Strain identifier

BacDive ID: 3044

Type strain: Yes

Species: Collinsella aerofaciens

Strain history: T. Mitsuoka V-61 <-- Takeda Chem. Ind., Ltd.; 1442 <-- ATCC 25986 <-- VPI 1003.

NCBI tax ID(s): 411903 (strain), 74426 (species)

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General

@ref: 1537

BacDive-ID: 3044

DSM-Number: 3979

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

description: Collinsella aerofaciens CCUG 28087 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
411903strain
74426species

strain history

@refhistory
1537<- ATCC <- W.E.C. Moore, VPI 1003
67770T. Mitsuoka V-61 <-- Takeda Chem. Ind., Ltd.; 1442 <-- ATCC 25986 <-- VPI 1003.

doi: 10.13145/bacdive3044.20230509.8.1

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 aerofaciens
  • full scientific name: Collinsella aerofaciens (Eggerth 1935) Kageyama et al. 1999

  • synonyms

    @refsynonym
    20215Bacteroides aerofaciens
    20215Eubacterium aerofaciens

@ref: 1537

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Coriobacteriaceae

genus: Collinsella

species: Collinsella aerofaciens

full scientific name: Collinsella aerofaciens (Eggerth 1935) Kageyama et al. 1999

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1537CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 0.0001 g/l NaOH (optional) Distilled water
1537FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
1537FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1537positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1537anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.982

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-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
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
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
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1537-+-+-+-----------+/-+-------+/---
1537-+-+-+/------------++----------
1537-+-+-+-----------++----------
1537---+-+-----------++------+/-+--

Isolation, sampling and environmental information

isolation

@refsample type
1537human faeces
49090Human feces
67770Human feces

isolation source categories

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

Safety information

risk assessment

  • @ref: 1537
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Eubacterium aerofaciens gene for 16S rRNA, partial sequenceAB0118161463ena411903
20218Collinsella aerofaciens gene for 16S ribosomal RNA, partial sequence, strain: JCM 10188AB6161311467ena74426

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Collinsella aerofaciens ATCC 25986 JCM 10188GCA_010509075completencbi411903
66792Collinsella aerofaciens ATCC 25986411903.6wgspatric411903
66792Collinsella aerofaciens ATCC 25986 strain JCM 10188411903.30completepatric411903
66792Collinsella aerofaciens strain NCTC1183874426.133wgspatric74426
66792Collinsella aerofaciens ATCC 25986640612206draftimg411903
66792Collinsella aerofaciens NCTC 118382814123380draftimg74426
67770Collinsella aerofaciens ATCC 25986GCA_000169035contigncbi411903
67770Collinsella aerofaciens NCTC11838GCA_900461335contigncbi74426

GC content

  • @ref: 67770
  • GC-content: 61
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.351no
flagellatedno97.899no
gram-positiveyes93.765no
anaerobicyes99.669yes
aerobicno98.638yes
halophileno86.894no
spore-formingno93.623no
thermophileno91.234no
glucose-utilyes86.098no
glucose-fermentyes79.402no

External links

@ref: 1537

culture collection no.: CCUG 28087, JCM 10188, DSM 3979, ATCC 25986, VPI 1003, KCTC 3647, NCTC 11838

straininfo link

  • @ref: 72564
  • straininfo: 38740

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology6954878Characterization of NADP-dependent 7 beta-hydroxysteroid dehydrogenases from Peptostreptococcus productus and Eubacterium aerofaciens.Hirano S, Masuda NAppl Environ Microbiol10.1128/aem.43.5.1057-1063.19821982Cations, Divalent/pharmacology, Enzyme Induction, Eubacterium/*enzymology, Hot Temperature, Hydrogen-Ion Concentration, Hydroxysteroid Dehydrogenases/isolation & purification/*metabolism, Kinetics, Molecular Weight, Peptostreptococcus/*enzymology, Ursodeoxycholic Acid/metabolismStress
Phylogeny10319476Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.Kageyama A, Benno Y, Nakase TInt J Syst Bacteriol10.1099/00207713-49-2-5571999Bacteria, Anaerobic/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eubacterium/*classification/genetics/isolation & purification/physiology, Feces/*microbiology, Genes, rRNA, Gram-Positive Asporogenous Rods/*classification/genetics/physiology, Humans, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Enzymology21181147Identification, cloning, heterologous expression, and characterization of a NADPH-dependent 7beta-hydroxysteroid dehydrogenase from Collinsella aerofaciens.Liu L, Aigner A, Schmid RDAppl Microbiol Biotechnol10.1007/s00253-010-3052-y2010Actinobacteria/chemistry/classification/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/*chemistry/*genetics/isolation & purification/metabolism, *Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics/metabolism, *Gene Expression, Hydroxysteroid Dehydrogenases/*chemistry/*genetics/isolation & purification/metabolism, Molecular Sequence Data, NADP/*metabolism, Phylogeny, Sequence Alignment, Substrate Specificity, Ursodeoxycholic Acid/metabolismPhylogeny
Phylogeny30871249Characterization a Novel Butyric Acid-Producing Bacterium Collinsella aerofaciens Subsp. Shenzhenensis Subsp. Nov.Qin P, Zou Y, Dai Y, Luo G, Zhang X, Xiao LMicroorganisms10.3390/microorganisms70300782019
Genetics32299873Complete Genome Sequence of Collinsella aerofaciens JCM 10188(T).Tourlousse DM, Sakamoto M, Miura T, Narita K, Ohashi A, Uchino Y, Yamazoe A, Kameyama K, Terauchi J, Ohkuma M, Kawasaki H, Sekiguchi YMicrobiol Resour Announc10.1128/MRA.00134-202020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1537Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3979)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3979
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
49090Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28087)https://www.ccug.se/strain?id=28087
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
72564Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38740.1StrainInfo: A central database for resolving microbial strain identifiers