Strain identifier

BacDive ID: 159351

Type strain: Yes

Species: Scrofimicrobium canadense

Strain Designation: WB03_NA08

Strain history: B. Abt; DSMZ, Germany; DSM 105338 (=WB03_NA08) <-- E. Allen-Vercoe; Univ. of Guelph, Canada.

NCBI tax ID(s): 2652290 (species)

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General

@ref: 66174

BacDive-ID: 159351

DSM-Number: 105338

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

description: Scrofimicrobium canadense WB03_NA08 is an anaerobe, mesophilic bacterium that was isolated from wild boar.

NCBI tax id

  • NCBI tax id: 2652290
  • Matching level: species

strain history

@refhistory
66174<- E. Allen-Vercoe, Dept. Molecular and Cellular Biology, College of Biological Science, University of Guelph;
67770B. Abt; DSMZ, Germany; DSM 105338 (=WB03_NA08) <-- E. Allen-Vercoe; Univ. of Guelph, Canada.

doi: 10.13145/bacdive159351.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Scrofimicrobium
  • species: Scrofimicrobium canadense
  • full scientific name: Scrofimicrobium canadense Wylensek et al. 2021

@ref: 66174

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Scrofimicrobium

species: Scrofimicrobium canadense

full scientific name: Scrofimicrobium canadense

strain designation: WB03_NA08

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell lengthcell shape
69480no90.133
69480100positive
69645positive1-2 µmrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66174WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
69645Nutrient agar (NA)yes
69645Wilkins-Chalgren Anaerobe brothyessupplemented with L-cysteine and DTT (0.05% and 0.02% (w/v), respectively)
69645modified YCFAyes

culture temp

@refgrowthtypetemperaturerange
66174positivegrowth37mesophilic
67770positivegrowth37mesophilic
69645positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe94.818
69645facultative anaerobe

spore formation

@refspore formationconfidence
69480no99.999
69481no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose+builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol+builds acid from
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6964517234glucose+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6964530089acetateyes
6964515740formateyes
6964524996lactateyes
6964530031succinateyes

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
66174--+--+/-+-++-+/-++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
66174wild boarStratford, OntarioCanadaCANNorth America43.3667-80.9833
67770Feces of a farmed wild boar in MoservilleOntarioCanadaCANNorth America
69645Wild boar fecesMoserville, OntarioCanadaCANNorth AmericaNutrient Agar3-4 days37aerobic

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Suidae (Pig,Swine)

Sequence information

16S sequences

  • @ref: 66174
  • description: Actinomycetaceae bacterium DSM 105338 16S ribosomal RNA gene, partial sequence
  • accession: MN537492
  • length: 1444
  • database: ena
  • NCBI tax ID: 2652290

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Scrofimicrobium canadense WB03_NA08GCA_009696615contigncbi2652290
66792Actinomycetaceae bacterium WB03_NA082606625.3wgspatric2652290
69645Whole genome shotgunVULO00000000ncbi2652290

GC content

  • @ref: 67770
  • GC-content: 53.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.795no
gram-positiveyes93.625no
anaerobicno83.221no
aerobicno82.369no
halophileno87.89no
spore-formingno93.393no
glucose-utilyes84.129no
flagellatedno98.304no
thermophileno97.595yes
glucose-fermentyes78.936no

External links

@ref: 66174

culture collection no.: DSM 105338, JCM 34392

straininfo link

  • @ref: 111849
  • straininfo: 397303

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
66174Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105338Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105338)
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/
68367Automatically annotated from API 20A
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
69645David Wylensek, Thomas C. A. Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R. Lesker, Sara B. Hernández, Viktoria Heine, Eva M. Buhl, Paul M. D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J. Taverne-Thiele, Marcel Giesbers, Jerry M. Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M. Ridlon, Tobias A. M. Gulder, Jörg Overmann, Thomas ClavelA collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity10.1038/s41467-020-19929-w
111849Reimer, 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-ID397303.1