Enterocloster clostridioformis (DSM 933, ATCC 25537, CCUG 16791)

Name: Enterocloster clostridioformis (DSM 933, ATCC 25537, CCUG 16791)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2569

Type strain

Strain Designation T90

Culture col. no. DSM 933 ATCC 25537 CCUG 16791 NCTC 11224 CIP 104318 7 more

NCBI tax ID(s) 1531

Special Collections DSMZ CCUG JCM CIP

History <- C. Kaneuchi <- ATCC <- L. Holdeman, VPI 0316 <- M.P. Bryant, T90 C. Kaneuchi <-- ATCC 25537 <-- L. V. Holdeman VPI 0316 <-- M. P. Bryant.

Links

Enterocloster clostridioformis T90 is an anaerobe, mesophilic prokaryote that was isolated from calf rumen.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92923

ATCC 25537,CCUG 16791,DSM 933,JCM 1291,CCRC 14545,NCIMB 11018,NCTC 11224,CCM 6066,CIP 104318,BCRC 14545,VTT E-052777

@ref 20215

Last LPSN update 2026-02-09 11:18:18

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Enterocloster

Species Enterocloster clostridioformis

Full scientific name Enterocloster clostridioformis (Burri and Ankersmit 1906) Haas and Blanchard 2020

Synonyms (4)

"Bacteroides clostridiiformis"
"Bacterium clostridiiforme"
Clostridium clostridioforme
Clostridium clostridiiforme

BacDive ID	Other strains from **Enterocloster clostridioformis** (2)	Type strain
130916	E. clostridioformis YL32, DSM 26114
158909	E. clostridioformis H4_30, DSM 108191

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
471	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)	Range
471	positive	growth	37	mesophilic
46527	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
471	anaerobe
46527	anaerobe
125439	anaerobe	99.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68367	gelatinase	-		from API 20A
68367	urease	-	3.5.1.5	from API 20A

API 20A

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type
471	calf rumen
46527	Calf rumen
67770	Calf rumen

Taxonmaps

69479

Global distribution of 16S sequence M59089 (>99% sequence identity) for Enterocloster clostridioformis subclade from Microbeatlas

Aquatic Samples	1136
Soil Samples	492
Animal Samples	71851
Plant Samples	358
Total Samples	73837

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
471	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
124043	ASM2029748v1 assembly for Enterocloster clostridioformis FDAARGOS_1529	contig	GCA_020297485	1531.157		1531	74.07
67770	57530_A01 assembly for Enterocloster clostridioformis NCTC11224	contig	GCA_900447015	1531.20	2858553787	1531	72.21
67770	IMG-taxon 2593339147 annotated assembly for Enterocloster clostridioformis ATCC 25537	scaffold	GCA_900113155	1531.116	2593339147	1531	44.93

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium clostridioforme strain ATCC 25537 16S ribosomal RNA gene, partial sequence	JF313109	1310	1531
20218	Clostridium clostridioforme strain DSM 933 16S ribosomal RNA gene, partial sequence	HM245937	845	1531
471	Clostridium clostridioforme strain ATCC 25537 16S ribosomal RNA gene, partial sequence	M59089	1476	1531
67770	[Clostridium] clostridioforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 1291	LC036310	1493	1531

GC content

@ref	GC-content (mol%)	Method
471	48.8
67770	48.8	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: Enterocloster clostridioformis ATCC 25537
NCBI: GCA_900113155

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	82.00	no
125439	motility	BacteriaNetⓘ	yes	82.30	no
125439	gram_stain	BacteriaNetⓘ	variable	70.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] clostridioforme strain NCTC11224
PATRIC: 1531.20

