025-06404-7	2025
	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
	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
	Changes in the gut microbiome due to diarrhea in neonatal Korean indigenous calves.	Ku JY, Lee MJ, Jung Y, Choi HJ, Park J.	Front Microbiol	10.3389/fmicb.2025.1511430	2025
	KH-R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB.	Fukui K, Murakawa T, Baba S, Kumasaka T, Yano T.	Nat Commun	10.1038/s41467-025-62302-y	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
	A systematic review of microbial markers for risk prediction of colorectal neoplasia.	Yu L, Zhao G, Wang L, Zhou X, Sun J, Li X, Zhu Y, He Y, Kofonikolas K, Bogaert D, Dunlop M, Zhu Y, Theodoratou E, Li X.	Br J Cancer	10.1038/s41416-022-01740-7	2022
	Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025
Phylogeny	Gut Microbial and Associated Metabolite Markers for Colorectal Cancer Diagnosis.	Alhhazmi AA, Alhamawi RM, Almisned RM, Almutairi HA, Jan AA, Kurdi SM, Almutawif YA, Mohammed-Saeid W.	Microorganisms	10.3390/microorganisms11082037	2023
	Impact of Gut Dysbiosis on the Risk of Non-Small-Cell Lung Cancer.	Wei YF, Huang MS, Huang CH, Yeh YT, Hung CH.	Int J Environ Res Public Health	10.3390/ijerph192315991	2022
Phylogeny	Gut microbiome and metabolome signatures in liver cirrhosis-related complications.	Sharma SP, Gupta H, Kwon GH, Lee SY, Song SH, Kim JS, Park JH, Kim MJ, Yang DH, Park H, Won SM, Jeong JJ, Oh KK, Eom JA, Lee KJ, Yoon SJ, Ham YL, Baik GH, Kim DJ, Suk KT.	Clin Mol Hepatol	10.3350/cmh.2024.0349	2024
	Disease-associated microbiome signature species in the gut.	Li J, Li J, O'Toole PW.	PNAS Nexus	10.1093/pnasnexus/pgae352	2024
	A systematic review of microbiome-derived biomarkers for early colorectal cancer detection.	Zwezerijnen-Jiwa FH, Sivov H, Paizs P, Zafeiropoulou K, Kinross J.	Neoplasia	10.1016/j.neo.2022.100868	2023
	Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity.	Hieta J, Benchraka C, Parnanen K, Houttu N, Mokkala K, Lotankar M, Kataja EL, Lahti L, Laitinen K.	Brain Behav Immun Health	10.1016/j.bbih.2025.101042	2025
Transcriptome	Lactiplantibacillus plantarum Attenuates Diet-Induced Obesity and Insulin Resistance Through Gut Microbiota-Driven PPAR/PI3K-Axis Modulation.	Gao Y, Zhu A, Li J, Liu H, Li X, Zhang H.	Microb Biotechnol	10.1111/1751-7915.70227	2025
	De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.	Klaes S, White C, Alvarez-Cohen L, Adrian L, Ding C.	Environ Microbiome	10.1186/s40793-025-00767-6	2025
	Corrigendum to "Fecal Clostridium Symbiosum for Noninvasive Detection of Early and Advanced Colorectal Cancer: Test and Validation Studies" [Ebiomedicine 25 (2017) 32-40].	Xie YH, Gao QY, Cai GX, Sun XM, Zou TH, Chen HM, Yu SY, Qiu YW, Gu WQ, Chen XY, Cui Y, Sun D, Liu ZJ, Cai SJ, Xu J, Chen YX, Fang JY.	EBioMedicine	10.1016/j.ebiom.2018.02.014	2018
Metabolism	Study of sulfoglycolysis in Enterococcus gilvus reveals a widespread bifurcated pathway for dihydroxypropanesulfonate degradation.	Chen Y, Chu R, Ma K, Jiang L, Yang Q, Li Z, Hu M, Guo Q, Lu F, Wei Y, Zhang Y, Tong Y.	iScience	10.1016/j.isci.2024.111010	2024
Metabolism	Changing Gastrointestinal Transit Time Alters Microbiome Composition and Bile Acid Metabolism: A Cross-Over Study in Healthy Volunteers.	Hillman EBM, Baumgartner M, Carson D, Amos GCA, Wazir I, Khan HA, Khan MA, Rijpkema S, Walters JRF, Wellington EMH, Arasaradnam R, Lewis SJ.	Neurogastroenterol Motil	10.1111/nmo.70075	2025
	The Yin-Yang Pharmacomicrobiomics on Treatment Response in Inflammatory Arthritides: A Narrative Review.	Peretti S, Torracchi S, Russo E, Bonomi F, Fiorentini E, Aoufy KE, Bruni C, Lepri G, Orlandi M, Chimenti MS, Guiducci S, Amedei A, Matucci-Cerinic M, Bellando Randone S.	Genes (Basel)	10.3390/genes14010089	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
Genetics	Population-based metagenomics analysis reveals altered gut microbiome in sarcopenia: data from the Xiangya Sarcopenia Study.	Wang Y, Zhang Y, Lane NE, Wu J, Yang T, Li J, He H, Wei J, Zeng C, Lei G.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13037	2022
	Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.	Chen Z, Zhang Z, Nie BN, Huang W, Zhu Y, Zhang L, Xu M, Wang M, Yuan C, Liu N, Wang X, Tian J, Ba Q, Wang Z.	mSystems	10.1128/msystems.01188-24	2025
Enzymology	Role of Anaerobic Blood Cultures in Neonatal Bacteremia.	Messbarger N, Neemann K.	J Pediatric Infect Dis Soc	10.1093/jpids/pix088	2018
	Interleukin-2 mediated associations between gut microbiota and acute myeloid leukemia: A population-based mediation Mendelian randomization study.	Luo C, Zhang W, Zhu J, Qiu T, Fang Q.	Heliyon	10.1016/j.heliyon.2024.e33194	2024
	Positive modulation of a new reconstructed human gut microbiota by Maitake extract helpfully boosts the intestinal environment in vitro.	De Giani A, Perillo F, Baeri A, Finazzi M, Facciotti F, Di Gennaro P.	PLoS One	10.1371/journal.pone.0301822	2024
	Alleviation of Hyperuricemia by Strictinin in AML12 Mouse Hepatocytes Treated with Xanthine and in Mice Treated with Potassium Oxonate.	Huang KC, Chang YT, Pranata R, Cheng YH, Chen YC, Kuo PC, Huang YH, Tzen JTC, Chen RJ.	Biology (Basel)	10.3390/biology12020329	2023
	The release patterns and potential prebiotic characteristics of soluble and insoluble dietary fiber-bound polyphenols from pinot noir grape pomace in vitro digestion and fermentation.	Li Y, Chen X, Wang G, Xu L, Liu Y, Yuan C, Li J.	Food Chem X	10.1016/j.fochx.2025.102694	2025
	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
	Mucosal homeostasis is altered in the ileum of gnotobiotic mice.	Greig CJ, Alper A, Goodman AL, Cowles RA.	J Surg Res	10.1016/j.jss.2018.05.055	2018
	Metformin-Associated Gastrointestinal Adverse Events Are Reduced by Probiotics: A Meta-Analysis.	Szymczak-Pajor I, Drzewoski J, Wenclewska S, Sliwinska A.	Pharmaceuticals (Basel)	10.3390/ph17070898	2024
	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
Phylogeny	Salivary and fecal microbiota: potential new biomarkers for early screening of colorectal polyps.	Zhang L, Feng Z, Li Y, Lv C, Li C, Hu Y, Fu M, Song L.	Front Microbiol	10.3389/fmicb.2023.1182346	2023
	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
Pathogenicity	Sulforaphane-driven reprogramming of gut microbiome and metabolome ameliorates the progression of hyperuricemia.	Wang R, Halimulati M, Huang X, Ma Y, Li L, Zhang Z.	J Adv Res	10.1016/j.jare.2022.11.003	2023
	Maternal group B Streptococcus decreases infant length and alters the early-life microbiome: a prospective cohort study.	Li S, Liang Q, Qing W, Fang Z, Yuan C, Pan S, Xie H, Li X, Chen M, He Y, Zhou H, Wang Q.	Ann Med	10.1080/07853890.2024.2442070	2025
Genetics	Genome-scale metabolic modelling of human gut microbes to inform rational community design.	Molina Ortiz JP, McClure DD, Holmes A, Rice SA, Read MN, Shanahan ER.	Gut Microbes	10.1080/19490976.2025.2534673	2025
	Microbial and metabolic profiles associated with HPV infection and cervical intraepithelial neoplasia: a multi-omics study.	Pu X, Wang X, Wang J, Gu Z, Zhu H, Li C.	Microbiol Spectr	10.1128/spectrum.00192-25	2025
	Pterostilbene Protects against Osteoarthritis through NLRP3 Inflammasome Inactivation and Improves Gut Microbiota as Evidenced by In Vivo and In Vitro Studies.	Lee YC, Chang YT, Cheng YH, Pranata R, Hsu HH, Chen YL, Chen RJ.	J Agric Food Chem	10.1021/acs.jafc.3c09749	2024
	Gut dysbiosis patterns in CVID patients with noninfectious complications observed in a germ-free mouse model through fecal microbiota transplantation.	Hajjar J, Voigt AY, Conner ME, Swennes AG, Fowler S, Calarge C, Mendonca DD, Armstrong D, Chang CY, Walter JE, Butte MJ, Savidge T, Oh J, Kheradmand F, Petrosino JF.	J Hum Immun	10.70962/jhi.20250040	2025
Metabolism	Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.	Thomson P, Medina DA, Ortuzar V, Gotteland M, Garrido D.	Food Res Int	10.1016/j.foodres.2018.04.008	2018
Genetics	Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.	Zheng X, Xu L, Tang Q, Shi K, Wang Z, Shi L, Ding Y, Yin Z, Zhang X.	Genes (Basel)	10.3390/genes15080970	2024
	Ligilactobacillus agilis W70: a probiotic with capacity to enhance ammonia assimilation in the rumen.	Duan X, Vigors S, Ma R, Ma L, Gu J, Bu D.	Front Microbiol	10.3389/fmicb.2024.1498109	2024
Phylogeny	Distinct gut microbiomes in Thai patients with colorectal polyps.	Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S.	World J Gastroenterol	10.3748/wjg.v30.i27.3336	2024
	The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.	Zhang L, Wang S, Wong MCS, Mok CKP, Ching JYL, Mak JWY, Chen C, Huo B, Yan S, Cheung CP, Chiu EOL, Fung EYT, Cheong PK, Chan FKL, Ng SC.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00804-9	2025
	Sucralose Promotes Colitis-Associated Colorectal Cancer Risk in a Murine Model Along With Changes in Microbiota.	Li X, Liu Y, Wang Y, Li X, Liu X, Guo M, Tan Y, Qin X, Wang X, Jiang M.	Front Oncol	10.3389/fonc.2020.00710	2020
	Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients.	Hoang T, Kim MJ, Park JW, Jeong SY, Lee J, Shin A.	BMC Cancer	10.1186/s12885-022-09735-6	2022
	Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.	Li C, Guo X, He Y, Wang J, Hao J, Liu X.	Ann Med	10.1080/07853890.2024.2337712	2024
	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
Pathogenicity	Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.	Gao Y, Borjihan Q, Zhang W, Li L, Wang D, Bai L, Zhu S, Chen Y.	Nutrients	10.3390/nu17050801	2025
Metabolism	Characterization of a two-component kinase that initiates the bacterial catabolism of hydroxyphenylethanones.	Dexter GN, Grigg JC, Zahn M, Wheatley EJ, Lian J, Mohn WW, Eltis LD.	J Biol Chem	10.1016/j.jbc.2025.110210	2025
	The microbiome compositional and functional differences between rectal mucosa and feces.	Yin X-F, Ye T, Chen H-L, Liu J, Mu X-F, Li H, Wang J, Hu Y-J, Cao H, Kang W-Q.	Microbiol Spectr	10.1128/spectrum.03549-23	2024
Genetics	Microbiome-based therapeutics towards healthier aging and longevity.	Kadyan S, Park G, Singh TP, Patoine C, Singar S, Heise T, Domeier C, Ray C, Kumar M, Behare PV, Chakrabarty P, Efron P, Sheffler J, Nagpal R.	Genome Med	10.1186/s13073-025-01493-x	2025
Metabolism	Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway.	Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D.	iScience	10.1016/j.isci.2020.101510	2020
	Gut microbiota and gastrointestinal tumors: insights from a bibliometric analysis.	Chen C, Wang X, Han X, Peng L, Zhang Z.	Front Microbiol	10.3389/fmicb.2025.1558490	2025
