Name: Clostridium scindens JCM 10418
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/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

Other strains from Clostridium scindens

C. scindens 19, CCUG 45363, JCM 6567, CIP 106687, ... (type strain)
C. scindens BL-389-WT-3D, DSM 100975
C. scindens JCM 10419
C. scindens JCM 10420
C. scindens JCM 10421
C. scindens JCM 10422
C. scindens JCM 10423

Section

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	14-12-2023 (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

[Ref.: #67770]

Temperature range

mesophilic

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	ENA	29347 tax ID
[Ref.: #67770]	Clostridium scindens 16S rRNA, partial sequence, strain:JCM 10418	AB020727	1453	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	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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] scindens VPI12708 NCBI: GCA_027941655.1
[Ref.: #69480]	motile	no	85.07	no
[Ref.: #69480]	flagellated	no	92.915	no
[Ref.: #69480]	gram-positive	yes	91.799	no
[Ref.: #69480]	anaerobic	yes	99.003	no
[Ref.: #69480]	aerobic	no	98.035	no
[Ref.: #69480]	halophile	no	81.086	no
[Ref.: #69480]	spore-forming	yes	61.35	no
[Ref.: #69480]	glucose-ferment	yes	65.588	no
[Ref.: #69480]	thermophile	no	99.342	no
[Ref.: #69480]	glucose-util	yes	91.808	no

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 )

* These data were automatically processed and therefore are not curated

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[Clostridium] scindens VPI12708

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