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	67.73	no
125438	anaerobic	anaerobicⓘ	yes	86.96	yes
125438	spore-forming	spore-formingⓘ	yes	57.39	no
125438	aerobic	aerobicⓘ	no	95.79	yes
125438	thermophilic	thermophileⓘ	no	94.66	yes
125438	flagellated	motile2+ⓘ	no	82.49	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
Genetics	Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing.	Hosoda T, Suzuki M, Matsuno T, Matsui K, Ohyama K, Doi Y.	Microbiol Spectr	10.1128/spectrum.01014-25	2025
	Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.	Duong JT, Hayden HS, Verster AJ, Pope CE, Miller C, Kelsi Penewit, Salipante SJ, Rowe SM, Solomon GM, Nichols D, Kelly A, Schwarzenberg SJ, Freedman SD, Hoffman LR.	J Cyst Fibros	10.1016/j.jcf.2025.05.006	2025
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
	A case of bacteremia caused by Dialister micraerophilus with Enterocloster clostridioformis and Eggerthella lenta in a patient with pyometra.	Kitagawa H, Tadera K, Omori K, Nomura T, Shigemoto N, Ohge H.	BMC Infect Dis	10.1186/s12879-024-08999-6	2024
	Age and aging process alter the gut microbes.	Zhanbo Q, Jing Z, Shugao H, Yinhang W, Jian C, Xiang Y, Feimin Z, Jian L, Xinyue W, Wei W, Shuwen H.	Aging (Albany NY)	10.18632/aging.205728	2024
Pathogenicity	Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function.	Beresford-Jones BS, Suyama S, Clare S, Soderholm A, Xia W, Sardar P, Lee J, Harcourt K, Lawley TD, Pedicord VA.	Microbiome	10.1186/s40168-025-02050-9	2025
Pathogenicity	Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut.	Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B.	Nat Commun	10.1038/s41467-025-56332-9	2025
	Co-Colonization of Non-difficile Clostridial Species in Antibiotic-Associated Diarrhea Caused by Clostridioides difficile.	Salas-Trevino D, Flores-Trevino S, Cisneros-Rendon C, Dominguez-Rivera CV, Camacho-Ortiz A.	Antibiotics (Basel)	10.3390/antibiotics14040397	2025
	The effect of culturing temperature on the growth of the most dominant bacterial species of human gut microbiota and harmful bacterial species.	Shimokawa H, Sakakibara H, Ami Y, Hirano R, Kurihara S.	Biosci Microbiota Food Health	10.12938/bmfh.2024-087	2025
Genetics	Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.	Bryson S, Sisson Z, Nelson B, Grove J, Reister E, Liachko I, Auch B, Graiziger C, Khoruts A.	Gut Microbes	10.1080/19490976.2025.2559019	2025
	Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.	Qie J, Cao M, Xu M, Zhang Y, Luo L, Sun C, Ke D, Yuan S, Jia W, Qiu T, Li T, Du X, Xiao C, Hong Z, Zhang B.	mSystems	10.1128/msystems.01091-25	2025
	Clinical Utility of Plasma Microbial Cell-Free DNA Surveillance in Neutropenic Patients with Acute Myeloid Leukemia Undergoing Outpatient Chemotherapy: A Case Series.	Lampou M, Trull EC, Warren HM, Ghebremichael MS, Nakka R, Floyd DJ, Fathi AT, Brunner AM, Mansour MK.	Diagnostics (Basel)	10.3390/diagnostics15131715	2025
	Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.	Dike CR, Duan Q, Ahmed F, Denson LA, Haslam D, Minar P, Ollberding NJ, Papachristou GI, Setchell KDR, Thompson T, Vitale DS, Zhao X, Abu-El-Haija M.	J Pediatr Gastroenterol Nutr	10.1002/jpn3.70135	2025
Pathogenicity	Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression.	Jacobsen GE, Gonzalez EE, Mendygral P, Faust KM, Hazime H, Fernandez I, Santander AM, Quintero MA, Jiang C, Damas OM, Deshpande AR, Kerman DH, Proksell S, Sendzischew Shane M, Sussman DA, Ghaddar B, Cickovsk T, Abreu MT.	Inflamm Bowel Dis	10.1093/ibd/izae316	2025