	Data-driven prediction of colonization outcomes for complex microbial communities.	Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L.	Nat Commun	10.1038/s41467-024-46766-y	2024
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
	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
	Isolation, complete characterization and phylogeography of the first bacteriophage against Vibrio neocaledonicus, which encodes a pyruvate phosphate dikinase and represents a novel viral family.	Chen X, Liu R, Wang W, Liu Y, Sun J, Shao H, McMinn A, Wang M, Liang Y.	Microb Genom	10.1099/mgen.0.001403	2025
	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
	The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac.	Ng HY, Liao Y, Zhang R, Chan KH, To WP, Hui CH, Seto WK, Leung WK, Hung IFN, Lam TTY, Cheung KS.	Int J Mol Sci	10.3390/ijms25052583	2024
Genetics	Evaluating the probiotic effects of spraying lactiplantibacillus plantarum P-8 in neonatal piglets.	Yao G, Zhao Z, Yang C, Zuo B, Sun Z, Wang J, Zhang H.	BMC Microbiol	10.1186/s12866-024-03332-2	2024
	Harnessing gut-derived bioactives and AI diagnostics for the next generation of type 2 diabetes solutions.	Tseyslyer Y, Malyi V, Saifullina M, Tsyryuk O, Shvets Y, Penchuk Y, Kovalchuk I, Kovalchuk O, Korotkyi O, Bulda V, Lazarieva O.	Front Endocrinol (Lausanne)	10.3389/fendo.2025.1699954	2025
	A Systematic Review of the Gastrointestinal Microbiome: A Game Changer in Colorectal Cancer.	Eastmond AK, Shetty C, Rizvi SMHA, Sharaf J, Williams KD, Tariq M, Acharekar MV, Guerrero Saldivia SE, Unnikrishnan S, Chavarria YY, Akindele AO, Jalkh AP, Balani P.	Cureus	10.7759/cureus.28545	2022
Enzymology	Diet and gut microbial associations in irritable bowel syndrome according to disease subtype.	Wang Y, Ma W, Mehta R, Nguyen LH, Song M, Drew DA, Asnicar F, Huttenhower C, Segata N, Wolf J, Spector T, Berry S, Staller K, Chan AT.	Gut Microbes	10.1080/19490976.2023.2262130	2023
	Microbiota-gut-brain axis impairment in the pathogenesis of stroke: implication as a potent therapeutic target.	Muhammad M, Muchimapura S, Wattanathorn J.	Biosci Microbiota Food Health	10.12938/bmfh.2022-067	2023
	Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.	Choi JY, Shim B, Park Y, Kang YA.	Korean J Intern Med	10.3904/kjim.2023.097	2023
Enzymology	Fecal Clostridium symbiosum for Noninvasive Detection of Early and Advanced Colorectal Cancer: Test and Validation Studies.	Xie YH, Gao QY, Cai GX, Sun, Sun XM, Zou TH, Chen HM, Yu SY, Qiu YW, Gu WQ, Chen XY, Cui Y, Sun D, Liu ZJ, Cai SJ, Xu J, Chen YX, Fang JY.	EBioMedicine	10.1016/j.ebiom.2017.10.005	2017
	Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.	Tuerhongjiang G, Guo M, Qiao X, Liu J, Xi W, Wei Y, Liu P, Lou B, Wang C, Sun L, Yuan X, Liu H, Xiong Y, Ma Y, Li H, Zhou B, Li L, Yuan Z, Wu Y, She J.	Small Sci	10.1002/smsc.202300337	2024
	Designing function-specific minimal microbiomes from large microbial communities.	Raghu AK, Palanikumar I, Raman K.	NPJ Syst Biol Appl	10.1038/s41540-024-00373-1	2024
Phylogeny	Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes.	Kardos G, Laczko L, Kaszab E, Timmer B, Szarka K, Prepost E, Banyai K.	Antibiotics (Basel)	10.3390/antibiotics13070573	2024
	The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients.	MacDonald T, Dunn KA, MacDonald J, Langille MGI, Van Limbergen JE, Bielawski JP, Kulkarni K.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1102501	2023
	Dietary D-xylose promotes intestinal health by inducing phage production in Escherichia coli.	Hu J, Wu Y, Kang L, Liu Y, Ye H, Wang R, Zhao J, Zhang G, Li X, Wang J, Han D.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00445-w	2023
	Landscapes of gut microbiome and bile acid signatures and their interaction in HBV-associated acute-on-chronic liver failure.	Bao Z, Wei R, Zheng X, Zhang T, Bi Y, Shen S, Zou P, Zhang J, Yan H, Li MD, Yang Z, Gao H.	Front Microbiol	10.3389/fmicb.2023.1185993	2023
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
Pathogenicity	Effects of Different Carbohydrate Content Diet on Gut Microbiota and Aortic Calcification in Diabetic Mice.	Shen X, Guo G, Feng G, Wang Z.	Diabetes Metab Syndr Obes	10.2147/dmso.s456571	2024
Enzymology	Reversal of the extreme coenzyme selectivity of Clostridium symbiosum glutamate dehydrogenase.	Sharkey MA, Gori A, Capone M, Engel PC.	FEBS J	10.1111/j.1742-4658.2012.08681.x	2012
	Synergistic Antioxidant Effect of Prebiotic Ginseng Berries Extract and Probiotic Strains on Healthy and Tumoral Colorectal Cell Lines.	De Giani A, Oldani M, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Int J Mol Sci	10.3390/ijms24010373	2022
	Correlations between Intestinal Microbiota and Clinical Characteristics in Colorectal Adenoma/Carcinoma.	Lin C, Li B, Tu C, Chen X, Guo M.	Biomed Res Int	10.1155/2022/3140070	2022
	Development of non-alcoholic steatohepatitis is associated with gut microbiota but not with oxysterol enzymes CH25H, EBI2, or CYP7B1 in mice.	Wyss J, Raselli T, Wyss A, Telzerow A, Rogler G, Krupka N, Yilmaz B, Schmidt TSB, Misselwitz B.	BMC Microbiol	10.1186/s12866-024-03195-7	2024
Metabolism	Structural analysis and insight into effector binding of the niacin-responsive repressor NiaR from Bacillus halodurans.	Lee DW, Park YW, Lee MY, Jeong KH, Lee JY.	Sci Rep	10.1038/s41598-020-78148-x	2020
Genetics	Pharmacological and Nutritional Modulation of Metabolome and Metagenome in Cardiometabolic Disorders.	Witkowska AM, Salem JE.	Biomolecules	10.3390/biom13091340	2023
Metabolism	Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.	Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M, Aichinger G, Hausmann B, Berry D, Richter A, Marko D, Mussmann M, Schleheck D, Stecher B, Loy A.	Microbiome	10.1186/s40168-025-02175-x	2025
	Macronutrient balance determines the human gut microbiome eubiosis: insights from in vitro gastrointestinal digestion and fermentation of eight pulse species.	Lee DB, Hwang IS.	Front Microbiol	10.3389/fmicb.2024.1512217	2024
	The Water Extract of Rhubarb Prevents Ischemic Stroke by Regulating Gut Bacteria and Metabolic Pathways.	Liu X, Wang Y, Tian Y, Hu J, Liu Z, Ma Y, Xu W, Wang W, Gao J, Wang T.	Metabolites	10.3390/metabo14040216	2024
	The Development and Evaluation of a Literature-Based Dietary Index for Gut Microbiota.	Kase BE, Liese AD, Zhang J, Murphy EA, Zhao L, Steck SE.	Nutrients	10.3390/nu16071045	2024
	Gut microbiota in patients with COVID-19 and type 2 diabetes: A culture-based method.	Petakh P, Kobyliak N, Kamyshnyi A.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1142578	2023
	Bile acid is a responsible host factor for high-fat diet-induced gut microbiota alterations in rats: proof of the "bile acid hypothesis".	Watanabe M, Fujita Y, Hagio M, Ishizuka S, Ogura Y, Hayashi T, Fukiya S, Yokota A.	Biosci Microbiota Food Health	10.12938/bmfh.2024-042	2025
Genetics	Connect the dots: sketching out microbiome interactions through networking approaches.	Fabbrini M, Scicchitano D, Candela M, Turroni S, Rampelli S.	Microbiome Res Rep	10.20517/mrr.2023.25	2023
	Enteropathogenic Escherichia coli induces Entamoeba histolytica superdiffusion movement on fibronectin by reducing traction forces.	Guo Y, Ye J, Shemesh A, Odeh A, Trebicz-Geffen M, Wolfenson H, Ankri S.	PLoS Pathog	10.1371/journal.ppat.1012618	2025
	Gut microbiome alterations in pulmonary hypertension in highlanders and lowlanders.	Dong W, Ma L, Huang Q, Yang X, Mei Z, Kong M, Sun Z, Zhang Z, Li J, Zou J, Chen D, Dai Y, Zhou D, Zheng Y, Kang L.	ERJ Open Res	10.1183/23120541.00617-2022	2023
Metabolism	Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth.	Mondal SI, Akter A, Draper LA, Ross RP, Hill C.	Int J Mol Sci	10.3390/ijms22115690	2021
	Deciphering microbial and metabolic influences in gastrointestinal diseases-unveiling their roles in gastric cancer, colorectal cancer, and inflammatory bowel disease.	Philip D, Hodgkiss R, Radhakrishnan SK, Sinha A, Acharjee A.	J Transl Med	10.1186/s12967-025-06552-w	2025
Pathogenicity	Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice.	Lee J, d'Aigle J, Atadja L, Quaicoe V, Honarpisheh P, Ganesh BP, Hassan A, Graf J, Petrosino J, Putluri N, Zhu L, Durgan DJ, Bryan RM, McCullough LD, Venna VR.	Circ Res	10.1161/circresaha.119.316448	2020
	Causal associations between gut microbiome and cardiovascular disease: A Mendelian randomization study.	Zhang Y, Zhang X, Chen D, Lu J, Gong Q, Fang J, Jiang J.	Front Cardiovasc Med	10.3389/fcvm.2022.971376	2022
	Differences in gut microbes in captive pangolins and the effects of captive breeding.	Jiao W, Liu L, Zeng Z, Li L, Chen J.	Front Microbiol	10.3389/fmicb.2022.1053925	2022
Pathogenicity	Microbial-derived imidazole propionate links the heart failure-associated microbiome alterations to disease severity.	Raju SC, Molinaro A, Awoyemi A, Jorgensen SF, Braadland PR, Nendl A, Seljeflot I, Ueland PM, McCann A, Aukrust P, Vestad B, Mayerhofer C, Broch K, Gullestad L, Lappegard KT, Halvorsen B, Kristiansen K, Hov JR, Troseid M.	Genome Med	10.1186/s13073-024-01296-6	2024
	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
	Effects of Polyphenols and Glucosinolates in Broccoli Extract on Human Gut Microorganisms Based on Simulation In Vitro.	Zhang Y, Jiang C, Huang S, Sun J, Song X, Nishanbaev SZ, Benito MJ, Wu Y.	ACS Omega	10.1021/acsomega.2c05523	2022
	Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.	Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E.	Microbiol Spectr	10.1128/spectrum.00336-23	2023
	A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer.	Zhang Q, Zhao H, Wu D, Cao D, Ma W.	BMC Microbiol	10.1186/s12866-020-01938-w	2020
	Leveraging explainable AI for gut microbiome-based colorectal cancer classification.	Rynazal R, Fujisawa K, Shiroma H, Salim F, Mizutani S, Shiba S, Yachida S, Yamada T.	Genome Biol	10.1186/s13059-023-02858-4	2023
	The gut microbiome in end-stage lung disease and lung transplantation.	Zhang S, Swarte JC, Gacesa R, Knobbe TJ, Kremer D, Jansen BH, de Borst MH, TransplantLines Investigators, Harmsen HJM, Erasmus ME, Verschuuren EAM, Bakker SJL, Gan CT, Weersma RK, Bjork JR.	mSystems	10.1128/msystems.01312-23	2024
	Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.	Avuthu N, Guda C.	Microbiol Spectr	10.1128/spectrum.00013-22	2022
	Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation.	Chatthanathon P, Leelahavanichkul A, Cheibchalard T, Wilantho A, Hirankarn N, Somboonna N.	Sci Rep	10.1038/s41598-024-77672-4	2024
