Strain identifier

BacDive ID: 3047

Type strain: Yes

Species: Collinsella intestinalis

Strain Designation: RCA56-68

Strain history: CIP <- 2001, JCM <- Y. Benno: strain RCA56-68

NCBI tax ID(s): 521003 (strain), 147207 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4990

BacDive-ID: 3047

DSM-Number: 13280

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

description: Collinsella intestinalis RCA56-68 is an anaerobe, mesophilic bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
147207species
521003strain

strain history

@refhistory
4990<- Y. Benno; RCA 56-68
67770Y. Benno RCA56-68.
120256CIP <- 2001, JCM <- Y. Benno: strain RCA56-68

doi: 10.13145/bacdive3047.20230509.8.1

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 intestinalis
  • full scientific name: Collinsella intestinalis Kageyama and Benno 2000

@ref: 4990

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Coriobacteriaceae

genus: Collinsella

species: Collinsella intestinalis

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

strain designation: RCA56-68

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.743
69480100positive
120256nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4990PYG 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
40616MEDIUM 137 - for Ruminococcus hansenii and Rarobacter incanusyesDistilled water make up to (940.000 ml);Glucose (5.000 g);Yeast extract(10.000 g);Peptone (5.000 g);Resazurin (1.000 mg);Tween 80 (1.000 ml);Tryptone (5.000g);Beef extract (5.000 g);Cysteine hydrochloride (0.500 g);Di Potassium monohydrogenophosphate (2.0
120256CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137

culture temp

@refgrowthtypetemperaturerange
4990positivegrowth37mesophilic
40616positivegrowth37mesophilic
56722positivegrowth37mesophilic
67770positivegrowth37mesophilic
120256positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4990anaerobe
56722anaerobe
69480anaerobe99.567

spore formation

@refspore formationconfidence
69481no100
69480no99.994

murein

  • @ref: 4990
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

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-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
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
4990-+-------++-----++---+---++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4990human fecesJapanJPNAsia
56722Human fecesJapanJPNAsia
67770Human feces
120256Human, Feces

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49901Risk group (German classification)
1202561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Collinsella intestinalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10643AB5584891466ena147207
4990Hepatitis C virus gene for core protein, partial cds, clone:N5AB030163300ena11103
67770Collinsella sp. RCA56-68 gene for 16S rRNAAB0310631459ena521003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Collinsella intestinalis DSM 13280521003.7wgspatric521003
66792Collinsella intestinalis DSM 132802562617146draftimg521003
67770Collinsella intestinalis DSM 13280GCA_000156175scaffoldncbi521003

GC content

  • @ref: 4990
  • GC-content: 64.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.812no
anaerobicyes98.532yes
halophileno69.531no
spore-formingno95.628no
glucose-utilyes86.129no
aerobicno99.286no
thermophileno96.399yes
motileno95.881no
flagellatedno98.201no
glucose-fermentyes75.444no

External links

@ref: 4990

culture collection no.: CCUG 45296, CIP 106914, DSM 13280, JCM 10643, RCA 56-68

straininfo link

  • @ref: 72567
  • straininfo: 49453

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4990Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13280)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13280
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
40616Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19097
56722Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45296)https://www.ccug.se/strain?id=45296
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
72567Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49453.1StrainInfo: A central database for resolving microbial strain identifiers
120256Curators of the CIPCollection of Institut Pasteur (CIP 106914)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106914