Strain identifier

BacDive ID: 1613

Type strain: Yes

Species: Bacteroides coprosuis

Strain Designation: PC 139

Strain history: CCUG 50528 <-- T. R. Whitehead PC 139.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7330

BacDive-ID: 1613

DSM-Number: 18011

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

description: Bacteroides coprosuis PC 139 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pig faeces, swine manure.

NCBI tax id

NCBI tax idMatching level
679937strain
151276species

strain history

@refhistory
7330<- A. P. Rooney <- T. R. Whitehead; PC 139
67770CCUG 50528 <-- T. R. Whitehead PC 139.

doi: 10.13145/bacdive1613.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides coprosuis
  • full scientific name: Bacteroides coprosuis Whitehead et al. 2005

@ref: 7330

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides coprosuis

full scientific name: Bacteroides coprosuis Whitehead et al. 2005 emend. Hahnke et al. 2016

strain designation: PC 139

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31598negative1.9 µm1 µmrod-shapedno
69480no91.259
69480negative99.999

colony morphology

  • @ref: 7330
  • incubation period: 2-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_18011_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7330
  • 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

@refgrowthtypetemperaturerange
7330positivegrowth37mesophilic
31598positivegrowth25-37mesophilic
31598positiveoptimum37mesophilic
58893positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7330anaerobe
31598anaerobe
58893anaerobe
69480anaerobe98.922

spore formation

@refspore formationconfidence
31598no
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3159817234glucose+carbon source
3159817306maltose+carbon source
315984853esculin+hydrolysis
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
31598acid phosphatase+3.1.3.2
31598alpha-galactosidase+3.2.1.22
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
7330---+-++--+------+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7330pig faeces, swine manurenear PeoriaUSAUSANorth America
58893Swine manure,storage pitIllinois,near PeoriaUSAUSANorth America1998
67770Swine-manure storage pits

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_411.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15892;96_278;97_307;98_341;99_411&stattab=map
  • Last taxonomy: Bacteroides coprosuis subclade
  • 16S sequence: AF319778
  • Sequence Identity:
  • Total samples: 11064
  • soil counts: 733
  • aquatic counts: 1370
  • animal counts: 8819
  • plant counts: 142

Safety information

risk assessment

  • @ref: 7330
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31598Bacteroides coprosuis strain PC139 16S ribosomal RNA gene, partial sequenceAF3197781523nuccore679937
7330Bacteroides coprosuis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13475AB5106991490ena151276

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides coprosuis DSM 18011679937.3wgspatric679937
66792Bacteroides coprosuis PC 139, DSM 180112503982039draftimg679937
67770Bacteroides coprosuis DSM 18011GCA_000212915chromosomencbi679937

GC content

@refGC-contentmethod
733036.4
733035.0sequence analysis
6777036.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.607yes
flagellatedno97.005no
gram-positiveno96.843no
anaerobicyes96.167no
aerobicno96.866yes
halophileno73.907no
spore-formingno95.345yes
thermophileno97.354yes
glucose-utilyes89.289yes
glucose-fermentyes65.918no

External links

@ref: 7330

culture collection no.: DSM 18011, CCUG 50528, JCM 13475, NRRL B-41113

straininfo link

  • @ref: 71258
  • straininfo: 281441

literature

  • topic: Phylogeny
  • Pubmed-ID: 16280519
  • title: Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits.
  • authors: Whitehead TR, Cotta MA, Collins MD, Falsen E, Lawson PA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63869-0
  • year: 2005
  • mesh: Animals, Bacteroides/classification/genetics/*isolation & purification, DNA, Ribosomal/genetics, Manure/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Swine/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7330Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18011)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18011
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
31598Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2788628776041
58893Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50528)https://www.ccug.se/strain?id=50528
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
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
71258Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281441.1StrainInfo: A central database for resolving microbial strain identifiers