Strain identifier

BacDive ID: 2748

Type strain: Yes

Species: Clostridium scindens

Strain Designation: 19

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

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

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General

@ref: 2276

BacDive-ID: 2748

DSM-Number: 5676

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

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

NCBI tax id

NCBI tax idMatching level
411468strain
29347species

strain history

@refhistory
2276<- ATCC <- L.V. Holdeman, VPI 13733 <- V. Bokkenheuser, 19
67770G. N. Morris.
122518CIP <- 2000, JCM <- G.N. Morris

doi: 10.13145/bacdive2748.20230509.8.1

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

@refgram stainconfidencecell shapemotility
69480positive100
122518positiverod-shapedno

colony morphology

@refincubation period
567422 days
122518

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2276WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: 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
2276CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: 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
122518CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
2276positivegrowth35mesophilic
56742positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2276anaerobe
56742anaerobe
69480anaerobe99.999
122518anaerobe

spore formation

@refspore formationconfidence
69480no99.466
122518no

compound production

@refcompound
227620-alpha hydroxysteroid dehydrogenase
2276steroid desmolase
22767-ß dehydrogenase
22767-alpha dehydroxylase

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1225184853esculin-hydrolysis
12251817632nitrate-reduction
12251816301nitrite-reduction
12251817632nitrate+respiration

metabolite production

  • @ref: 122518
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
122518oxidase-
122518beta-galactosidase-3.2.1.23
122518gelatinase-
122518amylase-
122518caseinase-3.4.21.50
122518catalase-1.11.1.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122518----------++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
2276human faecesUSAUSANorth America
56742Human fecesUSAUSANorth AmericaNew York
67770Human feces
122518Human, FecesUnited States of AmericaUSANorth AmericaNew York

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
22761Risk group (German classification)
1225182Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium scindens 16S rRNA gene, partial, strain DSM 5676Y181861490ena29347
20218Clostridium scindens 16S rRNA, partial sequence, strain:JCM 6567AB0208831453ena29347
20218Clostridium scindens gene for 16S ribosomal RNA, partial sequenceAB9107471496ena29347
2276Clostridium scindens 16S ribosomal RNA gene, partial sequenceAF2622381529ena29347

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] scindens ATCC 35704GCA_004295125completencbi411468
66792Clostridium scindens ATCC 35704411468.9wgspatric411468
66792[Clostridium] scindens ATCC 35704411468.41completepatric411468
66792Lachnoclostridium scindens ATCC 35704641736197draftimg411468
67770[Clostridium] scindens ATCC 35704GCA_000154505scaffoldncbi411468

GC content

@refGC-contentmethod
227645.0
6777045thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes64no
flagellatedno95.153no
gram-positiveyes93.729no
anaerobicyes99.708yes
aerobicno98.482yes
halophileno81.083no
spore-formingyes53.692no
thermophileno99.377yes
glucose-utilyes90.543no
motileno88.658no
glucose-fermentyes72.865no

External links

@ref: 2276

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

straininfo link

  • @ref: 72278
  • straininfo: 40833

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10843034Assignment 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 YInt J Syst Evol Microbiol10.1099/00207713-50-3-9712000Base 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/*metabolismEnzymology
Enzymology23646168Characterization of a novel metal-dependent D-psicose 3-epimerase from Clostridium scindens 35704.Zhang W, Fang D, Xing Q, Zhou L, Jiang B, Mu WPLoS One10.1371/journal.pone.00629872013Amino 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, TemperatureMetabolism
Metabolism27598572Production 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 TJ Agric Food Chem10.1021/acs.jafc.6b033472016Bacillus 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, TemperatureEnzymology
Metabolism29217478Identification 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 JMBiochim Biophys Acta Mol Cell Biol Lipids10.1016/j.bbalip.2017.12.0012017*Bacterial Proteins/biosynthesis/chemistry/genetics/isolation & purification, Bile Acids and Salts/*metabolism, *Clostridium/genetics/metabolism, *Flavoproteins/biosynthesis/chemistry/genetics/isolation & purification, Humans, Intestines/microbiologyEnzymology
Enzymology29572237The desA and desB genes from Clostridium scindens ATCC 35704 encode steroid-17,20-desmolase.Devendran S, Mythen SM, Ridlon JMJ Lipid Res10.1194/jlr.M0839492018Cloning, Molecular, Clostridium/*enzymology/*genetics, Kinetics, Steroid 17-alpha-Hydroxylase/*genetics/*metabolism, Substrate SpecificityMetabolism
Metabolism30737348Clostridium 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 JMAppl Environ Microbiol10.1128/AEM.00052-192019Amino 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 SequencingGenetics
Metabolism32179626Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible (bai) Operon.Reed AD, Nethery MA, Stewart A, Barrangou R, Theriot CMJ Bacteriol10.1128/JB.00039-202020Antibiosis, 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, SymbiosisPathogenicity
Phylogeny33512312Sporofaciens 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 FKInt J Syst Evol Microbiol10.1099/ijsem.0.0046732021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2276Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5676)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5676
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
56742Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45363)https://www.ccug.se/strain?id=45363
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
72278Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40833.1StrainInfo: A central database for resolving microbial strain identifiers
122518Curators of the CIPCollection of Institut Pasteur (CIP 106687)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106687