Strain identifier

BacDive ID: 8577

Type strain: Yes

Species: Mycobacterium rutilum

Strain Designation: czh-117

Strain history: CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain czh-117

NCBI tax ID(s): 1305864 (strain), 370526 (species)

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General

@ref: 16674

BacDive-ID: 8577

DSM-Number: 45405

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

description: Mycobacterium rutilum czh-117 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1305864strain
370526species

strain history

@refhistory
16674<- CIP <- Q. X. Li, Honolulu, Hawai, USA; czh-117
67770CIP 109271 <-- Q. X. Li czh-117.
122323CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain czh-117

doi: 10.13145/bacdive8577.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium rutilum

@ref: 16674

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium rutilum

full scientific name: Mycobacterium rutilum Hennessee et al. 2009 emend. Nouioui et al. 2018

strain designation: czh-117

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32638positiverod-shapedno
69480no92.007
69480positive100
122323rod-shapedno

multimedia

  • @ref: 16674
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45405.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16674MIDDLEBROOK 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
36355MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122323CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16674positivegrowth28mesophilic
32638positivegrowth28-45
32638positiveoptimum37mesophilic
36355positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32638aerobe
122323obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.399

halophily

@refsaltgrowthtested relationconcentration
32638NaClpositivegrowth2.5-5.0 %
32638NaClpositiveoptimum3.75 %

observation

  • @ref: 32638
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263817234glucose+carbon source
3263829864mannitol+carbon source
3263830911sorbitol+carbon source
3263817151xylitol+carbon source
3263818222xylose+carbon source
12232317632nitrate-reduction
12232316301nitrite-reduction

metabolite production

  • @ref: 122323
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32638alpha-galactosidase+3.2.1.22
32638catalase+1.11.1.6
32638urease+3.5.1.5
122323oxidase+
122323catalase+1.11.1.6
122323urease+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
122323--++-+-++-++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16674soilOahu, HawaiUSAUSANorth America
67770Soil from an urban park in HonoluluHIUSAUSANorth America
122323Environment, SoilOahu, HawaiiUnited States of AmericaUSANorth America2004

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166741Risk group (German classification)
1223231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16674
  • description: Mycobacterium rutilum strain czh-117 16S ribosomal RNA gene, partial sequence
  • accession: DQ370011
  • length: 1418
  • database: ena
  • NCBI tax ID: 370526

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium rutilum DSM 45405GCA_900108565chromosomencbi370526
66792Mycolicibacterium rutilum JCM 16371GCA_001314185contigncbi1305864
66792Mycobacterium rutilum strain DSM 45405370526.3completepatric370526
66792Mycolicibacterium rutilum JCM 163711305864.5wgspatric1305864
66792Mycolicibacterium rutilum JCM 163712734481975draftimg1305864
66792Mycolicibacterium rutilum DSM 454052636415969draftimg370526

GC content

  • @ref: 67770
  • GC-content: 68.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno77no
gram-positiveyes89.41yes
anaerobicno99.394yes
halophileno87.728no
spore-formingno78.194no
glucose-utilyes86.912yes
aerobicyes88.792yes
motileno90.29no
flagellatedno97.804yes
thermophileno99.65yes
glucose-fermentno90.395no

External links

@ref: 16674

culture collection no.: DSM 45405, ATCC BAA 1375, CIP 109271, JCM 16371, DSM 4505

straininfo link

  • @ref: 77961
  • straininfo: 47851

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
16674Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45405)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45405
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
36355Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6993
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)
77961Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47851.1StrainInfo: A central database for resolving microbial strain identifiers
122323Curators of the CIPCollection of Institut Pasteur (CIP 109271)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109271