	Phage Targeting Neonatal Meningitis E. coli K1 In Vitro in the Intestinal Microbiota of Pregnant Donors and Impact on Bacterial Populations.	Antoine C, Laforet F, Goya-Jorge E, Gonza I, Lebrun S, Douny C, Duprez JN, Fall A, Taminiau B, Scippo ML, Daube G, Thiry D, Delcenserie V.	Int J Mol Sci	10.3390/ijms241310580	2023
	Microbial succession at weaning is guided by microbial metabolism of host glycans.	Lubin JB, Planet PJ, Silverman MA.	Microbiome	10.1186/s40168-025-02193-9	2025
	Disease-associated microbiome signature species in the gut.	Li J, Li J, O'Toole PW.	PNAS Nexus	10.1093/pnasnexus/pgae352	2024
Phylogeny	Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa.	Haas KN, Blanchard JL.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003698	2020
	Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging-oriented single-cell sequencing.	Gao J, Sun D, Li B, Yang C, Wang W.	mLife	10.1002/mlf2.12041	2022
	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
Metabolism	Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.	Park S, Li C, Wu X, Zhang T.	Int J Mol Sci	10.3390/ijms241713329	2023
	Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.	Serrano-Gomez G, Yanez F, Soler Z, Pons-Tarin M, Mayorga L, Herrera-deGuise C, Borruel N, Rodriguez-Sinovas A, Consegal M, Manjon I, Vega-Abellaneda S, Manichanh C.	Biomark Res	10.1186/s40364-025-00802-1	2025
Metabolism	Gut Bacteria Involved in Ellagic Acid Metabolism To Yield Human Urolithin Metabotypes Revealed.	Iglesias-Aguirre CE, Garcia-Villalba R, Beltran D, Frutos-Lison MD, Espin JC, Tomas-Barberan FA, Selma MV.	J Agric Food Chem	10.1021/acs.jafc.2c08889	2023
	Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.	Guedon G, Charron-Bourgoin F, Lacroix T, Hamadouche T, Soler N, Douzi B, Chiapello H, Leblond-Bourget N.	Sci Rep	10.1038/s41598-025-99981-y	2025
	Spaceflight alters host-gut microbiota interactions.	Gonzalez E, Lee MD, Tierney BT, Lipieta N, Flores P, Mishra M, Beckett L, Finkelstein A, Mo A, Walton P, Karouia F, Barker R, Jansen RJ, Green SJ, Weging S, Kelliher J, Singh NK, Bezdan D, Galazska J, Brereton NJB.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00545-1	2024
	Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME).	Liu L, Narrowe AB, Firrman JA, Mahalak KK, Bobokalonov JT, Lemons JMS, Bittinger K, Daniel S, Tanes C, Mattei L, Friedman ES, Soares JW, Kobori M, Zeng WB, Tomasula PM.	Foods	10.3390/foods12112105	2023
	The gut microbiome is associated with susceptibility to febrile malaria in Malian children.	Van Den Ham KM, Bower LK, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW.	Nat Commun	10.1038/s41467-024-52953-8	2024
Metabolism	Comparison of gnotobiotic communities reveals milk-adapted metabolic functions and unexpected amino acid metabolism by the pre-weaning microbiome.	Lubin JB, Silverman MA, Planet PJ.	Gut Microbes	10.1080/19490976.2024.2387875	2024
	The role of the gut microbiota in chemotherapy response, efficacy and toxicity: a systematic review.	Bohm D, Russ E, Guchelaar HJ, Ziemons J, Penders J, Smidt ML, van Best N, Deenen MJ.	NPJ Precis Oncol	10.1038/s41698-025-01034-0	2025
	Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis.	Mbaye B, Magdy Wasfy R, Borentain P, Tidjani Alou M, Mottola G, Bossi V, Caputo A, Gerolami R, Million M.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1279354	2023
	Isolation, Characterization, and Epizootiology of Clostridioides cuniculi from Immunodeficient Mice with Enteric Disease.	Funk A, Crawford A, Nickerson K, Janke L, Stringer T, Sun Y, Marsh A, Inoue M, Savage C, Emmons J, Henderson K, Tang L, Pisharath H.	J Am Assoc Lab Anim Sci	10.30802/aalas-jaalas-25-030	2025
