Strain identifier

BacDive ID: 3050

Type strain: Yes

Species: Collinsella tanakaei

Strain history: Y. Watanabe A40 (=YIT 12063).

NCBI tax ID(s): 742742 (strain), 626935 (species)

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General

@ref: 16260

BacDive-ID: 3050

DSM-Number: 22478

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

description: Collinsella tanakaei DSM 22478 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces .

NCBI tax id

NCBI tax idMatching level
626935species
742742strain

strain history

@refhistory
16260<- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan <- F. Nagai and M. Morotomi
67770Y. Watanabe A40 (=YIT 12063).

doi: 10.13145/bacdive3050.20230509.8.1

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 tanakaei
  • full scientific name: Collinsella tanakaei Nagai et al. 2010

@ref: 16260

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Coriobacteriaceae

genus: Collinsella

species: Collinsella tanakaei

full scientific name: Collinsella tanakaei Nagai et al. 2010

type strain: yes

Morphology

cell morphology

  • @ref: 29633
  • gram stain: positive
  • cell length: 1-3.3 µm
  • cell width: 0.5-1 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 29633
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16260PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) 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 Arginine 1.0 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 Vitamin K1 NaOH Tween 80 Distilled water
16260COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
16260positivegrowth37mesophilic
29633positivegrowth37mesophilic
29633positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29633positivegrowth7
29633positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16260obligate anaerobe
29633anaerobe

spore formation

  • @ref: 29633
  • spore formation: no

observation

  • @ref: 29633
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2963317057cellobiose+carbon source
2963317234glucose+carbon source
2963317716lactose+carbon source
2963317306maltose+carbon source
2963337684mannose+carbon source
2963317814salicin+carbon source
2963317992sucrose+carbon source
296334853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose+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
16260-+---++---++/-----+++--+---++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16260human faeces (healthy Japanese adult)TokyoJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4770.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_147;96_2358;97_2871;98_3575;99_4770&stattab=map
  • Last taxonomy: Collinsella tanakaei subclade
  • 16S sequence: AB601001
  • Sequence Identity:
  • Total samples: 5052
  • soil counts: 49
  • aquatic counts: 106
  • animal counts: 4896
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16260
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Collinsella tanakaei gene for 16S ribosomal RNA, partial sequenceAB6010011469ena742742
16260Collinsella tanakaei gene for 16S rRNA, partial sequence, strain: YIT 12063AB4908071491ena742742

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Collinsella tanakaei YIT 12063742742.3wgspatric742742
66792Collinsella tanakaei YIT 120632513237344draftimg742742
67770Collinsella tanakaei YIT 12063GCA_000225705scaffoldncbi742742

GC content

@refGC-contentmethod
1626060.8-61
6777060.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.678no
flagellatedno97.668no
gram-positiveyes91.917yes
anaerobicyes98.62yes
aerobicno98.338yes
halophileno78.237no
spore-formingno88.902no
thermophileno95.529no
glucose-utilyes88.988yes
glucose-fermentyes78.104no

External links

@ref: 16260

culture collection no.: DSM 22478, JCM 16071, YIT 12063, KCTC 15132

straininfo link

  • @ref: 72570
  • straininfo: 398191

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20023061Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces.Nagai F, Watanabe Y, Morotomi MInt J Syst Evol Microbiol10.1099/ijs.0.017533-02009Actinobacteria/*classification/enzymology/genetics/*isolation & purification, Adult, Bacterial Proteins/metabolism, Base Composition, Catalase/metabolism, DNA, Bacterial/genetics, Feces/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Urease/metabolismMetabolism
Phylogeny30806613Collinsella vaginalis sp. nov. strain Marseille-P2666(T), a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis.Diop A, Diop K, Tomei E, Armstrong N, Bretelle F, Raoult D, Fenollar F, Fournier PEInt J Syst Evol Microbiol10.1099/ijsem.0.0032212019Actinobacteria/*classification/isolation & purification, Adult, Bacterial Typing Techniques, Base Composition, DNA, Bacterial, Fatty Acids/chemistry, Female, France, Humans, *Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Vagina/microbiology, Vaginosis, Bacterial/*microbiologyPathogenicity
Metabolism33938389Completion of the gut microbial epi-bile acid pathway.Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JMGut Microbes10.1080/19490976.2021.19072712021Actinobacteria/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/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16260Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22478)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22478
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
29633Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126023
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
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
72570Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398191.1StrainInfo: A central database for resolving microbial strain identifiers