Clostridium scindens (VPI 12708, JCM 10418)

Name: Clostridium scindens (VPI 12708, JCM 10418)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160948

Type strain

Culture col. no. VPI 12708 JCM 10418

NCBI tax ID(s) 29347

Special Collections JCM

History JCM <-- F. Takamine <-- P. B. Hylemon <-- VPI 12708.

Links

Clostridium scindens JCM 10418 is a bacterium that was isolated from Feces of colon-cancer patient.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 88187

JCM 10418

@ref 20215

Last LPSN update 2026-05-29 08:44:34

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium scindens

Full scientific name Clostridium scindens Morris et al. 1985

BacDive ID	Other strains from **Clostridium scindens** (7)	Type strain
2748	C. scindens 19, CCUG 45363, JCM 6567, CIP 106687, DSM ... (type strain)
159178	C. scindens BL-389-WT-3D, DSM 100975
160949	C. scindens JCM 10419
160951	C. scindens JCM 10420
160952	C. scindens JCM 10421
160953	C. scindens JCM 10422
160954	C. scindens JCM 10423

Morphology

Culture and growth conditions

Culture temp

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

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate anaerobe	99.857

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Host species
67770	Feces of colon-cancer patient	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AB971816 (>99% sequence identity) for [Clostridium] scindens subclade from Microbeatlas

Aquatic Samples	837
Soil Samples	346
Animal Samples	78797
Plant Samples	225
Total Samples	80205

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM2794165v1 assembly for [Clostridium] scindens VPI12708	complete	GCA_027941655	29347.195	29347	97.69

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Clostridium scindens 16S rRNA, partial sequence, strain:JCM 10418	AB020727	1453	29347
67770	[Clostridium] scindens gene for 16S ribosomal RNA, partial sequence, strain: JCM 10418	AB971816	1399	29347
124043	Eubacterium sp. VPI 12708 16S ribosomal RNA gene, partial sequence.	AF262236	1531	29347

