Strain identifier

BacDive ID: 3046

Type strain: Yes

Species: Collinsella stercoris

Strain Designation: RCA55-54

Strain history: CIP <- 2001, JCM <- Y. Benno, Japan: strain RCA55-54

NCBI tax ID(s): 445975 (strain), 147206 (species)

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General

@ref: 4989

BacDive-ID: 3046

DSM-Number: 13279

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

description: Collinsella stercoris RCA55-54 is an anaerobe, mesophilic bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
147206species
445975strain

strain history

@refhistory
4989<- Y. Benno; RCA 55-54
67770Y. Benno RCA55-54.
123314CIP <- 2001, JCM <- Y. Benno, Japan: strain RCA55-54

doi: 10.13145/bacdive3046.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Coriobacteriaceae
  • genus: Collinsella
  • species: Collinsella stercoris
  • full scientific name: Collinsella stercoris Kageyama and Benno 2000

@ref: 4989

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Coriobacteriaceae

genus: Collinsella

species: Collinsella stercoris

full scientific name: Collinsella stercoris Kageyama and Benno 2000 emend. Nouioui et al. 2018

strain designation: RCA55-54

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.038
69480100positive
123314nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4989PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
123314CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137

culture temp

@refgrowthtypetemperaturerange
4989positivegrowth37mesophilic
56721positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4989anaerobe
56721anaerobe
69480anaerobe99.076

spore formation

@refspore formationconfidence
69481no100
69480no99.995

murein

  • @ref: 4989
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
4989---+-----+------+/-+---+/----+/-+/---
4989---+-----+------++---+---++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4989human fecesJapanJPNAsia
56721Human fecesJapanJPNAsia
67770Human feces
123314Human, FecesJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49891Risk group (German classification)
1233141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Collinsella stercoris gene for 16S ribosomal RNA, partial sequence, strain: JCM 10641AB5584881466ena147206
4989Hepatitis C virus gene for core protein, partial cds, clone:N3AB030161300ena11103
67770Collinsella sp. RCA55-54 gene for 16S rRNAAB0310611458ena445975

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Collinsella stercoris DSM 13279 FDAARGOS_1572GCA_020735465completencbi445975
66792Collinsella stercoris DSM 13279445975.6wgspatric445975
66792Collinsella stercoris DSM 13279642979321draftimg445975
67770Collinsella stercoris DSM 13279GCA_000156215scaffoldncbi445975
66792Collinsella stercoris DSM 13279GCA_025149625completencbi147206
66792Collinsella stercoris strain DSM 13279147206.16completepatric147206
66792Collinsella stercoris DSM 13279 strain FDAARGOS_1572445975.14completepatric445975
66792Collinsella stercoris DSM 13279 strain FDAARGOS_1572445975.13completepatric445975

GC content

  • @ref: 4989
  • GC-content: 61.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.15no
gram-positiveyes90.733no
anaerobicyes99.107yes
aerobicno99.316yes
halophileno84.244no
spore-formingno94.452no
motileno94.753no
thermophileno96.586yes
glucose-utilyes86.663no
glucose-fermentyes75.353no

External links

@ref: 4989

culture collection no.: DSM 13279, JCM 10641, CCUG 45295, CIP 106913, RCA 55-54

straininfo link

  • @ref: 72566
  • straininfo: 49452

literature

  • topic: Metabolism
  • Pubmed-ID: 33938389
  • title: Completion of the gut microbial epi-bile acid pathway.
  • authors: Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM
  • journal: Gut Microbes
  • DOI: 10.1080/19490976.2021.1907271
  • year: 2021
  • mesh: Actinobacteria/genetics, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/*metabolism, Clostridium/*enzymology/*genetics/*metabolism, Clostridium Infections/microbiology, DNA, Bacterial, Gastrointestinal Microbiome, Humans, Hydroxysteroid Dehydrogenases/*genetics/*metabolism, Lithocholic Acid/metabolism, NADP/metabolism, Phylogeny, Recombinant Proteins/genetics/metabolism
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4989Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13279)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13279
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
56721Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45295)https://www.ccug.se/strain?id=45295
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/
68380Automatically annotated from API rID32A
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72566Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49452.1StrainInfo: A central database for resolving microbial strain identifiers
123314Curators of the CIPCollection of Institut Pasteur (CIP 106913)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106913