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, mesophilic, Gram-positive, rod-shaped

description: Mycobacterium crocinum czh-42 is an aerobe, mesophilic, Gram-positive 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/bacdive8574.20230509.8.1

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 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 shapemotilityconfidence
32638positiverod-shapedno
69480no95.368
69480positive99.999
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

@refgrowthtypetemperaturerange
16806positivegrowth37mesophilic
32638positivegrowth28-37mesophilic
32638positiveoptimum32.5mesophilic
37495positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32638aerobe
118791obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

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: ena
  • 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

traitpredictionconfidencetraining_data
spore-formingno75no
flagellatedno98.278yes
flagellatedno98.278yes
flagellatedno98.278yes
gram-positiveyes87.653no
gram-positiveyes87.653no
gram-positiveyes87.653no
anaerobicno99.154yes
anaerobicno99.154yes
anaerobicno99.154yes
aerobicyes90.033yes
aerobicyes90.033yes
aerobicyes90.033yes
halophileno94.792no
halophileno94.792no
halophileno94.792no
spore-formingno83.097no
spore-formingno83.097no
spore-formingno83.097no
motileno92.818no
motileno92.818no
motileno92.818no
glucose-fermentno88.557no
glucose-fermentno88.557no
glucose-fermentno88.557no
thermophileno99.661yes
thermophileno99.661yes
thermophileno99.661yes
glucose-utilyes83.453yes
glucose-utilyes83.453yes
glucose-utilyes83.453yes

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)
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