	Types and viral load of human papillomavirus, and vaginal microbiota in vaginal intraepithelial neoplasia: a cross-sectional study.	Zhou FY, Zhou Q, Zhu ZY, Hua KQ, Chen LM, Ding JX.	Ann Transl Med	10.21037/atm-20-622	2020
Genetics	Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis.	Candeliere F, Musmeci E, Amaretti A, Sola L, Raimondi S, Rossi M.	Microbiome Res Rep	10.20517/mrr.2022.19	2023
	Differences in Compositions of Oral and Fecal Microbiota between Patients with Obesity and Controls.	Stefura T, Zapala B, Gosiewski T, Skomarovska O, Dudek A, Pedziwiatr M, Major P.	Medicina (Kaunas)	10.3390/medicina57070678	2021
Enzymology	Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid.	Parthasarathy A, Parthasarathy A, Pierik AJ, Kahnt J, Zelder O, Buckel W.	Biochemistry	10.1021/bi1020056	2011
	Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers.	Coker OO, Liu C, Wu WKK, Wong SH, Jia W, Sung JJY, Yu J.	Microbiome	10.1186/s40168-021-01208-5	2022
Phylogeny	From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.	Huang F, Lyu B, Xie F, Li F, Xing Y, Han Z, Lai J, Ma J, Zou Y, Zeng H, Xu Z, Gao P, Luo Y, Bolund L, Tong G, Fengping X.	Front Microbiol	10.3389/fmicb.2024.1366744	2024
	Exploring Gut Microbiota and the Influence of Physical Activity Interventions on Overweight and Obese Children and Adolescents: A Systematic Review.	Morgado MC, Sousa M, Coelho AB, Costa JA, Seabra A.	Healthcare (Basel)	10.3390/healthcare11172459	2023
	The Potential Role of Boron in the Modulation of Gut Microbiota Composition: An In Vivo Pilot Study.	Senturk NB, Kasapoglu B, Sahin E, Ozcan O, Ozansoy M, Ozansoy MB, Siyah P, Sezerman U, Sahin F.	Pharmaceuticals (Basel)	10.3390/ph17101334	2024
	Gut Microbiota-Butyrate-PPARgamma Axis Modulates Adipose Regulatory T Cell Population.	Chen B, Guan L, Wu C, Gong Y, Wu L, Zhang M, Cao Z, Chen Y, Yang C, Wang B, Li Y, Li B, Bi Y, Ning G, Wang J, Wang W, Liu R.	Adv Sci (Weinh)	10.1002/advs.202411086	2025
Enzymology	Crystal structure of a chimaeric bacterial glutamate dehydrogenase.	Oliveira T, Sharkey MA, Engel PC, Khan AR.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x16007305	2016
	Microbiome modulation in the prevention and management of colorectal cancer: a systematic review of clinical interventions.	Fratila TD, Ismaiel A, Dumitrascu DL.	Med Pharm Rep	10.15386/mpr-2526	2023
	Design, synthesis, and evaluation of inhibitors of pyruvate phosphate dikinase.	Wu C, Dunaway-Mariano D, Mariano PS.	J Org Chem	10.1021/jo3018473	2013
	Fecal Microbiota and Associated Volatile Organic Compounds Distinguishing No-Adenoma from High-Risk Colon Adenoma Adults.	Katsaounou K, Yiannakou D, Nikolaou E, Brown C, Vogazianos P, Aristodimou A, Chi J, Costeas P, Agapiou A, Frangou E, Tsiaoussis G, Potamitis G, Antoniades A, Shammas C, Apidianakis Y.	Metabolites	10.3390/metabo13070819	2023
	Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.	Nychas E, Marfil-Sanchez A, Chen X, Mirhakkak M, Li H, Jia W, Xu A, Nielsen HB, Nieuwdorp M, Loomba R, Ni Y, Panagiotou G.	Microbiome	10.1186/s40168-024-01990-y	2025
Phylogeny	Development of a Novel Metagenomic Biomarker for Prediction of Upper Gastrointestinal Tract Involvement in Patients With Crohn's Disease.	Kwak MS, Cha JM, Shin HP, Jeon JW, Yoon JY.	Front Microbiol	10.3389/fmicb.2020.01162	2020
	Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.	Wang Y, Chen J, Ni Y, Liu Y, Gao X, Tse MA, Panagiotou G, Xu A.	Gut Microbes	10.1080/19490976.2024.2416928	2024
	MicrobiotaProcess: A comprehensive R package for deep mining microbiome.	Xu S, Zhan L, Tang W, Wang Q, Dai Z, Zhou L, Feng T, Chen M, Wu T, Hu E, Yu G.	Innovation (Camb)	10.1016/j.xinn.2023.100388	2023
	The antioxidant tempol transforms gut microbiome to resist obesity in female C3H mice fed a high fat diet.	Choudhuri R, Sowers AL, Chandramouli GVR, Gamson J, Krishna MC, Mitchell JB, Cook JA.	Free Radic Biol Med	10.1016/j.freeradbiomed.2021.12.006	2022
	Gut microbiota from coronary artery disease patients contributes to vascular dysfunction in mice by regulating bile acid metabolism and immune activation.	Liu H, Tian R, Wang H, Feng S, Li H, Xiao Y, Luan X, Zhang Z, Shi N, Niu H, Zhang S.	J Transl Med	10.1186/s12967-020-02539-x	2020
	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
Enzymology	X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA.	Shimekake Y, Hirato Y, Funabashi R, Okazaki S, Goto M, Furuichi T, Suzuki H, Kera Y, Takahashi S.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x20013333	2020
Enzymology	Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications.	Aleshina YA, Aleshin VA.	Int J Mol Sci	10.3390/ijms25084341	2024
	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
	New mechanisms for bacterial degradation of sulfoquinovose.	Wei Y, Tong Y, Zhang Y.	Biosci Rep	10.1042/bsr20220314	2022
	Waterborne Human Pathogenic Viruses in Complex Microbial Communities: Environmental Implication on Virus Infectivity, Persistence, and Disinfection.	Zhang M, Altan-Bonnet N, Shen Y, Shuai D.	Environ Sci Technol	10.1021/acs.est.2c00233	2022
	A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients.	Obuya S, Elkholy A, Avuthu N, Behring M, Bajpai P, Agarwal S, Kim HG, El-Nikhely N, Akinyi P, Orwa J, Afaq F, Abdalla M, Michael A, Farouk M, Bateman LB, Fouad M, Saleh M, Guda C, Manne U, Arafat W.	J Gastrointest Oncol	10.21037/jgo-22-116	2022
Metabolism	Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation.	Schroder L, Kaiser S, Flemer B, Hamm J, Hinrichsen F, Bordoni D, Rosenstiel P, Sommer F.	Nutrients	10.3390/nu12103032	2020
	Sustained Drug Treatment Alters the Gut Microbiota in Rheumatoid Arthritis.	Mei L, Yang Z, Zhang X, Liu Z, Wang M, Wu X, Chen X, Huang Q, Huang R.	Front Immunol	10.3389/fimmu.2021.704089	2021
Metabolism	Modular coenzyme specificity: a domain-swopped chimera of glutamate dehydrogenase.	Sharkey MA, Engel PC.	Proteins	10.1002/prot.22433	2009
	Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate.	Ferreira S, Pereira R, Liu F, Vilaca P, Rocha I.	Biotechnol Biofuels	10.1186/s13068-019-1565-x	2019
Enzymology	CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.	Wakabayashi T, Oide M, Nakasako M.	Sci Rep	10.1038/s41598-024-61793-x	2024
	Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production.	Volf J, Crhanova M, Karasova D, Faldynova M, Kubasova T, Seidlerova Z, Sebkova A, Zeman M, Juricova H, Matiasovicova J, Foltyn M, Tvrdon Z, Rychlik I.	Microorganisms	10.3390/microorganisms9071480	2021
	Clinical Significance of Probiotics for Children with Idiopathic Nephrotic Syndrome.	Yamaguchi T, Tsuji S, Akagawa S, Akagawa Y, Kino J, Yamanouchi S, Kimata T, Hashiyada M, Akane A, Kaneko K.	Nutrients	10.3390/nu13020365	2021
	Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship?	Lee KW, Shin JS, Lee CM, Han HY, O Y, Kim HW, Cho TJ.	Nutrients	10.3390/nu15051131	2023
Genetics	Global compositional and functional states of the human gut microbiome in health and disease.	Lee S, Portlock T, Le Chatelier E, Garcia-Guevara F, Clasen F, Onate FP, Pons N, Begum N, Harzandi A, Proffitt C, Rosario D, Vaga S, Park J, von Feilitzen K, Johansson F, Zhang C, Edwards LA, Lombard V, Gauthier F, Steves CJ, Gomez-Cabrero D, Henrissat B, Lee D, Engstrand L, Shawcross DL, Proctor G, Almeida M, Nielsen J, Mardinoglu A, Moyes DL, Ehrlich SD, Uhlen M, Shoaie S.	Genome Res	10.1101/gr.278637.123	2024
Genetics	Monensin Alters the Functional and Metabolomic Profile of Rumen Microbiota in Beef Cattle.	Ogunade I, Schweickart H, Andries K, Lay J, Adeyemi J.	Animals (Basel)	10.3390/ani8110211	2018
	Immune cells: the key mediator between the gut microbiota and osteoporosis.	Ma T, Zhang T, Peng C, Liu K, Xiong Y, Chen K, Peng N, Wei Z, Kuang J, Ou L.	Front Immunol	10.3389/fimmu.2025.1680021	2025
Enzymology	Clostridium symbiosum as a cause of bloodstream infection in an immunocompetent patient.	Decousser JW, Bartizel C, Zamni M, Fadel N, Doucet-Populaire F.	Anaerobe	10.1016/j.anaerobe.2007.04.003	2007
	Potent and specific antibiotic combination therapy against Clostridioides difficile.	Chioti VT, McWhorter KL, Blue TC, Li Y, Xu F, Jeffrey PD, Davis KM, Seyedsayamdost MR.	Nat Chem Biol	10.1038/s41589-024-01651-z	2024
	A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers.	Xu J, Zheng Z, Yang L, Li R, Ma X, Zhang J, Yin F, Liu L, Xu Q, Shen Q, Shen X, Wu C, Liu J, Qin N, Sheng J, Jin P, Jin P.	Cell Biosci	10.1186/s13578-022-00940-1	2022
	Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer.	Wu X, Tang Z, Zhao R, Wang Y, Wang X, Liu S, Zou H.	Front Oncol	10.3389/fonc.2023.1218056	2023
	Tumor bacterial markers diagnose the initiation and four stages of colorectal cancer.	Cai P, Xiong J, Sha H, Dai X, Lu J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1123544	2023
Enzymology	A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach.	Barberio B, Facchin S, Patuzzi I, Ford AC, Massimi D, Valle G, Sattin E, Simionati B, Bertazzo E, Zingone F, Savarino EV.	Gut Microbes	10.1080/19490976.2022.2028366	2022
	Mechanisms Linking the Gut-Muscle Axis With Muscle Protein Metabolism and Anabolic Resistance: Implications for Older Adults at Risk of Sarcopenia.	Prokopidis K, Chambers E, Ni Lochlainn M, Witard OC.	Front Physiol	10.3389/fphys.2021.770455	2021
	Different gut microbiota in U.S. formula-fed infants consuming a meat vs. dairy-based complementary foods: A randomized controlled trial.	Tang M, Ma C, Weinheimer-Haus EM, Robertson CE, Kofonow JM, Berman LM, Waljee A, Zhu J, Frank DN, Krebs NF.	Front Nutr	10.3389/fnut.2022.1063518	2022
	Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review.	Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.804644	2022
Enzymology	[Epidemiological study on cigar-shaped clostridia isolated in a local Japanese general hospital].	Daimon Y, Tanaka K, Watanabe K.	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi1970.82.205	2008
Genetics	Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake.	Xie Y, Sun H, Xue M, Liu J.	Anim Microbiome	10.1186/s42523-022-00170-3	2022
	Ten-Week Sucralose Consumption Induces Gut Dysbiosis and Altered Glucose and Insulin Levels in Healthy Young Adults.	Mendez-Garcia LA, Bueno-Hernandez N, Cid-Soto MA, De Leon KL, Mendoza-Martinez VM, Espinosa-Flores AJ, Carrero-Aguirre M, Esquivel-Velazquez M, Leon-Hernandez M, Viurcos-Sanabria R, Ruiz-Barranco A, Cota-Arce JM, Alvarez-Lee A, De Leon-Nava MA, Melendez G, Escobedo G.	Microorganisms	10.3390/microorganisms10020434	2022
