Strain identifier

BacDive ID: 8512

Type strain: Yes

Species: Mycobacterium kubicae

Strain Designation: 941078

Strain history: CIP <- 2000, W.R. Butler, CDC, Atlanta, USA: strain 941078

NCBI tax ID(s): 120959 (species)

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General

@ref: 11939

BacDive-ID: 8512

DSM-Number: 44627

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, rod-shaped

description: Mycobacterium kubicae 941078 is a mesophilic, rod-shaped bacterium that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 120959
  • Matching level: species

strain history

@refhistory
11939<- CIP <- W. R. Butler, CDC
362562000, W.R. Butler, CDC, Atlanta, USA: strain 941078
67770CIP 106428 <-- W. R. Butler CDC 941078.
120508CIP <- 2000, W.R. Butler, CDC, Atlanta, USA: strain 941078

doi: 10.13145/bacdive8512.20250331.9.3

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 kubicae
  • full scientific name: Mycobacterium kubicae Floyd et al. 2000

@ref: 11939

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium kubicae

full scientific name: Mycobacterium kubicae Floyd et al. 2000 emend. Nouioui et al. 2018

strain designation: 941078

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
120508rod-shapedno
125438positive90.814
125439positive92

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11939MIDDLEBROOK 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
36256MEDIUM 55 - for Mycobacteriumyes
120508CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55
120508CIP Medium 96yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=96

culture temp

@refgrowthtypetemperature
11939positivegrowth37
36256positivegrowth37
67770positivegrowth37
120508positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
120508606565hippurate-hydrolysis
12050817632nitrate-reduction
12050816301nitrite-reduction

metabolite production

  • @ref: 120508
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
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
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
120508oxidase-
120508beta-galactosidase-3.2.1.23
120508catalase+1.11.1.6
120508gamma-glutamyltransferase-2.3.2.2
120508urease-3.5.1.5
68382beta-glucuronidase-3.2.1.31

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120508--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11939human sputumSouth CarolinaUSAUSANorth America
60684Human sputum
67770Human sputum
120508Sputum

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119392Risk group (German classification)
1205081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene, partial sequenceAF547941542nuccore120959
20218Mycobacterium kubicae 16S ribosomal RNA gene and internal transcribed spacer, partial sequenceDQ275612266nuccore120959
11939Mycobacterium kubicae 16S ribosomal RNA gene, partial sequenceAF1339021321nuccore120959
11939Mycobacterium kubicae strain CIP 106428 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM0222001792nuccore120959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium kubicae JCM 13573GCA_015689175completencbi120959
66792Mycobacterium kubicae JCM 13573GCA_010723135contigncbi120959
66792Mycobacterium kubicae strain CIP 106428120959.3wgspatric120959
66792Mycobacterium kubicae strain JCM 13573120959.24completepatric120959
66792Mycobacterium kubicae strain JCM 13573120959.18wgspatric120959
67770Mycobacterium kubicae CIP 106428GCA_002101745contigncbi120959
66792Mycobacterium kubicae DSM 44627GCA_025821825contigncbi120959

GC content

  • @ref: 67770
  • GC-content: 66
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.6
125439BacteriaNetgram_stainReaction to gram-stainingpositive92
125439BacteriaNetmotilityAbility to perform movementno77.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesno52.8
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.814no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.988no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.835no
125438spore-formingspore-formingAbility to form endo- or exosporesno59.662no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5yes
125438motile2+flagellatedAbility to perform flagellated movementno88no

External links

@ref: 11939

culture collection no.: DSM 44627, ATCC 700732, CDC 941078, CIP 106428, CCUG 55639, JCM 13573

straininfo link

  • @ref: 77902
  • straininfo: 44109

literature

  • topic: Phylogeny
  • Pubmed-ID: 11034491
  • title: Mycobacterium kubicae sp. nov., a slowly growing, scotochromogenic Mycobacterium.
  • authors: Floyd MM, Gross WM, Bonato DA, Silcox VA, Smithwick RW, Metchock B, Crawford JT, Butler WR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-5-1811
  • year: 2000
  • mesh: Base Sequence, Chromatography, High Pressure Liquid, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Molecular Sequence Data, Mycobacterium/chemistry/*classification/*growth & development/physiology, Mycolic Acids/analysis, Phylogeny, Pigments, Biological/*analysis, RNA, Ribosomal, 16S/genetics, Sequence Alignment, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11939Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44627)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44627
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
36256Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18558
60684Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55639)https://www.ccug.se/strain?id=55639
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
77902Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44109.1StrainInfo: A central database for resolving microbial strain identifiers
120508Curators of the CIPCollection of Institut Pasteur (CIP 106428)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106428
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1