Genetics	Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.	Park R, Chevalier C, Kieser S, Marizzoni M, Paquis A, Armand S, Scheffler M, Allali G, Assal F, Momjian S, Frisoni GB.	PLoS One	10.1371/journal.pone.0330251	2025
Phylogeny	Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection.	Bi Y, Wang Y, Li W, Chen Y, Qin J, Zheng H.	BMC Microbiol	10.1186/s12866-024-03709-3	2025
	Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae.	Lin X, Hu T, Wu Z, Li L, Wang Y, Wen D, Liu X, Li W, Liang H, Jin X, Xu X, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y.	Imeta	10.1002/imt2.174	2024
	Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo.	Deyaert S, Poppe J, Dai Vu L, Baudot A, Bubeck S, Bayne T, Krishnan K, Giusto M, Moltz S, Van den Abbeele P.	Metabolites	10.3390/metabo14090497	2024
	Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.	Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligne B, Titecat M.	Int J Mol Sci	10.3390/ijms25042164	2024
	Genomic characterization of prophage elements in Clostridium clostridioforme: an understudied component of the intestinal microbiome.	Humphrey S, Marouli A, Thummler K, Mullin M, Pritchard L, Wall DM.	Microbiology (Reading)	10.1099/mic.0.001486	2024
	The Use of Fecal Microbiota Transplant in Overcoming and Modulating Resistance to Anti-PD-1 Therapy in Patients with Skin Cancer.	Vongsavath T, Rahmani R, Tun KM, Manne V.	Cancers (Basel)	10.3390/cancers16030499	2024
	Experience with dalbavancin use in various gram-positive infections within Aberdeen Royal Infirmary OPAT service.	McSorley JC, Reyes D, Tonna I, Bateman V.	Infection	10.1007/s15010-023-02152-2	2024
	Colorectal cancer-specific microbiome in peripheral circulation and cancer tissues.	Yan S, Liu T, Zhao H, Zhao C, Zhu Y, Dai W, Sun W, Wang H, Sun J, Zhao L, Xu D.	Front Microbiol	10.3389/fmicb.2024.1422536	2024
	High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome.	Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.	Antibiotics (Basel)	10.3390/antibiotics12121667	2023
Genetics	Gut resistome of NSCLC patients treated with immunotherapy.	Iwan E, Grenda A, Bomba A, Bielinska K, Wasyl D, Kieszko R, Rolska-Kopinska A, Chmielewska I, Krawczyk P, Rybczynska-Tkaczyk K, Olejnik M, Milanowski J.	Front Genet	10.3389/fgene.2024.1378900	2024
Genetics	Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing.	Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M.	Animals (Basel)	10.3390/ani13142303	2023
	Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.	Tamburini FB, Tripathi A, Gold MP, Yang JC, Biancalani T, McBride JM, Keir ME, Gardenia Study Group.	J Crohns Colitis	10.1093/ecco-jcc/jjae084	2024
Genetics	Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study.	Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R.	Microorganisms	10.3390/microorganisms11102437	2023
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
	Maternal Faecalibacterium pathobionts and low-fiber diets synergize to impact offspring health: implications for atopic dermatitis	Lee D, Park J, Park S, Hwang J, Kim S, Kee S, Kim H.	Microbiome		2025
Genetics	Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.	Zhang C, Liu Z, Yu H, Shen Y, Lu L, Kong F, Sun W, Wei X, Jin L, Ge L, Zeng B.	Front Microbiol	10.3389/fmicb.2025.1537286	2025
	Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury.	Li J, Barnes S, Lefkowitz E, Yarar-Fisher C.	Physiol Genomics	10.1152/physiolgenomics.00107.2023	2024