	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
	MS-20 enhances the gut microbiota-associated antitumor effects of anti-PD1 antibody.	Lee PJ, Hung CM, Yang AJ, Hou CY, Chou HW, Chang YC, Chu WC, Huang WY, Kuo WC, Yang CC, Lin KI, Hung KH, Chang LC, Lee KY, Kuo HP, Lu KM, Lai HC, Kuo ML, Chen WJ.	Gut Microbes	10.1080/19490976.2024.2380061	2024
	Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population.	Jeyaram K, Lahti L, Tims S, Heilig HGHJ, van Gelder AH, de Vos WM, Smidt H, Zoetendal EG.	Nat Commun	10.1038/s41467-025-56014-6	2025
	Immunological design of commensal communities to treat intestinal infection and inflammation.	Brown RL, Larkinson MLY, Clarke TB.	PLoS Pathog	10.1371/journal.ppat.1009191	2021
Phylogeny	Gut microbial features and dietary fiber intake predict gut microbiota response to resistant starch supplementation.	Devarakonda SLS, Superdock DK, Ren J, Johnson LM, Loinard-Gonzalez AAP, Poole AC.	Gut Microbes	10.1080/19490976.2024.2367301	2024
Metabolism	Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males.	Hermes GDA, Reijnders D, Kootte RS, Goossens GH, Smidt H, Nieuwdorp M, Blaak EE, Zoetendal EG.	Sci Rep	10.1038/s41598-020-64574-4	2020
	Effects of Complementary Feeding With Different Protein-Rich Foods on Infant Growth and Gut Health: Study Protocol.	Tang M, Matz KL, Berman LM, Davis KN, Melanson EL, Frank DN, Hendricks AE, Krebs NF.	Front Pediatr	10.3389/fped.2021.793215	2021
	Integrated analysis of microbe-host interactions in Crohn's disease reveals potential mechanisms of microbial proteins on host gene expression.	Sudhakar P, Andrighetti T, Verstockt S, Caenepeel C, Ferrante M, Sabino J, Verstockt B, Vermeire S.	iScience	10.1016/j.isci.2022.103963	2022
	Meta-analysis of the microbial biomarkers in the gut-lung crosstalk in COVID-19, community-acquired pneumonia and Clostridium difficile infections.	Aishwarya S, Gunasekaran K.	Lett Appl Microbiol	10.1111/lam.13798	2022
	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
Genetics	Circulating Short-Chain Fatty Acids Are Positively Associated with Adiposity Measures in Chinese Adults.	Wang Y, Wang H, Howard AG, Meyer KA, Tsilimigras MCB, Avery CL, Sha W, Sun S, Zhang J, Su C, Wang Z, Zhang B, Fodor AA, Gordon-Larsen P.	Nutrients	10.3390/nu12072127	2020
Metabolism	Swiveling domain mechanism in pyruvate phosphate dikinase.	Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O.	Biochemistry	10.1021/bi701848w	2007
	A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.	Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V.	Nucleic Acids Res	10.1093/nar/gkae399	2024
Genetics	Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder.	Kovtun AS, Averina OV, Angelova IY, Yunes RA, Zorkina YA, Morozova AY, Pavlichenko AV, Syunyakov TS, Karpenko OA, Kostyuk GP, Danilenko VN.	Biomedicines	10.3390/biomedicines10092162	2022
	Rhubarb Enema Increasing Short-Chain Fatty Acids that Improves the Intestinal Barrier Disruption in CKD May Be Related to the Regulation of Gut Dysbiosis.	Ji C, Lu F, Wu Y, Lu Z, Mo Y, Han L, Lin Q, Liu X, Zou C.	Biomed Res Int	10.1155/2022/1896781	2022
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
Enzymology	The contribution of tryptophan residues to conformational changes in clostridial glutamate dehydrogenase--W64 and W449 as mediators of the cooperative response to glutamate.	Hamza MA, Martin SR, Engel PC.	FEBS J	10.1111/j.1742-4658.2007.05940.x	2007
	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
	Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape.	Grant ET, Parrish A, Boudaud M, Hunewald O, Hirayama A, Ollert M, Fukuda S, Desai MS.	Microbiome	10.1186/s40168-024-01898-7	2024
	A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data.	Chen EZ, Bushman FD, Li H.	Stat Biosci	10.1007/s12561-016-9148-x	2017
	Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function.	Hassouneh SA, Loftus M, Yooseph S.	Front Microbiol	10.3389/fmicb.2021.673632	2021
	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
	Puerarin improves skeletal muscle strength by regulating gut microbiota in young adult rats.	Yang W, Gao B, Qin L, Wang X.	J Orthop Translat	10.1016/j.jot.2022.08.009	2022
	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
	Both Disease Activity and HLA-B27 Status Are Associated With Gut Microbiome Dysbiosis in Spondyloarthritis Patients.	Berland M, Meslier V, Berreira Ibraim S, Le Chatelier E, Pons N, Maziers N, Thirion F, Gauthier F, Plaza Onate F, Furet JP, Leboime A, Said-Nahal R, Levenez F, Galleron N, Quinquis B, Langella P, Ehrlich SD, Breban M.	Arthritis Rheumatol	10.1002/art.42289	2023
	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
	Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report.	Wei S, Jespersen ML, Baunwall SMD, Myers PN, Smith EM, Dahlerup JF, Rasmussen S, Nielsen HB, Licht TR, Bahl MI, Hvas CL.	Microbiome	10.1186/s40168-022-01394-w	2022
	The gut-cardiovascular connection: new era for cardiovascular therapy.	Cheng CK, Huang Y.	Med Rev (2021)	10.1515/mr-2021-0002	2021
	Lactobacillus rhamnosus Probio-M9 Improves the Quality of Life in Stressed Adults by Gut Microbiota.	Zheng Y, Yu Z, Zhang W, Sun T.	Foods	10.3390/foods10102384	2021
	The Gut Microbiota-Related Antihyperglycemic Effect of Metformin.	Szymczak-Pajor I, Drzewoski J, Kozlowska M, Krekora J, Sliwinska A.	Pharmaceuticals (Basel)	10.3390/ph18010055	2025
	The impact of complementary feeding foods of animal origin on growth and the risk of overweight in infants.	Tang M.	Anim Front	10.1093/af/vfz037	2019
	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
	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
Pathogenicity	Chitin Glucan Shifts Luminal and Mucosal Microbial Communities, Improve Epithelial Barrier and Modulates Cytokine Production In Vitro.	Calatayud M, Verstrepen L, Ghyselinck J, Van den Abbeele P, Marzorati M, Modica S, Ranjanoro T, Maquet V.	Nutrients	10.3390/nu13093249	2021
	Millet-based supplement restored gut microbial diversity of acute malnourished pigs.	Li X, Hui Y, Leng B, Ren J, Song Y, Che L, Peng X, Huang B, Liu S, Li L, Nielsen DS, Li Y, Dai X, Zhao S.	PLoS One	10.1371/journal.pone.0250423	2021
	Crosstalk between the Gut and Brain in Ischemic Stroke: Mechanistic Insights and Therapeutic Options.	Huang W, Zhu L, Song W, Zhang M, Teng L, Wu M.	Mediators Inflamm	10.1155/2022/6508046	2022
	Fecal Enterotoxigenic Bacteroides fragilis-Peptostreptococcus stomatis-Parvimonas micra Biomarker for Noninvasive Diagnosis and Prognosis of Colorectal Laterally Spreading Tumor.	Shen X, Li J, Li J, Zhang Y, Li X, Cui Y, Gao Q, Chen X, Chen Y, Fang JY.	Front Oncol	10.3389/fonc.2021.661048	2021
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
Phenotype	Moving beyond microbiome-wide associations to causal microbe identification.	Surana NK, Kasper DL.	Nature	10.1038/nature25019	2017
	An Examination by Site-Directed Mutagenesis of Putative Key Residues in the Determination of Coenzyme Specificity in Clostridial NAD-Dependent Glutamate Dehydrogenase.	Griffin J, Engel PC.	Enzyme Res	10.4061/2011/595793	2011
	Diversity of Intestinal Clostridium coccoides Group in the Japanese Population, as Demonstrated by Reverse Transcription-Quantitative PCR.	Kurakawa T, Ogata K, Matsuda K, Tsuji H, Kubota H, Takada T, Kado Y, Asahara T, Takahashi T, Nomoto K.	PLoS One	10.1371/journal.pone.0126226	2015
Enzymology	Detection of multiple active site domain motions in transient-state component time courses of the Clostridium symbiosum L-glutamate dehydrogenase-catalyzed oxidative deamination reaction.	Tally JF, Maniscalco SJ, Saha SK, Fisher HF.	Biochemistry	10.1021/bi0202068	2002
	The fecal microbiota of patients with pancreatic ductal adenocarcinoma and autoimmune pancreatitis characterized by metagenomic sequencing.	Zhou W, Zhang, Li Z, Jiang H, Li J, Ren R, Gao X, Li J, Wang X, Wang W, Yang Y.	J Transl Med	10.1186/s12967-021-02882-7	2021
	Standardized Astragalus Mongholicus Bunge-Curcuma Aromatica Salisb. Extract Efficiently Suppresses Colon Cancer Progression Through Gut Microbiota Modification in CT26-Bearing Mice.	Gu J, Sun R, Wang Q, Liu F, Tang D, Chang X.	Front Pharmacol	10.3389/fphar.2021.714322	2021
Phylogeny	Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis.	Huh JW, Roh TY.	BMC Microbiol	10.1186/s12866-020-01887-4	2020
	Relationship between changes in microbiota induced by resveratrol and its anti-diabetic effect on type 2 diabetes.	Fernandez-Quintela A, Macarulla MT, Gomez-Zorita S, Gonzalez M, Milton-Laskibar I, Portillo MP.	Front Nutr	10.3389/fnut.2022.1084702	2022
	Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging.	Sun L, Li Z, Hu C, Ding J, Zhou Q, Pang G, Wu Z, Yang R, Li S, Li J, Cai J, Sun Y, Li R, Zhen H, Sun S, Zhang J, Fang M, Chen Z, Lv Y, Cao Q, Sun Y, Gong R, Huang Z, Duan Y, Liu H, Dong J, Li J, Ruan J, Lu H, He B, Li N, Li T, Xue W, Li Y, Shen J, Yang F, Zhao C, Liang Q, Zhang M, Chen C, Gong H, Hou Y, Wang J, Zhang Y, Yang H, Zhu S, Xiao L, Jin Z, Guo H, Zhao P, Brix S, Xu X, Jia H, Kristiansen K, Yang Z, Nie C.	Aging Cell	10.1111/acel.14028	2023
	Infection leaves a genetic and functional mark on the gut population of a commensal bacterium.	Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2023.04.005	2023
Metabolism	Compositional change of gut microbiome and osteocalcin expressing endothelial progenitor cells in patients with coronary artery disease.	Toya T, Ozcan I, Corban MT, Sara JD, Marietta EV, Ahmad A, Horwath IE, Loeffler DL, Murray JA, Lerman LO, Lerman A.	PLoS One	10.1371/journal.pone.0249187	2021
Enzymology	Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion.	Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H.	Biochemistry	10.1021/bi0484522	2005
Genetics	Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate Producers.	Elmen L, Zlamal JE, Scott DA, Lee RB, Chen DJ, Colas AR, Rodionov DA, Peterson SN.	Front Microbiol	10.3389/fmicb.2020.00892	2020
	Conversion of phosphoenolpyruvate to pyruvate in Thermoanaerobacterium saccharolyticum.	Cui J, Maloney MI, Olson DG, Lynd LR.	Metab Eng Commun	10.1016/j.mec.2020.e00122	2020
Phylogeny	Bacteremia caused by Clostridium symbiosum.	Elsayed S, Zhang K.	J Clin Microbiol	10.1128/jcm.42.9.4390-4392.2004	2004
Genetics	Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.	Schirmer M, Strazar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2023.12.013	2024
