Archive BacDiveID:10.13145/bacdive2748.20221219.7.1

Strain identifier

BacDive ID: 2748

Type strain:

Species: Clostridium scindens

Strain Designation: 19

Strain history: G. N. Morris.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 2276

BacDive-ID: 2748

DSM-Number: 5676

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Clostridium scindens 19 is an anaerobe, mesophilic bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax id	Matching level
29347	species
411468	strain

strain history

doi: 10.13145/bacdive2748.20221219.7.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Clostridium
species: Clostridium scindens
full scientific name: Clostridium scindens Morris et al. 1985

@ref: 2276

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium scindens

full scientific name: Clostridium scindens Morris et al. 1985

strain designation: 19

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 95.78

colony morphology

@ref: 56742
incubation period: 2 days

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
2276	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)	yes	https://mediadive.dsmz.de/medium/339	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339; with strain-specific modifications) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l D-Glucose 10.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
2276	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	yes	https://mediadive.dsmz.de/medium/110	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	range
2276	positive	growth	35	mesophilic
56742	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
2276	anaerobe
56742	anaerobe
69480	anaerobe	99.999

spore formation

@ref: 69480
spore formation: no
confidence: 82.483

compound production

@ref	compound
2276	20-alpha hydroxysteroid dehydrogenase
2276	steroid desmolase
2276	7-ß dehydrogenase
2276	7-alpha dehydroxylase

halophily

@ref: 69480
halophily level: non-halophilic
confidence: 99.434

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent	geographic location
2276	human faeces	USA	USA	North America
56742	Human feces	USA	USA	North America	New York
67770	Human feces

isolation source categories

Cat1	Cat2	Cat3
#Host	#Human
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

taxonmaps

@ref: 69479
File name: preview.99_1033.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_592;97_693;98_808;99_1033&stattab=map
Last taxonomy: [Clostridium] scindens subclade
16S sequence: Y18186
Sequence Identity:
Total samples: 80205
soil counts: 346
aquatic counts: 837
animal counts: 78797
plant counts: 225

Safety information

risk assessment

@ref: 2276
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Clostridium scindens 16S rRNA gene, partial, strain DSM 5676	Y18186	1490	ena	29347
20218	Clostridium scindens 16S rRNA, partial sequence, strain:JCM 6567	AB020883	1453	ena	29347
20218	Clostridium scindens gene for 16S ribosomal RNA, partial sequence	AB910747	1496	ena	29347
2276	Clostridium scindens 16S ribosomal RNA gene, partial sequence	AF262238	1529	ena	29347

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	[Clostridium] scindens ATCC 35704 ATCC 35704	GCA_004295125	complete	ncbi	411468
66792	Clostridium scindens ATCC 35704	411468.9	wgs	patric	411468
66792	[Clostridium] scindens ATCC 35704	411468.41	complete	patric	411468
66792	Lachnoclostridium scindens ATCC 35704	641736197	draft	img	411468
67770	[Clostridium] scindens ATCC 35704 ATCC 35704	GCA_000154505	scaffold	ncbi	411468
67770	[Clostridium] scindens ATCC 35704 chromosome, complete genome	CP036170		ena	411468
66792	uncultured Rhodobacteraceae bacterium ERR599014_bin.115_MetaBAT_v2.12.1_MAG	GCA_913043125	contig	patric	157276

GC content

@ref	GC-content	method
2276	45.0
67770	45	thermal denaturation, midpoint method (Tm)

External links

@ref: 2276

culture collection no.: CCUG 45363, JCM 6567, CIP 106687, DSM 5676, ATCC 35704, VPI 13733, BCRC 14551

straininfo link

@ref	passport
20218	http://www.straininfo.net/strains/159364
20218	http://www.straininfo.net/strains/111093

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	10843034	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	Base Composition, Bile Acids and Salts/metabolism, Clostridium/classification/enzymology/isolation & purification, DNA, Ribosomal/chemistry/genetics, Eubacterium/classification/enzymology, Feces/microbiology, Genes, rRNA, Humans, Hydroxysteroid Dehydrogenases, Molecular Sequence Data, Oxidoreductases, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Steroid Hydroxylases/*metabolism	Enzymology
Enzymology	23646168	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	Amino Acid Sequence, Carbohydrate Epimerases/chemistry/genetics/isolation & purification/metabolism, Cloning, Molecular, Clostridium/enzymology/genetics, Enzyme Stability, Fructose/metabolism, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Manganese/metabolism, Metals/metabolism, Molecular Sequence Data, Recombinant Proteins, Sequence Alignment, Substrate Specificity, Temperature	Metabolism
Metabolism	27598572	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	Bacillus subtilis/genetics/metabolism, Biocatalysis, Carbohydrate Epimerases/genetics/metabolism, Cloning, Molecular, Clostridium/classification/enzymology, Fructose/biosynthesis/metabolism, Gene Expression Regulation, Enzymologic, Hydrogen-Ion Concentration, Recombinant Fusion Proteins/genetics/metabolism, Spores, Bacterial/metabolism, Temperature	Enzymology
Metabolism	29217478	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	Bacterial Proteins/biosynthesis/chemistry/genetics/isolation & purification, Bile Acids and Salts/metabolism, Clostridium/genetics/metabolism, Flavoproteins/biosynthesis/chemistry/genetics/isolation & purification, Humans, Intestines/microbiology	Enzymology
Enzymology	29572237	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	Cloning, Molecular, Clostridium/enzymology/genetics, Kinetics, Steroid 17-alpha-Hydroxylase/genetics/metabolism, Substrate Specificity	Metabolism
Metabolism	30737348	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	Amino Acids/metabolism, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/metabolism, Carbohydrate Metabolism, Cholic Acid/metabolism, Clostridiales/genetics/growth & development/metabolism, Culture Media, DNA Repair, DNA, Bacterial/genetics/isolation & purification, Deoxycholic Acid/metabolism, Fermentation, Gastrointestinal Microbiome, Humans, Hydroxylation, Nutritional Requirements, Sequence Analysis, RNA, Whole Genome Sequencing	Genetics
Metabolism	32179626	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	Antibiosis, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/metabolism, Clostridiales/genetics/physiology, Clostridioides difficile/growth & development/physiology, Clostridium Infections/metabolism/microbiology, Clostridium histolyticum/genetics/*physiology, Humans, Operon, Species Specificity, Symbiosis	Pathogenicity
Phylogeny	33512312	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

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2276	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5676)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-5676
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
56742	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 45363)	https://www.ccug.se/strain?id=45363
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)