	Role of the gut microbiota in tumorigenesis and treatment.	Liu Q, Yang Y, Pan M, Yang F, Yu Y, Qian Z.	Theranostics	10.7150/thno.91700	2024
Genetics	A metagenome-wide study of the gut virome in chronic kidney disease.	Zhang P, Guo R, Ma S, Jiang H, Yan Q, Li S, Wang K, Deng J, Zhang Y, Zhang Y, Wang G, Chen L, Li L, Guo X, Zhao G, Yang L, Wang Y, Kang J, Sha S, Fan S, Cheng L, Meng J, Yu H, Chen F, He D, Wang J, Liu S, Shi H.	Theranostics	10.7150/thno.101601	2025
	Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.	Holman DB, Gzyl KE, Kommadath A.	mSystems	10.1128/msystems.01250-24	2024
	The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice	Viehof A, Haange S, Streidl T, Schubert K, Engelmann B, Haller D, Rolle-Kampczyk U, von Bergen M, Clavel T.	Microbiome Res Rep		2024
Metabolism	The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice.	Streidl T, Karkossa I, Segura Munoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T.	Gut Microbes	10.1080/19490976.2020.1854008	2021
	Culture-dependent screening of endospore-forming clostridia in infant feces.	Ingribelli E, Modrackova N, Tejnecky V, Killer J, Schwab C, Neuzil-Bunesova V.	BMC Microbiol	10.1186/s12866-023-03104-4	2023
	Contribution of bacterial and host factors to pathogen "blooming" in a gnotobiotic mouse model for Salmonella enterica serovar Typhimurium-induced enterocolitis.	Beutler M, Eberl C, Garzetti D, Herp S, Munch P, Ring D, Dolowschiak T, Brugiroux S, Schiller P, Hussain S, Basic M, Bleich A, Stecher B.	Infect Immun	10.1128/iai.00318-23	2024
Genetics	Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.	Tourlousse DM, Narita K, Miura T, Ohashi A, Matsuda M, Ohyama Y, Shimamura M, Furukawa M, Kasahara K, Kameyama K, Saito S, Goto M, Shimizu R, Mishima R, Nakayama J, Hosomi K, Kunisawa J, Terauchi J, Sekiguchi Y, Kawasaki H.	Microbiol Spectr	10.1128/spectrum.01915-21	2022
	Disease-specific loss of microbial cross-feeding interactions in the human gut.	Marcelino VR, Welsh C, Diener C, Gulliver EL, Rutten EL, Young RB, Giles EM, Gibbons SM, Greening C, Forster SC.	Nat Commun	10.1038/s41467-023-42112-w	2023
Pathogenicity	Gut microbiota composition is altered in postural orthostatic tachycardia syndrome and post-acute COVID-19 syndrome.	Hamrefors V, Kahn F, Holmqvist M, Carlson K, Varjus R, Gudjonsson A, Fedorowski A, Ohlsson B.	Sci Rep	10.1038/s41598-024-53784-9	2024
	Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.	Brochu E, Huletsky A, Boudreau DK, Raymond F, Berube E, Ouameur AA, Frenette J, Boissinot M, Corbeil J, Bergeron MG.	JAC Antimicrob Resist	10.1093/jacamr/dlad026	2023
	A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.	Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotna T, Ouattara DA, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A.	Nat Commun	10.1038/s41467-021-26963-9	2021
Pathogenicity	Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.	Xu SY, Feng XR, Zhao W, Bi YL, Diao QY, Tu Y.	Microbiome	10.1186/s40168-024-01844-7	2024
	Horizontal Transfer of Different erm(B)-Carrying Mobile Elements Among Streptococcus suis Strains With Different Serotypes.	Chen L, Huang J, Huang X, He Y, Sun J, Dai X, Wang X, Shafiq M, Wang L.	Front Microbiol	10.3389/fmicb.2021.628740	2021
	Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice.	von Strempel A, Weiss AS, Wittmann J, Salvado Silva M, Ring D, Wortmann E, Clavel T, Debarbieux L, Kleigrewe K, Stecher B.	PLoS Pathog	10.1371/journal.ppat.1011600	2023