	The influences of low protein diet on the intestinal microbiota of mice.	Masuoka H, Suda W, Tomitsuka E, Shindo C, Takayasu L, Horwood P, Greenhill AR, Hattori M, Umezaki M, Hirayama K.	Sci Rep	10.1038/s41598-020-74122-9	2020
Genetics	Alleviation of Metabolic Disturbance by Substituting Kanjang High in Bacillus for Salt through Modulation of Gut Microbiota in Estrogen-Deficient Rats.	Park S, Zhang T, Yue Y, Jeong SJ, Ryu MS, Wu X, Yang HJ, Jeong DY.	Foods	10.3390/foods11131951	2022
	EloR interacts with the lytic transglycosylase MltG at midcell in Streptococcus pneumoniae R6.	Winther AR, Kjos M, Herigstad ML, Havarstein LS, Straume D.	J Bacteriol	10.1128/jb.00691-20	2021
Pathogenicity	16S rRNA Sequencing and Metagenomics Study of Gut Microbiota: Implications of BDB on Type 2 Diabetes Mellitus.	Zhang L, Luo J, Li X, Guo S, Shi D.	Mar Drugs	10.3390/md18090469	2020
Genetics	XX sex chromosome complement modulates immune responses to heat-killed Streptococcus pneumoniae immunization in a microbiome-dependent manner.	Amato-Menker CJ, Hopen Q, Pettit A, Gandhi J, Hu G, Schafer R, Franko J.	Biol Sex Differ	10.1186/s13293-024-00597-0	2024
	Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism.	Minges A, Hoppner A, Groth G.	Protein Sci	10.1002/pro.3184	2017
	Database limitations for studying the human gut microbiome.	Dias CK, Starke R, Pylro VS, Morais DK.	PeerJ Comput Sci	10.7717/peerj-cs.289	2020
	A study of the correlation between stroke and gut microbiota over the last 20years: a bibliometric analysis.	Han S, Cai L, Chen P, Kuang W.	Front Microbiol	10.3389/fmicb.2023.1191758	2023
Enzymology	Identification of domain-domain docking sites within Clostridium symbiosum pyruvate phosphate dikinase by amino acid replacement.	Wei M, Li Z, Ye D, Herzberg O, Dunaway-Mariano D.	J Biol Chem	10.1074/jbc.m006149200	2000
	Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.	Hanson BT, Dimitri Kits K, Loffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A.	ISME J	10.1038/s41396-021-00968-0	2021
Enzymology	Investigation of the role of the domain linkers in separate site catalysis by Clostridium symbiosum pyruvate phosphate dikinase.	Wei M, Ye D, Dunaway-Mariano D.	Biochemistry	10.1021/bi0113061	2001
	In vitro Engineering of Novel Bioactivity in the Natural Enzymes.	Tiwari V.	Front Chem	10.3389/fchem.2016.00039	2016
Metabolism	Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase.	Ye D, Wei M, McGuire M, Huang K, Kapadia G, Herzberg O, Martin BM, Dunaway-Mariano D.	J Biol Chem	10.1074/jbc.m105631200	2001
	Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer.	Yuan Y, Chen Y, Yao F, Zeng M, Xie Q, Shafiq M, Noman SM, Jiao X.	Front Cell Dev Biol	10.3389/fcell.2021.736994	2021
Enzymology	2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum.	Hans M, Sievers J, Muller U, Bill E, Vorholt JA, Linder D, Buckel W.	Eur J Biochem	10.1046/j.1432-1327.1999.00748.x	1999
Metabolism	Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria.	Kim J, Hetzel M, Boiangiu CD, Buckel W.	FEMS Microbiol Rev	10.1016/j.femsre.2004.03.001	2004
Metabolism	Kinetic analysis of phenylalanine dehydrogenase mutants designed for aliphatic amino acid dehydrogenase activity with guidance from homology-based modelling.	Seah SY, Britton KL, Rice DW, Asano Y, Engel PC.	Eur J Biochem	10.1046/j.1432-1033.2003.03852.x	2003
Metabolism	Reciprocal Interactions between Epigallocatechin-3-gallate (EGCG) and Human Gut Microbiota In Vitro.	Liu Z, de Bruijn WJC, Bruins ME, Vincken JP.	J Agric Food Chem	10.1021/acs.jafc.0c03587	2020
Pathogenicity	Gut Microbiome Structure and Association with Host Factors in a Korean Population.	Lim MY, Hong S, Bang SJ, Chung WH, Shin JH, Kim JH, Nam YD.	mSystems	10.1128/msystems.00179-21	2021
	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
Metabolism	Microbial Metabolism of Theaflavin-3,3'-digallate and Its Gut Microbiota Composition Modulatory Effects.	Liu Z, de Bruijn WJC, Bruins ME, Vincken JP.	J Agric Food Chem	10.1021/acs.jafc.0c06622	2021
	Dysbiosis in Pediatrics Is Associated with Respiratory Infections: Is There a Place for Bacterial-Derived Products?	Ballarini S, Rossi GA, Principi N, Esposito S.	Microorganisms	10.3390/microorganisms9020448	2021
	Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.	Kumar S, Ma B, Tsai CJ, Nussinov R.	Proteins	10.1002/(sici)1097-0134(20000301)38:4<368::aid-prot3>3.0.co;2-r	2000
Pathogenicity	Clostridium clostridioforme and Atopobium minutum clinical isolates with vanB-type resistance in France.	Marvaud JC, Mory F, Lambert T.	J Clin Microbiol	10.1128/jcm.00308-11	2011
	Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families.	Yang J, Li D, Yang Z, Dai W, Feng X, Liu Y, Jiang Y, Li P, Li Y, Tang B, Zhou Q, Qiu C, Zhang C, Xu X, Feng S, Wang D, Wang H, Wang W, Zheng Y, Zhang L, Wang W, Zhou K, Li S, Yu P.	Gut Microbes	10.1080/19490976.2020.1712986	2020
	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
	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	Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase.	McGuire M, Huang K, Kapadia G, Herzberg O, Dunaway-Mariano D.	Biochemistry	10.1021/bi980920i	1998
Enzymology	A thermally sensitive loop in clostridial glutamate dehydrogenase detected by limited proteolysis.	Aghajanian S, Hovsepyan M, Geoghegan KF, Chrunyk BA, Engel PC.	J Biol Chem	10.1074/jbc.m206099200	2003
Metabolism	Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.	Stillman TJ, Migueis AM, Wang XG, Baker PJ, Britton KL, Engel PC, Rice DW.	J Mol Biol	10.1006/jmbi.1998.2335	1999
Metabolism	Single amino acid substitution in Bacillus sphaericus phenylalanine dehydrogenase dramatically increases its discrimination between phenylalanine and tyrosine substrates.	Seah SY, Britton KL, Rice DW, Asano Y, Engel PC.	Biochemistry	10.1021/bi020196a	2002
	Joint Asian Pacific Association of Gastroenterology (APAGE)-Asian Pacific Society of Digestive Endoscopy (APSDE) clinical practice guidelines on the use of non-invasive biomarkers for diagnosis of colorectal neoplasia.	Chan FKL, Wong MCS, Chan AT, East JE, Chiu HM, Makharia GK, Weller D, Ooi CJ, Limsrivilai J, Saito Y, Hang DV, Emery JD, Makmun D, Wu K, Ali RAR, Ng SC.	Gut	10.1136/gutjnl-2023-329429	2023
Phylogeny	Four cases of bacteremia caused by Oscillibacter ruminantium, a newly described species.	Sydenham TV, Arpi M, Klein K, Justesen US.	J Clin Microbiol	10.1128/jcm.03128-13	2014
	Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations.	Shen WX, Liang SR, Jiang YY, Chen YZ.	Patterns (N Y)	10.1016/j.patter.2022.100658	2023
Metabolism	Intersubunit communication in hybrid hexamers of K89L/A163G/S380A and C320S mutants of glutamate dehydrogenase from Clostridium symbiosum.	Goyal A, Aghajanian S, Hayden BM, Wang XG, Engel PC.	Biochemistry	10.1021/bi971419d	1997
	Competitive exclusion culture for swine	Nisbet DJ, Corrier DE, Stanker LH.	United States Department of Agriculture patents.		1999
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	Alteration of the quaternary structure of glutamate dehydrogenase from Clostridium symbiosum by a single mutation distant from the subunit interfaces.	Dean JL, Colfen H, Harding SE, Rice DW, Engel PC.	Eur Biophys J	10.1007/s002490050055	1997
Enzymology	The 3.0 A resolution crystal structure of glycosomal pyruvate phosphate dikinase from Trypanosoma brucei.	Cosenza LW, Bringaud F, Baltz T, Vellieux FM.	J Mol Biol	10.1016/s0022-2836(02)00113-4	2002
Metabolism	Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.	Minges A, Ciupka D, Winkler C, Hoppner A, Gohlke H, Groth G.	Sci Rep	10.1038/srep45389	2017
Enzymology	Cloning of a pyruvate phosphate dikinase from Trypanosoma cruzi.	Maldonado RA, Fairlamb AH.	Mol Biochem Parasitol	10.1016/s0166-6851(00)00362-5	2001
	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
	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
Metabolism	The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants.	Tanaka M, Sanefuji M, Morokuma S, Yoden M, Momoda R, Sonomoto K, Ogawa M, Kato K, Nakayama J.	Gut Microbes	10.1080/19490976.2019.1650997	2020
	Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice.	Parrish A, Boudaud M, Grant ET, Willieme S, Neumann M, Wolter M, Craig SZ, De Sciscio A, Cosma A, Hunewald O, Ollert M, Desai MS.	Nat Microbiol	10.1038/s41564-023-01464-1	2023
Metabolism	Contribution of an aspartate residue, D114, in the active site of clostridial glutamate dehydrogenase to the enzyme's unusual pH dependence.	Coughlan S, Wang XG, Britton KL, Stillman TJ, Rice DW, Chiaraluce R, Consalvi V, Scandurra R, Engel PC.	Biochim Biophys Acta	10.1016/s0167-4838(00)00200-4	2001
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
Enzymology	Quaternary organization of the Staphylothermus marinus phosphoenolpyruvate synthase: angular reconstitution from cryoelectron micrographs with molecular modeling.	Li W, Ottensmeyer FP, Harauz G.	J Struct Biol	10.1006/jsbi.2000.4322	2000
Enzymology	The NAD-dependent glutamate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum: cloning, sequencing, and expression of the enzyme gene(1).	Kujo C, Sakuraba H, Nunoura N, Ohshima T.	Biochim Biophys Acta	10.1016/s0167-4838(99)00192-2	1999
Enzymology	Use of protein engineering to explore subunit interactions in an allosteric enzyme: construction of inter-subunit hybrids in Clostridium symbiosum glutamate dehydrogenase.	Aghajanian S, Engel PC.	Protein Eng	10.1093/protein/11.7.569	1998
Enzymology	Kinetic studies on the binding of 1,N6-etheno-NAD+ to glutamate dehydrogenase from Clostridium symbiosum.	Basso LA, Engel PC, Walmsley AR.	Biochim Biophys Acta	10.1016/s0167-4838(97)00032-0	1997
Phylogeny	Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children.	Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan YM, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, Gordon JI.	Science	10.1126/science.aad3311	2016
Metabolism	The Prebiotic Effects of Oats on Blood Lipids, Gut Microbiota, and Short-Chain Fatty Acids in Mildly Hypercholesterolemic Subjects Compared With Rice: A Randomized, Controlled Trial.	Xu D, Feng M, Chu Y, Wang S, Shete V, Tuohy KM, Liu F, Zhou X, Kamil A, Pan D, Liu H, Yang X, Yang C, Zhu B, Lv N, Xiong Q, Wang X, Sun J, Sun G, Yang Y.	Front Immunol	10.3389/fimmu.2021.787797	2021
Pathogenicity	Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota.	Aljahdali NH, Sanad YM, Han J, Foley SL.	BMC Microbiol	10.1186/s12866-020-02008-x	2020
	Contribution of salt bridges toward protein thermostability.	Kumar S, Tsai CJ, Ma B, Nussinov R.	J Biomol Struct Dyn	10.1080/07391102.2000.10506606	2000
	mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.	Zeng Y, Li J, Wei C, Zhao H, Wang T.	Genome Biol	10.1186/s13059-022-02657-3	2022
Metabolism	Faecal microbial biomarkers in early diagnosis of colorectal cancer.	Olovo CV, Huang X, Zheng X, Xu M.	J Cell Mol Med	10.1111/jcmm.17010	2021
Enzymology	Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase from Aspergillus niger.	Prakash P, Walvekar AS, Punekar NS, Bhaumik P.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x14021499	2014
Metabolism	Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut.	Wang Y, Leong LEX, Keating RL, Kanno T, Abell GCJ, Mobegi FM, Choo JM, Wesselingh SL, Mason AJ, Burr LD, Rogers GB.	Gut Microbes	10.1080/19490976.2018.1534512	2019
Enzymology	Pyruvate phosphate dikinase from a thermophilic actinomyces Microbispora rosea subsp. aerata: purification, characterization and molecular cloning of the gene.	Eisaki N, Tatsumi H, Murakami S, Horiuchi T.	Biochim Biophys Acta	10.1016/s0167-4838(99)00057-6	1999
Enzymology	Construction of a dimeric form of glutamate dehydrogenase from Clostridium symbiosum by site-directed mutagenesis.	Pasquo A, Britton KL, Stillman TJ, Rice DW, Colfen H, Harding SE, Scandurra R, Engel PC.	Biochim Biophys Acta	10.1016/s0167-4838(96)00017-9	1996
	Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria.	Shiver AL, Culver R, Deutschbauer AM, Huang KC.	Nat Protoc	10.1038/s41596-021-00531-3	2021
Metabolism	Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site.	Minges A, Groth G.	PLoS One	10.1371/journal.pone.0181139	2017
Metabolism	Determination of the nucleotide binding site within Clostridium symbiosum pyruvate phosphate dikinase by photoaffinity labeling, site-directed mutagenesis, and structural analysis.	McGuire M, Carroll LJ, Yankie L, Thrall SH, Dunaway-Mariano D, Herzberg O, Jayaram B, Haley BH.	Biochemistry	10.1021/bi960275k	1996
Enzymology	Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 2. Site-directed mutagenesis of an essential arginine contained within an apparent P-loop.	Yankie L, Xu Y, Dunaway-Mariano D.	Biochemistry	10.1021/bi00007a012	1995
Enzymology	NADP+-dependent glutamate dehydrogenase in the Antarctic psychrotolerant bacterium Psychrobacter sp. TAD1. Characterization, protein and DNA sequence, and relationship to other glutamate dehydrogenases.	Di Fraia R, Wilquet V, Ciardiello MA, Carratore V, Antignani A, Camardella L, Glansdorff N, Di Prisco G.	Eur J Biochem	10.1046/j.1432-1327.2000.00972.x	2000
Phylogeny	First Korean case of Robinsoniella peoriensis bacteremia in a patient with aspiration pneumonia.	Jeon Y, Kim TS, Kim HB, Park KU, Song J, Kim EC.	Ann Lab Med	10.3343/alm.2012.32.5.370	2012
Metabolism	Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis.	Xu Y, Yankie L, Shen L, Jung YS, Mariano PS, Dunaway-Mariano D, Martin BM.	Biochemistry	10.1021/bi00007a011	1995
Proteome	Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family.	Yip KS, Britton KL, Stillman TJ, Lebbink J, de Vos WM, Robb FT, Vetriani C, Maeder D, Rice DW.	Eur J Biochem	10.1046/j.1432-1327.1998.2550336.x	1998
	Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness.	Albuquerque TA, Zurek L.	Front Microbiol	10.3389/fmicb.2014.00590	2014
	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
Pathogenicity	In Vitro Testing of Potential Entamoeba histolytica Pyruvate Phosphate Dikinase Inhibitors.	Saidin S, Othman N, Noordin R.	Am J Trop Med Hyg	10.4269/ajtmh.17-0132	2017
	Short-Chain Fatty Acids and Human Health: From Metabolic Pathways to Current Therapeutic Implications.	Facchin S, Bertin L, Bonazzi E, Lorenzon G, De Barba C, Barberio B, Zingone F, Maniero D, Scarpa M, Ruffolo C, Angriman I, Savarino EV.	Life (Basel)	10.3390/life14050559	2024
	Sequence of a Giardia lamblia gene coding for the glycolytic enzyme, pyruvate,phosphate dikinase.	Nevalainen L, Hrdy I, Muller M.	Mol Biochem Parasitol	10.1016/0166-6851(96)02604-7	1996
	Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity.	Han L, Zhao L, Zhou Y, Yang C, Xiong T, Lu L, Deng Y, Luo W, Chen Y, Qiu Q, Shang X, Huang L, Mo Z, Huang S, Huang S, Liu Z, Yang W, Zhai L, Ning Z, Lin C, Huang T, Cheng C, Zhong LLD, Li S, Li S, Bian Z, Fang X.	ISME J	10.1038/s41396-021-01123-5	2022
	Faecalibacterium prausnitzii Skews Human DC to Prime IL10-Producing T Cells Through TLR2/6/JNK Signaling and IL-10, IL-27, CD39, and IDO-1 Induction.	Alameddine J, Godefroy E, Papargyris L, Sarrabayrouse G, Tabiasco J, Bridonneau C, Yazdanbakhsh K, Sokol H, Altare F, Jotereau F.	Front Immunol	10.3389/fimmu.2019.00143	2019
Metabolism	Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth.	Gillis CC, Hughes ER, Spiga L, Winter MG, Zhu W, Furtado de Carvalho T, Chanin RB, Behrendt CL, Hooper LV, Santos RL, Winter SE.	Cell Host Microbe	10.1016/j.chom.2017.11.006	2018
Metabolism	Metagenome-wide association of gut microbiome features for schizophrenia.	Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, Jie Z, Zhao B, Xiao L, Yang L, Zhang T, Feng J, Guo L, He X, Chen Y, Chen C, Gao C, Xu X, Yang H, Wang J, Dang Y, Madsen L, Brix S, Kristiansen K, Jia H, Ma X.	Nat Commun	10.1038/s41467-020-15457-9	2020
Enzymology	Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.	Stillman TJ, Baker PJ, Britton KL, Rice DW, Rodgers HF.	J Mol Biol	10.1016/0022-2836(92)90481-x	1992
Pathogenicity	The Gut Microbiota and Vascular Aging: A State-of-the-Art and Systematic Review of the Literature.	Agnoletti D, Piani F, Cicero AFG, Borghi C.	J Clin Med	10.3390/jcm11123557	2022
Metabolism	Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine.	Zhang K, Li H, Cho KM, Liao JC.	Proc Natl Acad Sci U S A	10.1073/pnas.0912903107	2010
Enzymology	Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus glutamate dehydrogenase.	Rice DW, Yip KS, Stillman TJ, Britton KL, Fuentes A, Connerton I, Pasquo A, Scandura R, Engel PC.	FEMS Microbiol Rev	10.1111/j.1574-6976.1996.tb00230.x	1996
Phylogeny	Systematic evaluation of supervised classifiers for fecal microbiota-based prediction of colorectal cancer.	Ai L, Tian H, Chen Z, Chen H, Xu J, Fang JY.	Oncotarget	10.18632/oncotarget.14488	2017
Enzymology	The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity.	Lilley KS, Baker PJ, Britton KL, Stillman TJ, Brown PE, Moir AJ, Engel PC, Rice DW, Bell JE, Bell E.	Biochim Biophys Acta	10.1016/0167-4838(91)90001-g	1991
	The glutamate dehydrogenase gene of Clostridium symbiosum. Cloning by polymerase chain reaction, sequence analysis and over-expression in Escherichia coli.	Teller JK, Smith RJ, McPherson MJ, Engel PC, Guest JR.	Eur J Biochem	10.1111/j.1432-1033.1992.tb16912.x	1992
Metabolism	Mechanistic interpretation of tryptophan fluorescence quenching in the time courses of glutamate dehydrogenase catalyzed reactions.	Saha SK, Maniscalco SJ, Fisher HF.	Biochemistry	10.1021/bi9612531	1996
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
	Analysis of the mobilization functions of the vancomycin resistance transposon Tn1549, a member of a new family of conjugative elements.	Tsvetkova K, Marvaud JC, Lambert T.	J Bacteriol	10.1128/jb.00680-09	2010
Metabolism	Functional studies of a glutamate dehydrogenase with known three-dimensional structure: steady-state kinetics of the forward and reverse reactions catalysed by the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum.	Syed SE, Engel PC, Parker DM.	Biochim Biophys Acta	10.1016/0304-4165(91)90020-h	1991
Enzymology	Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 A resolution.	Knapp S, de Vos WM, Rice D, Ladenstein R.	J Mol Biol	10.1006/jmbi.1996.0900	1997
Enzymology	Molecular analysis of surface-associated enzymes of Porphyromonas gingivalis.	Gharbia SE, Shah HN.	Clin Infect Dis	10.1093/clinids/20.supplement_2.s160	1995
	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
Enzymology	The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.	Yip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V.	Structure	10.1016/s0969-2126(01)00251-9	1995
Enzymology	Exchange of domains of glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus and the mesophilic bacterium Clostridium difficile: effects on catalysis, thermoactivity and stability.	Lebbink JH, Eggen RI, Geerling AC, Consalvi V, Chiaraluce R, Scandurra R, de Vos WM.	Protein Eng	10.1093/protein/8.12.1287	1995
	Longitudinal Analysis of the Intestinal Microbiota in Persistently Stunted Young Children in South India.	Dinh DM, Ramadass B, Kattula D, Sarkar R, Braunstein P, Tai A, Wanke CA, Hassoun S, Kane AV, Naumova EN, Kang G, Ward HD.	PLoS One	10.1371/journal.pone.0155405	2016
	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	Structure of NADP(+)-dependent glutamate dehydrogenase from Escherichia coli--reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases.	Sharkey MA, Oliveira TF, Engel PC, Khan AR.	FEBS J	10.1111/febs.12439	2013
	Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.	Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, Porter N, Martens E, O'Connell R, Jacob V, Scherl E, Crawford C, Stephens WZ, Casjens SR, Longman RS, Round JL.	Cell Host Microbe	10.1016/j.chom.2019.01.008	2019
	Correlation of intron-exon organisation with the three-dimensional structure in glutamate dehydrogenase.	Teller JK, Baker PJ, Britton KL, Engel PC, Rice DW, Stillman TJ.	Biochim Biophys Acta	10.1016/0167-4838(94)00240-h	1995
Enzymology	A difference in the sequence of steps in the reactions catalyzed by two closely homologous forms of glutamate dehydrogenase.	Maniscalco SJ, Saha SK, Vicedomine P, Fisher HF.	Biochemistry	10.1021/bi9509098	1996
Metabolism	The mechanism of substrate and coenzyme binding to clostridial glutamate dehydrogenase during reductive amination.	Basso LA, Engel PC, Walmsley AR.	Eur J Biochem	10.1111/j.1432-1033.1995.603_b.x	1995
	The -SH Protection Method for Determining Accurate K(d) Values for Enzyme-Coenzyme Complexes of NAD-Dependent Glutamate Dehydrogenase and Engineered Mutants: Evidence for Nonproductive NADPH Complexes.	Griffin J, Engel PC.	Enzyme Res	10.4061/2010/951472	2010
Pathogenicity	In vitro activity of meropenem compared with imipenem, metronidazole, ampicillin, and ampicillin/sulbactam against anaerobes.	Schumacher U, Manncke B, Gerbracht K, Werner H.	Arzneimittelforschung		1994
