Strain identifier

BacDive ID: 8549

Type strain: Yes

Species: Mycobacterium aubagnense

Strain Designation: U8

Strain history: CIP <- 2004, M. Drancourt, Timone Hosp., Marseille, France: strain U8

NCBI tax ID(s): 319707 (species)

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General

@ref: 15461

BacDive-ID: 8549

DSM-Number: 45150

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

description: Mycobacterium aubagnense U8 is an aerobe, mesophilic bacterium that was isolated from bronchial aspiration.

NCBI tax id

  • NCBI tax id: 319707
  • Matching level: species

strain history

@refhistory
15461<- CIP; CIP 108543 <- M. Drancourt,Hosp. La Timone, Marseille,France; U8
363462004, M. Drancourt, Hosp. La Timone, Marseille, France: strain U8
67770CCUG 50186 <-- M. Drancourt U8.
116549CIP <- 2004, M. Drancourt, Timone Hosp., Marseille, France: strain U8

doi: 10.13145/bacdive8549.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium aubagnense
  • full scientific name: Mycobacterium aubagnense Adékambi et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium aubagnense

@ref: 15461

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium aubagnense

full scientific name: Mycobacterium aubagnense Adékambi et al. 2006

strain designation: U8

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.5
69480100positive
116549norod-shaped

colony morphology

  • @ref: 58776
  • incubation period: 2 days

multimedia

  • @ref: 15461
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45150.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15461MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
36346MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116549CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15461positivegrowth28mesophilic
36346positivegrowth30mesophilic
58776positivegrowth30mesophilic
67770positivegrowth28mesophilic
116549positivegrowth10-37
116549nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58776aerobe
116549obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.927

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
116549606565hippurate+hydrolysis
11654917632nitrate-reduction
11654916301nitrite-reduction
11654917632nitrate-respiration

antibiotic resistance

  • @ref: 116549
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116549
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116549oxidase-
116549beta-galactosidase-3.2.1.23
116549gelatinase-
116549amylase+
116549DNase-
116549caseinase-3.4.21.50
116549catalase+1.11.1.6
116549tween esterase+
116549gamma-glutamyltransferase-2.3.2.2
116549lecithinase-
116549lipase-
116549protease-
116549urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116549-+++-++++-++---++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116549++-+-++-+++----++----++-----++--++++-----+--++--++--++++++--+---+-----++++++----+++++--++++-+++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15461bronchial aspirationMarseilleFranceFRAEurope
58776Human bronchial aspirate/lavageAubagneFranceFRAEurope
67770Bronchial aspirate
116549Bronchial aspirationMarseilleFranceFRAEurope2001

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Aspirate
#Host Body-Site#Oral cavity and airways

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
154612Risk group (German classification)
1165491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium aubagnense strain CCUG 50186 16S ribosomal RNA gene, partial sequenceDQ987739528ena319707
15461Mycolicibacterium aubagnense strain CIP 108543 16S ribosomal RNA gene, partial sequenceAY8596831482ena319707

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium aubagnense JCM 15296GCA_010730955completencbi319707
66792Mycolicibacterium aubagnense strain DSM 45150319707.12wgspatric319707
66792Mycolicibacterium aubagnense strain JCM 15296319707.13wgspatric319707
67770Mycolicibacterium aubagnense DSM 45150GCA_005670695scaffoldncbi319707

GC content

  • @ref: 67770
  • GC-content: 64-66
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno95.282no
flagellatedno98.674no
gram-positiveyes89.316no
anaerobicno99.276yes
aerobicyes89.182yes
halophileno95.526no
spore-formingno89.678no
glucose-utilyes82.906no
thermophileno99.664yes
glucose-fermentno89.928no

External links

@ref: 15461

culture collection no.: JCM 15296, DSM 45150, CCUG 50186, CIP 108543

straininfo link

  • @ref: 77933
  • straininfo: 289774

literature

  • topic: Phylogeny
  • Pubmed-ID: 16403878
  • title: rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov.
  • authors: Adekambi T, Berger P, Raoult D, Drancourt M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63969-0
  • year: 2006
  • mesh: Anti-Bacterial Agents/pharmacology, Bacterial Proteins/*genetics, Chaperonin 60, Chaperonins/genetics, DNA-Directed RNA Polymerases/*genetics, *Genes, Bacterial, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Mycobacterium/chemistry/*classification/drug effects/physiology, Mycobacterium Infections/diagnosis/*microbiology, Species Specificity, Superoxide Dismutase/genetics
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15461Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45150)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45150
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
36346Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6177
58776Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50186)https://www.ccug.se/strain?id=50186
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/
68382Automatically annotated from API zym
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
77933Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289774.1StrainInfo: A central database for resolving microbial strain identifiers
116549Curators of the CIPCollection of Institut Pasteur (CIP 108543)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108543