Name: Clostridium scindens 19
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2748

Type strain:

Species: Clostridium scindens

Strain Designation: 19

Culture col. no.: CCUG 45363, JCM 6567, CIP 106687, DSM 5676, ATCC 35704, VPI 13733, BCRC 14551, CCRC 14551

Strain history: CIP <- 2000, JCM <- G.N. Morris

NCBI tax ID(s): 411468 (strain), 29347 (species)

SI-ID 40833

ATCC 35704, DSM 5676, JCM 6567, CCRC 14551, CCUG 45363, CIP 106687, BCRC 14551

Other strains from Clostridium scindens

C. scindens BL-389-WT-3D, DSM 100975
C. scindens JCM 10418, VPI 12708
C. scindens JCM 10419
C. scindens JCM 10420
C. scindens JCM 10421
C. scindens JCM 10422
C. scindens JCM 10423

Section

Clostridium scindens 19 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces.

Gram-positive
anaerobe
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 morphological and physiological properties Morphology

[Ref.: #122518]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #122518]	Cell shape	rod-shaped

[Ref.: #122518]	Motility	no

[Ref.: #56742]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2276]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)

[Ref.: #2276]

Culture medium growth

[Ref.: #2276]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2276]

Culture medium composition

expand / minimize

[Ref.: #2276]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #2276]

Culture medium growth

[Ref.: #2276]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2276]

Culture medium composition

expand / minimize

[Ref.: #122518]

Culture medium

CIP Medium 20

[Ref.: #122518]

Culture medium growth

[Ref.: #122518]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #2276]	growth	35 °C
[Ref.: #56742]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #2276]	Temperature range	mesophilic
[Ref.: #56742]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2276]	Oxygen tolerance	anaerobe
[Ref.: #56742]	Oxygen tolerance	anaerobe
[Ref.: #122518]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #122518]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.466

[Ref.: #2276]	Name of produced compound	20-alpha hydroxysteroid dehydrogenase
[Ref.: #2276]	Name of produced compound	steroid desmolase
[Ref.: #2276]	Name of produced compound	7-ß dehydrogenase
[Ref.: #2276]	Name of produced compound	7-alpha dehydroxylase

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122518]	esculin ChEBI	-	hydrolysis
[Ref.: #122518]	nitrate ChEBI	-	reduction
[Ref.: #122518]	nitrate ChEBI	+	respiration
[Ref.: #122518]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #122518]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #122518]	amylase	-
[Ref.: #122518]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #122518]	caseinase	-	3.4.21.50
[Ref.: #122518]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #122518]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122518]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122518]	9720	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #2276]	Sample type/isolated from	human faeces
[Ref.: #2276]	Country	USA
[Ref.: #2276]	Country ISO 3 Code	USA
[Ref.: #2276]	Continent	North America

[Ref.: #56742]	Sample type/isolated from	Human feces
[Ref.: #56742]	Geographic location (country and/or sea, region)	New York
[Ref.: #56742]	Country	USA
[Ref.: #56742]	Country ISO 3 Code	USA
[Ref.: #56742]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Human feces

[Ref.: #122518]	Sample type/isolated from	Human, Feces
[Ref.: #122518]	Geographic location (country and/or sea, region)	New York
[Ref.: #122518]	Country	United States of America
[Ref.: #122518]	Country ISO 3 Code	USA
[Ref.: #122518]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y18186 (>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 possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #2276]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122518]	Biosafety level	2	Risk group (French classification)

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.: #2276]	Clostridium scindens 16S ribosomal RNA gene, partial sequence	AF262238	1529	ENA	29347 tax ID
[Ref.: #20218]	Clostridium scindens 16S rRNA gene, partial, strain DSM 5676	Y18186	1490	ENA	29347 tax ID	*
[Ref.: #20218]	Clostridium scindens 16S rRNA, partial sequence, strain:JCM 6567	AB020883	1453	ENA	29347 tax ID	*
[Ref.: #20218]	Clostridium scindens gene for 16S ribosomal RNA, partial sequence	AB910747	1496	ENA	29347 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	[Clostridium] scindens ATCC 35704	GCA_000154505	scaffold	GenBank	411468 tax ID
[Ref.: #66792]	[Clostridium] scindens ATCC 35704	GCA_004295125	complete	GenBank	411468 tax ID	*
[Ref.: #66792]	Clostridium scindens ATCC 35704	411468.9	wgs	PATRIC	411468 tax ID	*
[Ref.: #66792]	[Clostridium] scindens ATCC 35704	411468.41	complete	PATRIC	411468 tax ID	*
[Ref.: #66792]	Lachnoclostridium scindens ATCC 35704	641736197	draft	JGI IMG/M	411468 tax ID	*

[Ref.: #2276]	GC-content	45.0 mol%
[Ref.: #67770]	GC-content	45 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: [Clostridium] scindens ATCC 35704 ATCC 35704 NCBI: GCA_004295125.1
[Ref.: #69481]	spore-forming	yes	64	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: [Clostridium] scindens ATCC 35704 ATCC 35704 NCBI: GCA_004295125.1
[Ref.: #69480]	flagellated	no	95.153	no
[Ref.: #69480]	gram-positive	yes	93.729	no
[Ref.: #69480]	anaerobic	yes	99.708	yes
[Ref.: #69480]	aerobic	no	98.482	yes
[Ref.: #69480]	halophile	no	81.083	no
[Ref.: #69480]	spore-forming	yes	53.692	no
[Ref.: #69480]	thermophile	no	99.377	yes
[Ref.: #69480]	glucose-util	yes	90.543	no
[Ref.: #69480]	motile	no	88.658	no
[Ref.: #69480]	glucose-ferment	yes	72.865	no

Availability in culture collections External links

[Ref.: #2276]

Culture collection no.

CCUG 45363, JCM 6567, CIP 106687, DSM 5676, ATCC 35704, VPI 13733, BCRC 14551, CCRC 14551

[Ref.: #72278]

SI-ID 40833

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse.	Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FK	Int J Syst Evol Microbiol	10.1099/ijsem.0.004673	2021	*
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	*
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	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	Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704.	Harris SC, Devendran S, Alves JMP, Mythen SM, Hylemon PB, Ridlon JM	Biochim Biophys Acta Mol Cell Biol Lipids	10.1016/j.bbalip.2017.12.001	2017	*
Metabolism	Production of d-Allulose with d-Psicose 3-Epimerase Expressed and Displayed on the Surface of Bacillus subtilis Spores.	He W, Jiang B, Mu W, Zhang T	J Agric Food Chem	10.1021/acs.jafc.6b03347	2016	*
Enzymology	Characterization of a novel metal-dependent D-psicose 3-epimerase from Clostridium scindens 35704.	Zhang W, Fang D, Xing Q, Zhou L, Jiang B, Mu W	PLoS One	10.1371/journal.pone.0062987	2013	*
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

#2276

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5676

#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 )

#56742 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45363

#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;

#68382

Automatically annotated from API zym .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72278

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-ID40833.1 )

#122518 Collection of Institut Pasteur ; Curators of the CIP; CIP 106687
* These data were automatically processed and therefore are not curated

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[Clostridium] scindens ATCC 35704 ATCC 35704

[Clostridium] scindens ATCC 35704 ATCC 35704

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