Metabolism	Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication.	Hulme H, Meikle LM, Strittmatter N, van der Hooft JJJ, Swales J, Bragg RA, Villar VH, Ormsby MJ, Barnes S, Brown SL, Dexter A, Kamat MT, Komen JC, Walker D, Milling S, Osterweil EK, MacDonald AS, Schofield CJ, Tardito S, Bunch J, Douce G, Edgar JM, Edrada-Ebel R, Goodwin RJA, Burchmore R, Wall DM.	Sci Adv	10.1126/sciadv.aax6328	2020
Metabolism	The biochemistry and enzymology of amino acid dehydrogenases.	Brunhuber NM, Blanchard JS.	Crit Rev Biochem Mol Biol	10.3109/10409239409083486	1994
	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
Enzymology	Insights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis.	Britton KL, Baker PJ, Borges KM, Engel PC, Pasquo A, Rice DW, Robb FT, Scandurra R, Stillman TJ, Yip KS.	Eur J Biochem	10.1111/j.1432-1033.1995.tb20515.x	1995
Metabolism	Identification and Characterization of a 25 kDa Protein That Is Indispensable for the Efficient Saccharification of Eisenia bicyclis in the Digestive Fluid of Aplysia kurodai.	Tsuji A, Kuwamura S, Shirai A, Yuasa K.	PLoS One	10.1371/journal.pone.0170669	2017
Enzymology	Energetics of pyruvate phosphate dikinase catalysis.	Mehl A, Xu Y, Dunaway-Mariano D.	Biochemistry	10.1021/bi00171a007	1994
	The role of electrostatic interactions on klentaq1 insight for domain separation.	Nurbaiti S, Martoprawiro MA, Akhmaloka, Hertadi R.	Bioinform Biol Insights	10.4137/bbi.s9390	2012
Metabolism	Kinetic evidence for separate site catalysis by pyruvate phosphate dikinase.	Thrall SH, Dunaway-Mariano D.	Biochemistry	10.1021/bi00171a008	1994
	Effect of intestinal bacteria on the virulence of Entamoeba histolytica.	Anaya-Velazquez F, Padilla-Vaca F.	Arch Med Res		1992
Metabolism	Characterisation of three novel alpha-L-arabinofuranosidases from a compost metagenome.	Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M.	BMC Biotechnol	10.1186/s12896-019-0510-1	2019
Enzymology	Allosteric behaviour of 1:5 hybrids of mutant subunits of Clostridium symbiosum glutamate dehydrogenase differing in their amino acid specificity.	Goyal A, Wang XG, Engel PC.	Biochem J	10.1042/0264-6021:3600651	2001
Enzymology	Sequential Extraction, Characterization, and Analysis of Pumpkin Polysaccharides for Their Hypoglycemic Activities and Effects on Gut Microbiota in Mice.	Wu HQ, Ma ZL, Zhang DX, Wu P, Guo YH, Yang F, Li DY.	Front Nutr	10.3389/fnut.2021.769181	2021
	Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.	Stillman TJ, Baker PJ, Britton KL, Rice DW.	J Mol Biol	10.1006/jmbi.1993.1665	1993
	Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis.	Britton KL, Baker PJ, Engel PC, Rice DW, Stillman TJ.	J Mol Biol	10.1006/jmbi.1993.1647	1993
Metabolism	Substrate binding domains in pyruvate phosphate dikinase.	Carroll LJ, Xu Y, Thrall SH, Martin BM, Dunaway-Mariano D.	Biochemistry	10.1021/bi00171a012	1994
Pathogenicity	An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness.	Marfil-Sanchez A, Zhang L, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M, Panagiotou G.	Gut Microbes	10.1080/19490976.2021.1993598	2021
Phylogeny	Assignment of the agent of Tyzzer's disease to Clostridium piliforme comb. nov. on the basis of 16S rRNA sequence analysis.	Duncan AJ, Carman RJ, Olsen GJ, Wilson KH.	Int J Syst Bacteriol	10.1099/00207713-43-2-314	1993
Metabolism	Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.	Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M.	Front Plant Sci	10.3389/fpls.2020.00754	2020
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
Metabolism	Identification of potential active-site residues in the human poly(ADP-ribose) polymerase.	Simonin F, Poch O, Delarue M, de Murcia G.	J Biol Chem	10.1016/s0021-9258(18)52907-0	1993
Metabolism	The mechanism of substrate and coenzyme binding to clostridial glutamate dehydrogenase during oxidative deamination.	Basso LA, Engel PC, Walmsley AR.	Eur J Biochem	10.1111/j.1432-1033.1993.tb17838.x	1993
	Structural relationship between the hexameric and tetrameric family of glutamate dehydrogenases.	Britton KL, Baker PJ, Rice DW, Stillman TJ.	Eur J Biochem	10.1111/j.1432-1033.1992.tb17357.x	1992
	Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.	Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, Andre S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sonderskov NB, MetaCardis Consortium, Kober L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clement K, Backhed F.	Nat Commun	10.1038/s41467-020-19589-w	2020
	Luciferase-based assay for adenosine: application to S-adenosyl-L-homocysteine hydrolase.	Burgos ES, Gulab SA, Cassera MB, Schramm VL.	Anal Chem	10.1021/ac203297z	2012
Metabolism	Characterization of the covalent enzyme intermediates formed during pyruvate phosphate dikinase catalysis.	Thrall SH, Mehl AF, Carroll LJ, Dunaway-Mariano D.	Biochemistry	10.1021/bi00058a014	1993
Metabolism	Detecting ricin: sensitive luminescent assay for ricin A-chain ribosome depurination kinetics.	Sturm MB, Schramm VL.	Anal Chem	10.1021/ac8026433	2009
Metabolism	Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.	Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.	Nat Med	10.1038/s41591-019-0405-7	2019
	Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. Implications for nucleotide specificity.	Baker PJ, Britton KL, Rice DW, Rob A, Stillman TJ.	J Mol Biol	10.1016/0022-2836(92)90848-e	1992
Pathogenicity	In vitro activity of nalidixic acid and its iron (III) complex on Entamoeba histolytica.	Anaya-Velazquez F, Padilla-Vaca F, Arias-Negrete S, Mendoza-Diaz G.	Trans R Soc Trop Med Hyg	10.1016/0035-9203(89)90498-7	1989
Metabolism	Subunit assembly and active site location in the structure of glutamate dehydrogenase.	Baker PJ, Britton KL, Engel PC, Farrants GW, Lilley KS, Rice DW, Stillman TJ.	Proteins	10.1002/prot.340120109	1992
	Limosilactobacillus reuteri administration alters the gut-brain-behavior axis in a sex-dependent manner in socially monogamous prairie voles.	Donovan M, Mackey CS, Lynch MDJ, Platt GN, Brown AN, Washburn BK, Trickey DJ, Curtis JT, Liu Y, Charles TC, Wang Z, Jones KM.	Front Microbiol	10.3389/fmicb.2023.1015666	2023
	Intestinal Flora Disruption and Novel Biomarkers Associated With Nasopharyngeal Carcinoma.	Jiang H, Li J, Zhang B, Huang R, Zhang J, Chen Z, Shang X, Li X, Nie X.	Front Oncol	10.3389/fonc.2019.01346	2019
Enzymology	Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum.	Rice DW, Hornby DP, Engel PC.	J Mol Biol	10.1016/0022-2836(85)90334-1	1985
Metabolism	C. difficile exploits a host metabolite produced during toxin-mediated disease.	Pruss KM, Sonnenburg JL.	Nature	10.1038/s41586-021-03502-6	2021
Enzymology	The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate.	Lilley KS, Engel PC.	Eur J Biochem	10.1111/j.1432-1033.1992.tb17079.x	1992
Enzymology	Coenzyme non-specific glutamate dehydrogenase from Chlorella pyrenoidosa 82T: electron microscopic studies.	Shatilov VR, Loseva LP, Tsuprun VL, Kaftanova AS, Kretovich WL.	Biochim Biophys Acta	10.1016/0167-4838(89)90227-6	1989
Phylogeny	Applying Data Mining to Classify Age by Intestinal Microbiota in 92 Healthy Men Using a Combination of Several Restriction Enzymes for T-RFLP Experiments.	Kobayashi T, Osaki T, Oikawa S.	Biosci Microbiota Food Health	10.12938/bmfh.33.65	2014
Metabolism	Absence of the KhpA and KhpB (JAG/EloR) RNA-binding proteins suppresses the requirement for PBP2b by overproduction of FtsA in Streptococcus pneumoniae D39.	Zheng JJ, Perez AJ, Tsui HT, Massidda O, Winkler ME.	Mol Microbiol	10.1111/mmi.13847	2017
	Fat, fibre and cancer risk in African Americans and rural Africans.	O'Keefe SJ, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, Puylaert PG, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, Nicholson JK, de Vos WM, Gaskins HR, Zoetendal EG.	Nat Commun	10.1038/ncomms7342	2015
	The Pyruvate-Phosphate Dikinase (C₄-SmPPDK) Gene From Suaeda monoica Enhances Photosynthesis, Carbon Assimilation, and Abiotic Stress Tolerance in a C₃ Plant Under Elevated CO₂ Conditions.	Yadav S, Rathore MS, Mishra A.	Front Plant Sci	10.3389/fpls.2020.00345	2020
Metabolism	Investigation into the Mode of Phosphate Activation in the 4-Hydroxy-4-Methyl-2-Oxoglutarate/4-Carboxy-4-Hydroxy-2-Oxoadipate Aldolase from Pseudomonas putida F1.	Mazurkewich S, Seah SY.	PLoS One	10.1371/journal.pone.0164556	2016
Enzymology	The biotin-dependent sodium ion pump glutaconyl-CoA decarboxylase from Fusobacterium nucleatum (subsp. nucleatum). Comparison with the glutaconyl-CoA decarboxylases from gram-positive bacteria.	Beatrix B, Bendrat K, Rospert S, Buckel W.	Arch Microbiol	10.1007/bf00276532	1990
	Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease.	Douglas GM, Hansen R, Jones CMA, Dunn KA, Comeau AM, Bielawski JP, Tayler R, El-Omar EM, Russell RK, Hold GL, Langille MGI, Van Limbergen J.	Microbiome	10.1186/s40168-018-0398-3	2018
Genetics	Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.	Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C.	Nat Microbiol	10.1038/s41564-017-0089-z	2018
Enzymology	Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme.	Wakamatsu T, Sakuraba H, Kitamura M, Hakumai Y, Fukui K, Ohnishi K, Ashiuchi M, Ohshima T.	Appl Environ Microbiol	10.1128/aem.02710-16	2017
Metabolism	Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties.	Neff CP, Rhodes ME, Arnolds KL, Collins CB, Donnelly J, Nusbacher N, Jedlicka P, Schneider JM, McCarter MD, Shaffer M, Mazmanian SK, Palmer BE, Lozupone CA.	Cell Host Microbe	10.1016/j.chom.2016.09.002	2016
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
Metabolism	Metformin elicits antitumour effect by modulation of the gut microbiota and rescues Fusobacterium nucleatum-induced colorectal tumourigenesis.	Huang X, Hong X, Wang J, Sun T, Yu T, Yu Y, Fang J, Xiong H.	EBioMedicine	10.1016/j.ebiom.2020.103037	2020
Metabolism	A sodium ion gradient as energy source for Peptostreptococcus asaccharolyticus.	Wohlfarth G, Buckel W.	Arch Microbiol	10.1007/bf00447055	1985
Enzymology	A monomeric mutant of Clostridium symbiosum glutamate dehydrogenase: comparison with a structured monomeric intermediate obtained during refolding.	Millevoi S, Pasquo A, Chiaraluce R, Consalvi V, Giangiacomo L, Britton KL, Stillman TJ, Rice DW, Engel PC.	Protein Sci	10.1002/pro.5560070414	1998
Metabolism	Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.	Vital M, Gao J, Rizzo M, Harrison T, Tiedje JM.	ISME J	10.1038/ismej.2014.179	2015
Metabolism	Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model.	Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI, Mehrabian M, Denu JM, Backhed F, Lusis AJ, Rey FE.	Nat Microbiol	10.1038/s41564-018-0272-x	2018
