Strain identifier

BacDive ID: 133523

Type strain: Yes

Species: Mycobacterium timonense

Strain Designation: 5351974

Strain history: CIP <- 2008, M. Drancourt, Timone Hosp., Marseille, France: strain 5351974

NCBI tax ID(s): 701043 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 29309

BacDive-ID: 133523

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive

description: Mycobacterium timonense 5351974 is a mesophilic, Gram-positive bacterium that was isolated from Human sputum.

NCBI tax id

  • NCBI tax id: 701043
  • Matching level: species

strain history

@refhistory
417492008, M. Drancourt, La Timone Hosp., Marseille, France: strain 5351974
67770CIP 109830 <-- M. Drancourt, La Timone Hosp., France; 5351974.
123548CIP <- 2008, M. Drancourt, Timone Hosp., Marseille, France: strain 5351974

doi: 10.13145/bacdive133523.20230509.8.1

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 timonense
  • full scientific name: Mycobacterium timonense Ben Salah et al. 2009

@ref: 29309

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Mycobacteriales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium timonense

strain designation: 5351974

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
29309positive0.9 µm0.45 µm
69480no93.539
69480positive100
123548negativenorod-shaped

pigmentation

  • @ref: 29309
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41749MEDIUM 93 - for Mycobacterium avium subsp. sylvaticumyesDistilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)
123548CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55
123548CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperaturerange
41749positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.962

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2930916947citrate+carbon source
2930933942ribose+carbon source
293094853esculin+hydrolysis
12354817632nitrate-reduction
12354816301nitrite-reduction

metabolite production

  • @ref: 123548
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29309acid phosphatase+3.1.3.2
29309alkaline phosphatase+3.1.3.1
123548oxidase-
123548catalase+1.11.1.6
123548urease-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
123548-+-+-+-++-++---+--+-

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
60920Human sputum2000MarseilleFranceFRAEurope
67770Sputum
123548Human, SplitMarseilleFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_402&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: JX976611
  • Sequence Identity:
  • Total samples: 24078
  • soil counts: 12779
  • aquatic counts: 4789
  • animal counts: 3677
  • plant counts: 2833

Safety information

risk assessment

  • @ref: 123548
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29309Mycobacterium timonense strain 3256799 16S ribosomal RNA gene, partial sequenceEF5910541440nuccore701043
67770Mycobacterium timonense strain CIP 109830 16S ribosomal RNA gene, partial sequenceJX9766111481ena701043

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium timonense CCUG 56329GCA_002086775contigncbi701043
66792Mycobacterium timonense JCM 30726GCA_010723675contigncbi701043
66792Mycobacterium timonense strain CCUG 56329701043.3wgspatric701043
66792Mycobacterium timonense strain JCM 30726701043.9wgspatric701043
66792Mycobacterium timonense CCUG 56329GCA_025821985contigncbi701043

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes89.248yes
anaerobicno99.504no
halophileno94.45no
spore-formingno84.325no
glucose-utilyes67.937no
flagellatedno98.987no
thermophileno98.075yes
motileno95.921no
aerobicyes90.805no
glucose-fermentno92.979no

External links

@ref: 29309

culture collection no.: CCUG 56329, CIP 109830, CSUR P32, JCM 30726, JCM 17325

straininfo link

  • @ref: 91485
  • straininfo: 364725

literature

  • topic: Phylogeny
  • Pubmed-ID: 19628609
  • title: Mycobacterium marseillense sp. nov., Mycobacterium timonense sp. nov. and Mycobacterium bouchedurhonense sp. nov., members of the Mycobacterium avium complex.
  • authors: Ben Salah I, Cayrou C, Raoult D, Drancourt M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010637-0
  • year: 2009
  • mesh: Bacterial Proteins/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*classification/enzymology/genetics/*isolation & purification, Mycobacterium avium-intracellulare Infection/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Respiratory System/microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
29309Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172572228776041
41749Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7617
60920Curators of the CCUGhttps://www.ccug.se/strain?id=56329Culture Collection University of Gothenburg (CCUG) (CCUG 56329)
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/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
91485Reimer, 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-ID364725.1
123548Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109830Collection of Institut Pasteur (CIP 109830)