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)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.2 (current version):
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.2 (current version)

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/bacdive8577.20241212.9.2

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
122323rod-shapedno
69480positive90.175

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

@refgrowthtypetemperature
16674positivegrowth28
32638positivegrowth28-45
32638positiveoptimum37
36355positivegrowth30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32638aerobe
122323obligate aerobe
69480aerobe90.123

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
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
12232335581indoleno
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32638alpha-galactosidase+3.2.1.22
32638catalase+1.11.1.6
32638urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
122323oxidase+
122323catalase+1.11.1.6
122323urease+3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382alkaline phosphatase-3.1.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122323--++-+-++-++---++---
16674--+/-+-+-+/-------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16674----+----++/-+--+-+/-+/---

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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno77no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.175no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.573no
69480spore-formingspore-formingAbility to form endo- or exosporesno55.957no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.123yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.5no
69480flagellatedmotile2+Ability to perform flagellated movementno87.5yes

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/
68369Automatically annotated from API 20NE
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
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