Strain identifier

BacDive ID: 210

Type strain: Yes

Species: Varibaculum cambriense

Strain Designation: R12359

Strain history: CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359

NCBI tax ID(s): 1123488 (strain), 184870 (species)

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General

@ref: 6116

BacDive-ID: 210

DSM-Number: 15806

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

description: Varibaculum cambriense R12359 is an anaerobe, mesophilic bacterium that was isolated from human postauricular abscess, 27 years old male.

NCBI tax id

NCBI tax idMatching level
184870species
1123488strain

strain history

@refhistory
6116<- E. Falsen, CCUG <- M. D. Collins, Univ. of Reading <- V. Hall
117109CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359

doi: 10.13145/bacdive210.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Varibaculum
  • species: Varibaculum cambriense
  • full scientific name: Varibaculum cambriense corrig. Hall et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Varibaculum cambriensis

@ref: 6116

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Varibaculum

species: Varibaculum cambriense

full scientific name: Varibaculum cambriense Hall et al. 2003 emend. Nouioui et al. 2018

strain designation: R12359

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.907
69480100positive
117109norod-shaped

colony morphology

  • @ref: 117109

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15806_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15806_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15806_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15806_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15806_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6116PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
6116COLUMBIA 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
42112MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
117109CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6116positivegrowth37mesophilic
42112positivegrowth37mesophilic
56585positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6116anaerobe
56585anaerobe
56585microaerophile
69480anaerobe97.849

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11710917108D-arabinose-degradation
11710915824D-fructose+degradation
11710917634D-glucose-degradation
11710965327D-xylose-degradation
11710917057cellobiose-degradation
11710917716lactose-degradation
11710917306maltose-degradation
11710917814salicin-degradation
11710917992sucrose-degradation
1171094853esculin-hydrolysis
11710917632nitrate+reduction
11710916301nitrite-reduction
11710935020tributyrin+hydrolysis

metabolite production

  • @ref: 117109
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
117109oxidase-
117109beta-galactosidase-3.2.1.23
117109gelatinase-
117109amylase-
117109DNase-
117109caseinase-3.4.21.50
117109catalase+1.11.1.6
117109tween esterase-
117109lecithinase-
117109lipase-
117109protease-
117109urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117109--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6116human postauricular abscess, 27 years old maleLondonUnited KingdomGBREurope
56585Human postauricular abscess,27-yr-old maleLondonUnited KingdomGBREurope1998
117109HumanCardiffUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body-Site#Other#Abscess
#Host Body-Site#Organ#Ear

taxonmaps

  • @ref: 69479
  • File name: preview.99_5423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_520;96_2630;97_3222;98_4047;99_5423&stattab=map
  • Last taxonomy: Varibaculum cambriense
  • 16S sequence: AM084231
  • Sequence Identity:
  • Total samples: 7892
  • soil counts: 30
  • aquatic counts: 56
  • animal counts: 7804
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61162Risk group (German classification)
1171091Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Varibaculum cambriensis partial 16S rRNA gene, strain CCUG 44998AJ4284021510ena184870
20218Varibaculum cambriense partial 16S rRNA gene, isolate CCUG 44998TAM0842311509ena184870
6116Varibaculum cambriensis 16S rRNA gene, type strain CCUG 44998TAJ4913261510ena184870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Varibaculum cambriense DSM 15806GCA_000420065contigncbi1123488
66792Varibaculum cambriense DSM 158061123488.3wgspatric1123488
66792Varibaculum cambriense DSM 158062524614732draftimg1123488

GC content

  • @ref: 6116
  • GC-content: 51.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.191no
flagellatedno96.825no
gram-positiveyes91.42no
anaerobicyes73.491no
aerobicno98.368no
halophileno82.933no
spore-formingno97.122no
thermophileno95.453yes
glucose-utilyes78.521no
glucose-fermentyes79.261no

External links

@ref: 6116

culture collection no.: DSM 15806, CCUG 44998, CIP 107344

straininfo link

  • @ref: 69893
  • straininfo: 25796

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12574260Characterization of some actinomyces-like isolates from human clinical sources: description of Varibaculum cambriensis gen nov, sp nov.Hall V, Collins MD, Lawson PA, Hutson RA, Falsen E, Inganas E, Duerden BJ Clin Microbiol10.1128/JCM.41.2.640-644.20032003Actinomycetaceae/classification/genetics/*isolation & purification, Humans, Phylogeny, RNA, Ribosomal, 16S/analysis/geneticsPathogenicity
Phylogeny27745752Varibaculum anthropi sp. nov. represented by three genetically different genomovars isolated from clinical material and emended description of the genus Varibaculum.Glaeser SP, Doijad S, Hijazin M, Chakraborty T, Falsen E, Hall V, Kampfer PSyst Appl Microbiol10.1016/j.syapm.2016.09.0022016Actinomycetaceae/*classification/*genetics/isolation & purification, Adolescent, Adult, Base Sequence, DNA, Bacterial/*genetics, Female, Genome, Bacterial/*genetics, Humans, Male, Middle Aged, Multilocus Sequence Typing, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6116Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15806)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15806
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
42112Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4769
56585Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44998)https://www.ccug.se/strain?id=44998
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 life 35: 676-683 201728604660
68382Automatically annotated from API zym
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
69893Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID25796.1StrainInfo: A central database for resolving microbial strain identifiers
117109Curators of the CIPCollection of Institut Pasteur (CIP 107344)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107344