Strain identifier

BacDive ID: 8574

Type strain: Yes

Species: Mycobacterium crocinum

Strain Designation: czh-42

Strain history: CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain czh-42

NCBI tax ID(s): 1305862 (strain), 388459 (species)

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General

@ref: 16806

BacDive-ID: 8574

DSM-Number: 45433

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped

description: Mycobacterium crocinum czh-42 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1305862strain
388459species

strain history

@refhistory
16806<- CIP; CIP 109269 <- Q. X. Li, Honolulu, Hawai, USA; czh-42
67770CIP 109269 <-- Q. X. Li czh-42.
118791CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain czh-42

doi: 10.13145/bacdive8574.20240916.9.1

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 crocinum
  • full scientific name: Mycobacterium crocinum Hennessee et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium crocinum

@ref: 16806

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium crocinum

full scientific name: Mycobacterium crocinum Hennessee et al. 2009

strain designation: czh-42

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32638positiverod-shapedno
118791no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16806MIDDLEBROOK 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
37495MEDIUM 55 - for Mycobacteriumyes
118791CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55
118791CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93
118791CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
16806positivegrowth37
32638positivegrowth28-37
32638positiveoptimum32.5
37495positivegrowth30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32638aerobe
118791obligate aerobe

halophily

  • @ref: 32638
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <5.0 %

observation

  • @ref: 32638
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263830089acetate+carbon source
3263822599arabinose+carbon source
3263818403L-arabitol+carbon source
3263823652dextrin+carbon source
3263828757fructose+carbon source
3263824265gluconate+carbon source
3263817234glucose+carbon source
3263824996lactate+carbon source
3263829864mannitol+carbon source
3263837684mannose+carbon source
3263817272propionate+carbon source
3263815361pyruvate+carbon source
3263833942ribose+carbon source
3263830031succinate+carbon source
3263827082trehalose+carbon source
3263853423tween 40+carbon source
3263853426tween 80+carbon source
3263818222xylose+carbon source
3263817632nitrate+reduction
11879117632nitrate+reduction
11879116301nitrite-reduction

metabolite production

  • @ref: 118791
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32638alkaline phosphatase+3.1.3.1
32638catalase+1.11.1.6
118791oxidase-
118791catalase-1.11.1.6
118791urease-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
118791-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16806soilHawai, OahuUSAUSANorth America
67770Non-contaminated soil from WahiawaHIUSAUSANorth America
118791Environment, SoilOahu, HawaiiUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
168061Risk group (German classification)
1187911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16806
  • description: Mycobacterium crocinum strain czh-42 16S ribosomal RNA gene, partial sequence
  • accession: DQ534008
  • length: 1398
  • database: nuccore
  • NCBI tax ID: 388459

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium crocinum JCM 16369GCA_001314145contigncbi1305862
66792Mycolicibacterium crocinum JCM 163691305862.4wgspatric1305862
66792Mycolicibacterium crocinum JCM 163692734481973draftimg1305862
66792Mycolicibacterium crocinum JCM 16369GCA_022370635completencbi388459
66792Mycolicibacterium crocinum DSM 45433GCA_025822435scaffoldncbi388459

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno75no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.428no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.067no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.907yes
69480spore-formingspore-formingAbility to form endo- or exosporesno55.939no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementno86.5yes

External links

@ref: 16806

culture collection no.: DSM 45433, ATCC BAA-1373, CIP 109269, JCM 16369

straininfo link

  • @ref: 77958
  • straininfo: 360726

literature

  • topic: Phylogeny
  • Pubmed-ID: 19196782
  • title: Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov.
  • authors: Hennessee CT, Seo JS, Alvarez AM, Li QX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65827-0
  • year: 2009
  • mesh: Genes, Bacterial/genetics, Hawaii, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/metabolism, Phenotype, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16806Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45433)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45433
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
32638Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2884928776041
37495Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6991
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
77958Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360726.1StrainInfo: A central database for resolving microbial strain identifiers
118791Curators of the CIPCollection of Institut Pasteur (CIP 109269)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109269