Pathogenicity	Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo.	Burckhardt JC, Chong DHY, Pett N, Tropini C.	Microbiome	10.1186/s40168-023-01496-z	2023
	In vitro interaction network of a synthetic gut bacterial community.	Weiss AS, Burrichter AG, Durai Raj AC, von Strempel A, Meng C, Kleigrewe K, Munch PC, Rossler L, Huber C, Eisenreich W, Jochum LM, Going S, Jung K, Lincetto C, Hubner J, Marinos G, Zimmermann J, Kaleta C, Sanchez A, Stecher B.	ISME J	10.1038/s41396-021-01153-z	2022
	Identification of bacterial lipopeptides as key players in IBS.	Petitfils C, Maurel S, Payros G, Hueber A, Agaiz B, Gazzo G, Marrocco R, Auvray F, Langevin G, Motta JP, Floch P, Tremblay-Franco M, Galano JM, Guy A, Durand T, Lachambre S, Durbec A, Hussein H, Decraecker L, Bertrand-Michel J, Saoudi A, Oswald E, Poisbeau P, Dietrich G, Melchior C, Boeckxstaens G, Serino M, Le Faouder P, Cenac N.	Gut	10.1136/gutjnl-2022-328084	2023
	Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.	Ye H, Borusak S, Eberl C, Krasenbrink J, Weiss AS, Chen SC, Hanson BT, Hausmann B, Herbold CW, Pristner M, Zwirzitz B, Warth B, Pjevac P, Schleheck D, Stecher B, Loy A.	Nat Commun	10.1038/s41467-023-41008-z	2023
	Single-cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a proinflammatory metabolic signature in male mice at late adulthood.	Lim JJ, Goedken M, Jin Y, Gu H, Cui JY.	Toxicol Sci	10.1093/toxsci/kfae047	2024
	Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria.	Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M.	Microbiome	10.1186/s40168-023-01541-x	2023
	Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation.	Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.	Sci Rep	10.1038/s41598-024-56242-8	2024
	Distinct Functional Metagenomic Markers Predict the Responsiveness to Anti-PD-1 Therapy in Chinese Non-Small Cell Lung Cancer Patients.	Fang C, Fang W, Xu L, Gao F, Hou Y, Zou H, Ma Y, Moll JM, Yang Y, Wang D, Huang Y, Ren H, Zhao H, Qin S, Zhong H, Li J, Liu S, Yang H, Wang J, Brix S, Kristiansen K, Zhang L.	Front Oncol	10.3389/fonc.2022.837525	2022
Pathogenicity	Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes.	Silamikele L, Silamikelis I, Ustinova M, Kalnina Z, Elbere I, Petrovska R, Kalnina I, Klovins J.	Front Endocrinol (Lausanne)	10.3389/fendo.2021.626359	2021
Pathogenicity	Infection, Dysbiosis and Inflammation Interplay in the COVID Era in Children.	Ailioaie LM, Ailioaie C, Litscher G.	Int J Mol Sci	10.3390/ijms241310874	2023
	Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.	Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T.	ISME Commun	10.1038/s43705-021-00017-z	2021
Metabolism	Mechanism of inhibition of tannic acid and related compounds on the growth of intestinal bacteria.	Chung KT, Lu Z, Chou MW	Food Chem Toxicol	10.1016/s0278-6915(98)00086-6	1998
	Enterocloster alcoholdehydrogenati sp. nov., a Novel Bacterial Species Isolated from the Feces of a Patient with Alcoholism.	Oikawa D, Fukui K, Aoki Y, Waki T, Takahashi S, Shimoyama T, Nakayama T.	Curr Microbiol	10.1007/s00284-023-03285-1	2023
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

References

#471	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 933
#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 )
#46527	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 16791
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#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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Enterocloster clostridioformis (DSM 933, ATCC 25537, CCUG 16791)

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