Strain identifier

BacDive ID: 8423

Type strain: Yes

Species: Mycobacterium cookii

Strain Designation: NZ2

Strain history: CIP <- 2000, W.R. Butler, CDC, Atlanta, USA <- ATCC <- J. Kazda: strain NZ2

NCBI tax ID(s): 1775 (species)

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General

@ref: 11271

BacDive-ID: 8423

DSM-Number: 43922

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

description: Mycobacterium cookii NZ2 is a mesophilic bacterium that was isolated from Sphagnum moss.

NCBI tax id

  • NCBI tax id: 1775
  • Matching level: species

strain history

@refhistory
11271<- A. F. Yassin <- ATCC <- J. Kazda, NZ2
67770CIP 105396 <-- W. R. Butler <-- ATCC 49103 <-- J. Kazda NZ2.
118740CIP <- 2000, W.R. Butler, CDC, Atlanta, USA <- ATCC <- J. Kazda: strain NZ2

doi: 10.13145/bacdive8423.20230509.8.1

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 cookii
  • full scientific name: Mycobacterium cookii Kazda et al. 1990

@ref: 11271

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium cookii

full scientific name: Mycobacterium cookii Kazda et al. 1990

strain designation: NZ2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.797
69480100positive
118740norod-shaped

multimedia

  • @ref: 11271
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43922.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11271MIDDLEBROOK 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
36374MEDIUM 55 - for Mycobacteriumyes
118740CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11271positivegrowth28mesophilic
36374positivegrowth30mesophilic
67770positivegrowth28mesophilic
118740positivegrowth22-30
118740nogrowth10psychrophilic
118740nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.94

metabolite utilization

  • @ref: 118740
  • Chebi-ID: 606565
  • metabolite: hippurate
  • utilization activity: -
  • kind of utilization tested: hydrolysis

metabolite production

  • @ref: 118740
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118740oxidase-
118740beta-galactosidase+3.2.1.23
118740gelatinase-
118740catalase+1.11.1.6
118740gamma-glutamyltransferase-2.3.2.2
118740urease-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
118740--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
11271Sphagnum mossSphagnumNew ZealandNZLAustralia and Oceania
54689Sphagnum mossNew ZealandNZLAustralia and Oceania
67770Sphagnum (Sphagnum falcatulum)Sphagnum falcatulumNew ZealandNZLAustralia and Oceania
118740Sphagnum mossNew ZealandNZLAustralia and Oceania

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Peat moss

taxonmaps

  • @ref: 69479
  • File name: preview.99_67899.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_196;97_213;98_34237;99_67899&stattab=map
  • Last taxonomy: Mycobacterium cookii
  • 16S sequence: AF480598
  • Sequence Identity:
  • Total samples: 1900
  • soil counts: 1596
  • aquatic counts: 84
  • animal counts: 180
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112711Risk group (German classification)
1187401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium cookii 16S ribosomal RNA gene, partial sequenceAF4805981471ena1775
20218Mycobacterium cookii partial 16S rRNAX538961459ena1775
20218Mycobacterium cookii strain CIP 105396 16S ribosomal RNA gene, partial sequenceAF547915556ena1775

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium cookii JCM 12404GCA_010727945completencbi1775
66792Mycobacterium cookii strain JCM 124041775.8completepatric1775
66792Mycobacterium cookii DSM 43922GCA_025822925scaffoldncbi1775

GC content

  • @ref: 67770
  • GC-content: 63.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.89no
flagellatedno98.555no
gram-positiveyes90.671no
anaerobicno98.814no
aerobicyes86.741no
halophileno95.989no
spore-formingno83.742no
glucose-utilyes58.617no
thermophileno98.419no
glucose-fermentno92.724no

External links

@ref: 11271

culture collection no.: CCUG 39182, DSM 43922, ATCC 49103, JCM 12404, CIP 105396

straininfo link

  • @ref: 77822
  • straininfo: 42291

literature

  • topic: Phylogeny
  • Pubmed-ID: 1697763
  • title: Mycobacterium cookii sp. nov.
  • authors: Kazda J, Stackebrandt E, Smida J, Minnikin DE, Daffe M, Parlett JH, Pitulle C
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-40-3-217
  • year: 1990
  • mesh: Base Sequence, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11271Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43922)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43922
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
36374Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17410
54689Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39182)https://www.ccug.se/strain?id=39182
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
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
77822Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42291.1StrainInfo: A central database for resolving microbial strain identifiers
118740Curators of the CIPCollection of Institut Pasteur (CIP 105396)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105396