GC content

@ref	GC-content (mol%)	Method
67770	47.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2794165v1 assembly for [Clostridium] scindens VPI12708
NCBI: GCA_027941655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.86	no
125439	motility	BacteriaNetⓘ	yes	69.61	no
125439	gram_stain	BacteriaNetⓘ	positive	57.89	no
125439	spore_formation	BacteriaNetⓘ	yes	67.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] scindens VPI12708
NCBI: GCA_027941655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	77.15	no
125438	anaerobic	anaerobicⓘ	yes	87.83	no
125438	aerobic	aerobicⓘ	no	94.48	no
125438	spore-forming	spore-formingⓘ	no	50.68	no
125438	thermophilic	thermophileⓘ	no	90.87	yes
125438	flagellated	motile2+ⓘ	no	67.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Clostridium scindens: history and current outlook for a keystone species in the mammalian gut involved in bile acid and steroid metabolism.	Daniel SL, Ridlon JM.	FEMS Microbiol Rev	10.1093/femsre/fuaf016	2025
Genetics	Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.	Olivos-Caicedo KY, Fernandez-Materan FV, Daniel SL, Anantharaman K, Ridlon JM, Alves JMP.	Microorganisms	10.3390/microorganisms13040857	2025
	Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid.	Vico-Oton E, Volet C, Jacquemin N, Dong Y, Hapfelmeier S, Meibom KL, Bernier-Latmani R.	BMC Microbiol	10.1186/s12866-024-03433-y	2024
	Genome sequences of nine Clostridium scindens strains isolated from human feces.	Fernandez-Materan FV, Olivos-Caicedo KY, Daniel SL, Walden KKO, Fields CJ, Hernandez AG, Alves JMP, Ridlon JM.	Microbiol Resour Announc	10.1128/mra.00848-24	2024
Metabolism	The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology.	Ridlon JM, Daniel SL, Gaskins HR.	J Lipid Res	10.1016/j.jlr.2023.100392	2023
Metabolism	A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery.	Chen Y, Chaudhari SN, Harris DA, Roberts CF, Moscalu A, Mathur V, Zhao L, Tavakkoli A, Devlin AS, Sheu EG.	Cell Host Microbe	10.1016/j.chom.2024.06.014	2024
Enzymology	Microbiota-derived bile acid metabolic enzymes and their impacts on host health	Ma H, Wang K, Jiang C.	Cell Insight		2025
	Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota.	Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A.	Microorganisms	10.3390/microorganisms9112254	2021
Metabolism	Conceptualizing the Vertebrate Sterolbiome.	Ridlon JM.	Appl Environ Microbiol	10.1128/aem.00641-20	2020
	Bile acids and their receptors in hepatic immunity.	Fiorucci S, Marchiano S, Distrutti E, Biagioli M.	Liver Res	10.1016/j.livres.2025.01.005	2025
	Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics.	McMillan AS, Theriot CM.	Gut Microbes	10.1080/19490976.2024.2393766	2024
Metabolism	The 7-alpha-dehydroxylation pathway: An integral component of gut bacterial bile acid metabolism and potential therapeutic target.	Wise JL, Cummings BP.	Front Microbiol	10.3389/fmicb.2022.1093420	2022
	Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids.	Lucas LN, Barrett K, Kerby RL, Zhang Q, Cattaneo LE, Stevenson D, Rey FE, Amador-Noguez D.	mSystems	10.1128/msystems.00805-21	2021
Metabolism	Clostridium scindens ATCC 35704: Integration of Nutritional Requirements, the Complete Genome Sequence, and Global Transcriptional Responses to Bile Acids.	Devendran S, Shrestha R, Alves JMP, Wolf PG, Ly L, Hernandez AG, Mendez-Garcia C, Inboden A, Wiley J, Paul O, Allen A, Springer E, Wright CL, Fields CJ, Daniel SL, Ridlon JM.	Appl Environ Microbiol	10.1128/aem.00052-19	2019
Enzymology	Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes.	Lee JW, Cowley ES, Wolf PG, Doden HL, Murai T, Caicedo KYO, Ly LK, Sun F, Takei H, Nittono H, Daniel SL, Cann I, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM.	Gut Microbes	10.1080/19490976.2022.2132903	2022
