Strain identifier

BacDive ID: 140126

Type strain: Yes

Species: Coprobacter secundus

Strain Designation: 177

Strain history: DSM 28864 <-- V. Shcherbakova; Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia <-- A. N. Shkoporov and B. A. Efimov; Russian Natl. Res. Med. Univ., Russia; 177.

NCBI tax ID(s): 1501392 (species)

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General

@ref: 42733

BacDive-ID: 140126

DSM-Number: 28864

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

description: Coprobacter secundus 177 is a mesophilic bacterium that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 1501392
  • Matching level: species

strain history

@refhistory
42733<- V. Shcherbakova, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia <- A.N. Shkoporov and B.A. Efimov; 177
67770DSM 28864 <-- V. Shcherbakova; Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia <-- A. N. Shkoporov and B. A. Efimov; Russian Natl. Res. Med. Univ., Russia; 177.

doi: 10.13145/bacdive140126.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Barnesiellaceae
  • genus: Coprobacter
  • species: Coprobacter secundus
  • full scientific name: Coprobacter secundus Shkoporov et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Gabonia massiliensis

@ref: 42733

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Barnesiellaceae

genus: Coprobacter

species: Coprobacter secundus

full scientific name: Coprobacter secundus Shkoporov et al. 2015

strain designation: 177

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 42733
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

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
42733--++-+---+------+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
42733human faecesRussiaRUSEurope
67770Stool of an 18-year-old healthy Russian female

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3340.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15878;96_1744;97_2085;98_2561;99_3340&stattab=map
  • Last taxonomy: Bacteroidales
  • 16S sequence: KJ572412
  • Sequence Identity:
  • Total samples: 13099
  • soil counts: 38
  • aquatic counts: 186
  • animal counts: 12866
  • plant counts: 9

Safety information

risk assessment

  • @ref: 42733
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Coprobacter secundus strain 177 16S ribosomal RNA gene, partial sequence
  • accession: KJ572412
  • length: 1290
  • database: ena
  • NCBI tax ID: 1501392

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Coprobacter secundus 1772630968585draftimg1501392
67770Coprobacter secundus 177GCA_000803105contigncbi1501392

GC content

@refGC-contentmethod
4273337.8sequence analysis
6777037.8genome sequence analysis

External links

@ref: 42733

culture collection no.: DSM 28864, VKM B-2857, JCM 33897

straininfo link

  • @ref: 96520
  • straininfo: 403723

literature

  • topic: Phylogeny
  • Pubmed-ID: 26377180
  • title: Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces.
  • authors: Shkoporov AN, Chaplin AV, Khokhlova EV, Shcherbakova VA, Motuzova OV, Bozhenko VK, Kafarskaia LI, Efimov BA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000617
  • year: 2015
  • mesh: Adolescent, Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Female, Gram-Negative Bacteria/classification/genetics/isolation & purification, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42733Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28864Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28864)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96520Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403723.1