Enzymology	A pH-dependent activation-inactivation equilibrium in glutamate dehydrogenase of Clostridium symbiosum.	Syed SE, Engel PC.	Biochem J	10.1042/bj2710351	1990
	Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups.	Tulstrup MV, Roager HM, Thaarup IC, Frandsen HL, Frokiaer H, Licht TR, Bahl MI.	Commun Biol	10.1038/s42003-018-0140-5	2018
	Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.	Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, Li H, Wu C, Hu C, Xu Q, Zhou J, Cai S, Wang D, Huang Y, Breban M, Qin N, Ehrlich SD.	Genome Biol	10.1186/s13059-017-1271-6	2017
Enzymology	Purification, characterisation and reconstitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria.	Buckel W, Semmler R.	Eur J Biochem	10.1111/j.1432-1033.1983.tb07760.x	1983
	An atypical lipoteichoic acid from Clostridium perfringens elicits a broadly cross-reactive and protective immune response.	Wenzel CQ, Mills DC, Dobruchowska JM, Vlach J, Nothaft H, Nation P, Azadi P, Melville SB, Carlson RW, Feldman MF, Szymanski CM.	J Biol Chem	10.1074/jbc.ra119.009978	2020
Enzymology	Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.	Spring S, Bunk B, Sproer C, Schumann P, Rohde M, Tindall BJ, Klenk HP.	ISME J	10.1038/ismej.2016.84	2016
Enzymology	Active site and remote contributions to catalysis in methylthioadenosine nucleosidases.	Thomas K, Cameron SA, Almo SC, Burgos ES, Gulab SA, Schramm VL.	Biochemistry	10.1021/bi501487w	2015
Genetics	Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia).	Rozanov AS, Bryanskaya AV, Malup TK, Meshcheryakova IA, Lazareva EV, Taran OP, Ivanisenko TV, Ivanisenko VA, Zhmodik SM, Kolchanov NA, Peltek SE.	BMC Genomics	10.1186/1471-2164-15-s12-s12	2014
Metabolism	The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary beta-mannans.	La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MO, Pope PB, Martens EC, Hachem MA, Westereng B.	Nat Commun	10.1038/s41467-019-08812-y	2019
Enzymology	Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora.	Ott SJ, Musfeldt M, Ullmann U, Hampe J, Schreiber S.	J Clin Microbiol	10.1128/jcm.42.6.2566-2572.2004	2004
Metabolism	Mixed disulfide formation at Cys141 leads to apparent unidirectional attenuation of Aspergillus niger NADP-glutamate dehydrogenase activity.	Walvekar AS, Choudhury R, Punekar NS.	PLoS One	10.1371/journal.pone.0101662	2014
Enzymology	Re-activation of Clostridium symbiosum glutamate dehydrogenase from subunits denatured by urea.	Aghajanian S, Engel PC.	Biochem J	10.1042/bj3260649	1997
Enzymology	Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model.	Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM, Thas O, De Weirdt R, Kerckhof FM, Van de Wiele T.	ISME J	10.1038/ismej.2012.158	2013
Enzymology	Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.	Syed SE, Hornby DP, Brown PE, Fitton JE, Engel PC.	Biochem J	10.1042/bj2980107	1994
Metabolism	Metabolic niche of a prominent sulfate-reducing human gut bacterium.	Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1312524110	2013
Metabolism	Bypassing isophthalate inhibition by modulating glutamate dehydrogenase (GDH): purification and kinetic characterization of NADP-GDHs from isophthalate-degrading Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4.	Vamsee-Krishna C, Phale PS.	J Bacteriol	10.1128/jb.01365-09	2010
	Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans.	Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S.	Cell	10.1016/j.cell.2020.09.009	2020
Genetics	Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.	Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1319470110	2013
Metabolism	Gut microbiome structure and metabolic activity in inflammatory bowel disease.	Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.	Nat Microbiol	10.1038/s41564-018-0306-4	2019
Metabolism	Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus.	Kim M, Le H, McInerney MJ, Buckel W.	J Bacteriol	10.1128/jb.02185-12	2013
Enzymology	The crystal structure of glutamate dehydrogenase from Clostridium symbiosum at 0.6 nm resolution.	Rice DW, Baker PJ, Farrants GW, Hornby DP.	Biochem J	10.1042/bj2420789	1987
Metabolism	Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium.	Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI.	Cell Host Microbe	10.1016/j.chom.2019.09.001	2019
Enzymology	Purification and properties of NADP-dependent glutamate dehydrogenase from Ruminococcus flavefaciens FD-1.	Duncan PA, White BA, Mackie RI.	Appl Environ Microbiol	10.1128/aem.58.12.4032-4037.1992	1992
Enzymology	Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase.	Tomita T, Kuzuyama T, Nishiyama M.	J Biol Chem	10.1074/jbc.m111.260265	2011
Pathogenicity	vanD and vanG-like gene clusters in a Ruminococcus species isolated from human bowel flora.	Domingo MC, Huletsky A, Giroux R, Picard FJ, Bergeron MG.	Antimicrob Agents Chemother	10.1128/aac.00584-07	2007
Metabolism	Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus.	Holmes DE, Risso C, Smith JA, Lovley DR.	ISME J	10.1038/ismej.2011.88	2012
Pathogenicity	Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon.	Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP.	Proc Natl Acad Sci U S A	10.1073/pnas.1001224107	2011
Metabolism	An archaeal tRNA-synthetase complex that enhances aminoacylation under extreme conditions.	Godinic-Mikulcic V, Jaric J, Hausmann CD, Ibba M, Weygand-Durasevic I.	J Biol Chem	10.1074/jbc.m110.168526	2011
Genetics	Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability.	Ramos Meyers G, Samouda H, Bohn T.	Nutrients	10.3390/nu14245361	2022
Metabolism	Characterizing DNA methyltransferases with an ultrasensitive luciferase-linked continuous assay.	Hemeon I, Gutierrez JA, Ho MC, Schramm VL.	Anal Chem	10.1021/ac200816m	2011
Metabolism	Functions for diverse metabolic activities in heterochromatin.	Su XB, Pillus L.	Proc Natl Acad Sci U S A	10.1073/pnas.1518707113	2016
Enzymology	Histone H2A and H4 N-terminal tails are positioned by the MEP50 WD repeat protein for efficient methylation by the PRMT5 arginine methyltransferase.	Burgos ES, Wilczek C, Onikubo T, Bonanno JB, Jansong J, Reimer U, Shechter D.	J Biol Chem	10.1074/jbc.m115.636894	2015
Enzymology	Urease-producing species of intestinal anaerobes and their activities.	Suzuki K, Benno Y, Mitsuoka T, Takebe S, Kobashi K, Hase J.	Appl Environ Microbiol	10.1128/aem.37.3.379-382.1979	1979
Metabolism	Gene cloning and characterization of the very large NAD-dependent l-glutamate dehydrogenase from the psychrophile Janthinobacterium lividum, isolated from cold soil.	Kawakami R, Sakuraba H, Ohshima T.	J Bacteriol	10.1128/jb.00496-07	2007
	Functional domain organization of the potato alpha-glucan, water dikinase (GWD): evidence for separate site catalysis as revealed by limited proteolysis and deletion mutants.	Mikkelsen R, Blennow A.	Biochem J	10.1042/bj20041119	2005
Metabolism	Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein.	Teplyakov A, Lim K, Zhu PP, Kapadia G, Chen CC, Schwartz J, Howard A, Reddy PT, Peterkofsky A, Herzberg O.	Proc Natl Acad Sci U S A	10.1073/pnas.0607587103	2006
Phylogeny	Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms.	Jalanka-Tuovinen J, Salonen A, Nikkila J, Immonen O, Kekkonen R, Lahti L, Palva A, de Vos WM.	PLoS One	10.1371/journal.pone.0023035	2011
Metabolism	Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.	Schmitzberger F, Smith AG, Abell C, Blundell TL.	J Bacteriol	10.1128/jb.185.14.4163-4171.2003	2003
Metabolism	Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile.	Kim J, Darley D, Selmer T, Buckel W.	Appl Environ Microbiol	10.1128/aem.00772-06	2006
Pathogenicity	Arginine residues on the opposite side of the active site stimulate the catalysis of ribosome depurination by ricin A chain by interacting with the P-protein stalk.	Li XP, Kahn PC, Kahn JN, Grela P, Tumer NE.	J Biol Chem	10.1074/jbc.m113.510966	2013
Metabolism	Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome.	Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS.	Elife	10.7554/elife.46540	2019
Metabolism	Establishment and development of ruminal hydrogenotrophs in methanogen-free lambs.	Fonty G, Joblin K, Chavarot M, Roux R, Naylor G, Michallon F.	Appl Environ Microbiol	10.1128/aem.00181-07	2007
Metabolism	Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.	Wendt KS, Schall I, Huber R, Buckel W, Jacob U.	EMBO J	10.1093/emboj/cdg358	2003
	The gdhB gene of Pseudomonas aeruginosa encodes an arginine-inducible NAD(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation.	Lu CD, Abdelal AT.	J Bacteriol	10.1128/jb.183.2.490-499.2001	2001
Enzymology	Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.	Belitsky BR, Sonenshein AL.	J Bacteriol	10.1128/jb.180.23.6298-6305.1998	1998
Phylogeny	Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.	Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J.	Appl Environ Microbiol	10.1128/aem.65.11.4799-4807.1999	1999
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
Metabolism	Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96.	Mavrodi OV, Mavrodi DV, Weller DM, Thomashow LS.	Appl Environ Microbiol	10.1128/aem.01215-06	2006
Metabolism	Studies on the carbohydrate metabolism of a gram-negative anaerobe (Bacteroides symbiosus) used in the culture of Entamoeba histolytica.	BRAGG PD, REEVES RE.	J Bacteriol	10.1128/jb.83.1.76-84.1962	1962
Genetics	Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection.	Yimagou EK, Tall ML, Baudoin JP, Raoult D, Bou Khalil JY.	New Microbes New Infect	10.1016/j.nmni.2019.100598	2019
Genetics	Description of 'Blautia phocaeensis' sp. nov. and 'Lachnoclostridium edouardi' sp. nov., isolated from healthy fresh stools of Saudi Arabia Bedouins by culturomics.	Traore SI, Azhar EI, Yasir M, Bibi F, Fournier PE, Jiman-Fatani AA, Delerce J, Cadoret F, Lagier JC, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2017.05.017	2017
Phylogeny	Clostridium fessum sp. nov., isolated from human faeces.	Seo B, Jeon K, Baek I, Lee YM, Baek K, Ko G.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004579	2021
Genetics	Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig.	Shin Y, Paek J, Kim H, Kook JK, Chang YH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004694	2019

References

#472	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 934
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Clostridium symbiosum (DSM 934, ATCC 14940, LSU (M. Sebald))

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