Metabolism	Bile Acid 7alpha-Dehydroxylating Gut Bacteria Secrete Antibiotics that Inhibit Clostridium difficile: Role of Secondary Bile Acids.	Kang JD, Myers CJ, Harris SC, Kakiyama G, Lee IK, Yun BS, Matsuzaki K, Furukawa M, Min HK, Bajaj JS, Zhou H, Hylemon PB.	Cell Chem Biol	10.1016/j.chembiol.2018.10.003	2019
Enzymology	Microbial Hydroxysteroid Dehydrogenases: From Alpha to Omega.	Doden HL, Ridlon JM.	Microorganisms	10.3390/microorganisms9030469	2021
Metabolism	A metabolic pathway for bile acid dehydroxylation by the gut microbiome.	Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA.	Nature	10.1038/s41586-020-2396-4	2020
	Biological tuners to reshape the bile acid pool for therapeutic purposes in non-alcoholic fatty liver disease.	Gillard J, Leclercq IA.	Clin Sci (Lond)	10.1042/cs20220697	2023
	Associations between Ileal Juice Bile Acids and Colorectal Advanced Adenoma.	Luu HN, Tran CT, Wang R, Nguyen MV, Tran MT, Tuong TT, Tran QH, Le LC, Pham HT, Vu HH, Bui NC, Ha HT, Trinh DT, Thomas CE, Adams-Haduch J, Velikokhatnaya L, Schoen RE, Xie G, Jia W, Boffetta P, Clemente JC, Yuan JM.	Nutrients	10.3390/nu15132930	2023
	Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium.	Reed AD, Theriot CM.	Microorganisms	10.3390/microorganisms9020371	2021
Metabolism	Consequences of bile salt biotransformations by intestinal bacteria.	Ridlon JM, Harris SC, Bhowmik S, Kang DJ, Hylemon PB.	Gut Microbes	10.1080/19490976.2015.1127483	2016
Enzymology	Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7alpha-dehydroxylating intestinal bacterium.	Ridlon JM, Hylemon PB.	J Lipid Res	10.1194/jlr.m020313	2012
Metabolism	In vitro and in vivo characterization of Clostridium scindens bile acid transformations.	Marion S, Studer N, Desharnais L, Menin L, Escrig S, Meibom A, Hapfelmeier S, Bernier-Latmani R.	Gut Microbes	10.1080/19490976.2018.1549420	2019
	Identification and Characterization of Major Bile Acid 7alpha-Dehydroxylating Bacteria in the Human Gut.	Kim KH, Park D, Jia B, Baek JH, Hahn Y, Jeon CO.	mSystems	10.1128/msystems.00455-22	2022
Enzymology	The desA and desB genes from Clostridium scindens ATCC 35704 encode steroid-17,20-desmolase.	Devendran S, Mythen SM, Ridlon JM.	J Lipid Res	10.1194/jlr.m083949	2018
Metabolism	Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12alpha-Hydroxysteroid Dehydrogenases from Bile Acid 7alpha-Dehydroxylating Human Gut Bacteria.	Doden H, Sallam LA, Devendran S, Ly L, Doden G, Daniel SL, Alves JMP, Ridlon JM.	Appl Environ Microbiol	10.1128/aem.00235-18	2018
Metabolism	Clostridium scindens baiCD and baiH genes encode stereo-specific 7alpha/7beta-hydroxy-3-oxo-delta4-cholenoic acid oxidoreductases.	Kang DJ, Ridlon JM, Moore DR, Barnes S, Hylemon PB.	Biochim Biophys Acta	10.1016/j.bbalip.2007.10.008	2008
Metabolism	Isolation and characterization of a bile acid inducible 7alpha-dehydroxylating operon in Clostridium hylemonae TN271.	Ridlon JM, Kang DJ, Hylemon PB.	Anaerobe	10.1016/j.anaerobe.2009.05.004	2010
	BaiCD gene cluster abundance is negatively correlated with Clostridium difficile infection.	Solbach P, Chhatwal P, Woltemate S, Tacconelli E, Buhl M, Gerhard M, Thoeringer CK, Vehreschild MJGT, Jazmati N, Rupp J, Manns MP, Bachmann O, Suerbaum S.	PLoS One	10.1371/journal.pone.0196977	2018
Metabolism	Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens.	Ridlon JM, Ikegawa S, Alves JM, Zhou B, Kobayashi A, Iida T, Mitamura K, Tanabe G, Serrano M, De Guzman A, Cooper P, Buck GA, Hylemon PB.	J Lipid Res	10.1194/jlr.m038869	2013
	The role of botanical triterpenoids and steroids in bile acid metabolism, transport, and signaling: Pharmacological and toxicological implications.	Luo Z, Zhou W, Xie T, Xu W, Shi C, Xiao Z, Si Y, Ma Y, Ren Q, Di L, Shan J.	Acta Pharm Sin B	10.1016/j.apsb.2024.04.027	2024
Metabolism	Metagenomic analysis of bile salt biotransformation in the human gut microbiome.	Das P, Marcisauskas S, Ji B, Nielsen J.	BMC Genomics	10.1186/s12864-019-5899-3	2019
