Name: Clostridium scindens JCM 10418
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 160948

Type strain:

Species: Clostridium scindens

Culture col. no.: JCM 10418, VPI 12708

Strain history: F. Takamine <-- P. B. Hylemon <-- VPI 12708.

NCBI tax ID(s): 29347 (species)

SI-ID 88187

JCM 10418

Special Collections

Other strains from Clostridium scindens

Section

When using BacDive for research please cite our paper

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

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium scindens**
	Full Scientific Name (LPSN)	Clostridium scindens Morris et al. 1985

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

anaerobe Confidence in %99.9

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Feces of colon-cancer patient
* marker position based on {}

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	[Clostridium] scindens gene for 16S ribosomal RNA, partial sequence, strain: JCM 10418	AB971816	1399	GenBank ENA	29347 tax ID
[Ref.: #67770]	Clostridium scindens 16S rRNA, partial sequence, strain:JCM 10418	AB020727	1453	GenBank ENA	29347 tax ID
[Ref.: #124043]	Eubacterium sp. VPI 12708 16S ribosomal RNA gene, partial sequence.	AF262236	1531	GenBank ENA	29347 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	[Clostridium] scindens VPI12708	GCA_027941655	complete	GenBank ENA	29347 tax ID	*

[Ref.: #67770]

GC-content

47.1 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] scindens VPI12708 NCBI: GCA_027941655.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	77.151	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	87.831	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	94.481	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	50.678	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	90.866	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	67.616	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] scindens VPI12708 NCBI: GCA_027941655
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	76.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	76.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	76.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	99.9

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 10418, VPI 12708

[Ref.: #113113]

SI-ID 88187

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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 .

#113113

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID88187.1 )

#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 .

* These data were automatically processed and therefore are not curated

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[Clostridium] scindens VPI12708

[Clostridium] scindens VPI12708

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