Strain identifier

BacDive ID: 8548

Type strain: Yes

Species: Mycobacterium phocaicum

Strain Designation: N4

Strain history: CIP <- 2004, M. Drancourt, Timone Hosp., Marseille, France: strain N4

NCBI tax ID(s): 319706 (species)

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General

@ref: 12346

BacDive-ID: 8548

DSM-Number: 45104

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

description: Mycobacterium phocaicum N4 is a microaerophile, mesophilic bacterium that was isolated from human bronchial aspirate.

NCBI tax id

  • NCBI tax id: 319706
  • Matching level: species

strain history

@refhistory
12346<- CCUG <- M. Drancourt, Timone, Marseille
363412004, M. Drancourt, La Timone Hosp., Marseille, France: strain N4
67770CCUG 50185 <-- M. Drancourt N4.
121803CIP <- 2004, M. Drancourt, Timone Hosp., Marseille, France: strain N4

doi: 10.13145/bacdive8548.20230509.8.1

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 phocaicum
  • full scientific name: Mycobacterium phocaicum Adékambi et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium phocaicum

@ref: 12346

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium phocaicum

full scientific name: Mycobacterium phocaicum Adékambi et al. 2006

strain designation: N4

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.583
69480100positive
121803norod-shaped

colony morphology

  • @ref: 58775
  • incubation period: 2 days

multimedia

  • @ref: 12346
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45104.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12346MIDDLEBROOK 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
36341MEDIUM 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)
121803CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperaturerange
12346positivegrowth37mesophilic
36341positivegrowth30mesophilic
58775positivegrowth37mesophilic
67770positivegrowth37mesophilic
121803positivegrowth22-37
121803nogrowth10psychrophilic
121803nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58775microaerophile
121803obligate aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.595

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121803606565hippurate+hydrolysis
12180317632nitrate+reduction
12180316301nitrite-reduction
12180317632nitrate-respiration

metabolite production

  • @ref: 121803
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121803oxidase-
121803beta-galactosidase-3.2.1.23
121803gelatinase-
121803amylase+
121803DNase-
121803caseinase-3.4.21.50
121803catalase+1.11.1.6
121803tween esterase+
121803gamma-glutamyltransferase-2.3.2.2
121803lecithinase-
121803lipase-
121803protease-
121803urease-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
121803-+++++----++-+-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121803-+----------------+--------------+---------------+----------+--+--------+------++---------+-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
12346human bronchial aspirateMarseilleFranceFRAEurope
58775Human bronchial aspirateMarseilleFranceFRAEurope
67770Bronchial aspirate
121803Bronchial aspirationMarseilleFranceFRAEurope1999

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123462Risk group (German classification)
1218031Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium phocaicum strain CCUG 50185 16S ribosomal RNA gene, partial sequenceDQ987741530ena319706
12346Mycolicibacterium phocaicum strain CIP 108542 16S ribosomal RNA gene, partial sequenceAY8596821482ena319706

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium phocaicum JCM 15301GCA_010731115completencbi319706
66792Mycolicibacterium phocaicum strain DSM 45104319706.12wgspatric319706
66792Mycolicibacterium phocaicum strain JCM 15301319706.13completepatric319706
67770Mycolicibacterium phocaicum DSM 45104GCA_005670655contigncbi319706

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno95.061no
flagellatedno98.589no
gram-positiveyes90.146no
anaerobicno99.266no
aerobicyes87.527yes
halophileno94.553no
spore-formingno85.421no
glucose-utilyes85.5no
thermophileno99.47no
glucose-fermentno90.84no

External links

@ref: 12346

culture collection no.: DSM 45104, CCUG 50185, CIP 108542, JCM 15301

straininfo link

  • @ref: 77932
  • straininfo: 289775

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
12346Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45104)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45104
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
36341Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6176
58775Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50185)https://www.ccug.se/strain?id=50185
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
77932Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289775.1StrainInfo: A central database for resolving microbial strain identifiers
121803Curators of the CIPCollection of Institut Pasteur (CIP 108542)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108542