Pathogenicity	A Gut-Restricted Lithocholic Acid Analog as an Inhibitor of Gut Bacterial Bile Salt Hydrolases.	Adhikari AA, Ramachandran D, Chaudhari SN, Powell CE, Li W, McCurry MD, Banks AS, Devlin AS.	ACS Chem Biol	10.1021/acschembio.1c00192	2021
	The Stickland Reaction Precursor trans-4-Hydroxy-l-Proline Differentially Impacts the Metabolism of Clostridioides difficile and Commensal Clostridia.	Reed AD, Fletcher JR, Huang YY, Thanissery R, Rivera AJ, Parsons RJ, Stewart AK, Kountz DJ, Shen A, Balskus EP, Theriot CM.	mSphere	10.1128/msphere.00926-21	2022
Metabolism	Identification and characterization of a bile acid 7alpha-dehydroxylation operon in Clostridium sp. strain TO-931, a highly active 7alpha-dehydroxylating strain isolated from human feces.	Wells JE, Hylemon PB.	Appl Environ Microbiol	10.1128/aem.66.3.1107-1113.2000	2000
Enzymology	Expression and characterization of a C24 bile acid 7 alpha-dehydratase from Eubacterium sp. strain VPI 12708 in Escherichia coli.	Dawson JA, Mallonee DH, Bjorkhem I, Hylemon PB.	J Lipid Res	10.1016/s0022-2275(20)39155-0	1996
Metabolism	Assessment of fecal bacteria with bile acid 7 alpha-dehydroxylating activity for the presence of bai-like genes.	Doerner KC, Takamine F, LaVoie CP, Mallonee DH, Hylemon PB.	Appl Environ Microbiol	10.1128/aem.63.3.1185-1188.1997	1997
Metabolism	Sequencing and expression of a gene encoding a bile acid transporter from Eubacterium sp. strain VPI 12708.	Mallonee DH, Hylemon PB.	J Bacteriol	10.1128/jb.178.24.7053-7058.1996	1996
Metabolism	Helicobacter hepaticus infection promotes hepatitis and preneoplastic foci in farnesoid X receptor (FXR) deficient mice.	Swennes AG, Sheh A, Parry NM, Muthupalani S, Lertpiriyapong K, Garcia A, Fox JG.	PLoS One	10.1371/journal.pone.0106764	2014
Metabolism	2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism.	Fader KA, Nault R, Zhang C, Kumagai K, Harkema JR, Zacharewski TR.	Sci Rep	10.1038/s41598-017-05656-8	2017
Enzymology	Characterization and regulation of the NADP-linked 7 alpha-hydroxysteroid dehydrogenase gene from Clostridium sordellii.	Coleman JP, Hudson LL, Adams MJ.	J Bacteriol	10.1128/jb.176.16.4865-4874.1994	1994
Metabolism	Role of N,N-Dimethylglycine and Its Catabolism to Sarcosine in Chromohalobacter salexigens DSM 3043.	Yang T, Shao YH, Guo LZ, Meng XL, Yu H, Lu WD.	Appl Environ Microbiol	10.1128/aem.01186-20	2020
Metabolism	Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243(T).	Harris SC, Devendran S, Mendez-Garcia C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JM	Gut Microbes	10.1080/19490976.2018.1458180	2018
Enzymology	Structure and functional characterization of a bile acid 7alpha dehydratase BaiE in secondary bile acid synthesis.	Bhowmik S, Chiu HP, Jones DH, Chiu HJ, Miller MD, Xu Q, Farr CL, Ridlon JM, Wells JE, Elsliger MA, Wilson IA, Hylemon PB, Lesley SA	Proteins	10.1002/prot.24971	2016
Enzymology	Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe.	Bhowmik S, Jones DH, Chiu HP, Park IH, Chiu HJ, Axelrod HL, Farr CL, Tien HJ, Agarwalla S, Lesley SA	Proteins	10.1002/prot.24353	2013
Phylogeny	Development and application of a polymerase chain reaction assay for the detection and enumeration of bile acid 7alpha-dehydroxylating bacteria in human feces.	Wells JE, Williams KB, Whitehead TR, Heuman DM, Hylemon PB	Clin Chim Acta	10.1016/s0009-8981(03)00115-3	2003
Metabolism	Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible (bai) Operon.	Reed AD, Nethery MA, Stewart A, Barrangou R, Theriot CM	J Bacteriol	10.1128/JB.00039-20	2020
Phylogeny	Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces.	Kitahara M, Takamine F, Imamura T, Benno Y	Int J Syst Evol Microbiol	10.1099/00207713-50-3-971	2000

References

#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 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 scindens (VPI 12708, JCM 10418)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_027941655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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