Strain identifier

BacDive ID: 8576

Type strain: Yes

Species: Mycobacterium rufum

Strain Designation: JS14

Strain history: CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans"

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General

@ref: 16675

BacDive-ID: 8576

DSM-Number: 45406

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

description: Mycobacterium rufum JS14 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
318424species
1305629strain

strain history

@refhistory
374962006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans"
16675<- CIP <- Q. X. Li,Honolulu,Hawai,USA ; JS14
67770CIP 109273 <-- Q. X. Li JS14.
122303CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans"

doi: 10.13145/bacdive8576.20230509.8.1

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 rufum
  • full scientific name: Mycobacterium rufum Hennessee et al. 2009
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium rufum

@ref: 16675

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium rufum

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

strain designation: JS14

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32638positiverod-shapedno
69480positive99.999
122303no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16675MIDDLEBROOK 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
37496MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122303CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16675positivegrowth28mesophilic
32638positivegrowth28mesophilic
32638positiveoptimum28mesophilic
37496positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32638aerobe
122303obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.997

observation

  • @ref: 32638
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263828757fructose+carbon source
3263817234glucose+carbon source
3263829864mannitol+carbon source
3263830911sorbitol+carbon source
3263827082trehalose+carbon source
3263817151xylitol+carbon source
3263818222xylose+carbon source
326384853esculin+hydrolysis
3263817632nitrate+reduction
12230317632nitrate+reduction
12230316301nitrite-reduction

metabolite production

  • @ref: 122303
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32638catalase+1.11.1.6
32638urease+3.5.1.5
122303oxidase-
122303catalase+1.11.1.6
122303urease+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
122303-++++++++-++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16675soilHawai, HiloUSAUSANorth America
67770Polycyclic aromatic hydrocarbon-contaminated soil of a former oil-gasification company site in HiloHIUSAUSANorth America
122303Environment, SoilHilo, HawaiiUnited States of AmericaUSANorth America2003

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6383.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_6383&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: AY943385
  • Sequence Identity:
  • Total samples: 4905
  • soil counts: 1619
  • aquatic counts: 1667
  • animal counts: 1470
  • plant counts: 149

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166751Risk group (German classification)
1223031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16675
  • description: Mycobacterium rufum strain JS14 16S ribosomal RNA gene, partial sequence
  • accession: AY943385
  • length: 1329
  • database: ena
  • NCBI tax ID: 318424

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium rufum JCM 16372GCA_001313925contigncbi1305629
66792Mycobacterium rufum JS14318424.3wgspatric318424
66792Mycolicibacterium rufum JCM 163721305629.4wgspatric1305629
66792Mycolicibacterium rufum JCM 163722734481965draftimg1305629
67770Mycolicibacterium rufum JS14GCA_000762985contigncbi318424
66792Mycolicibacterium rufum JCM 16372GCA_022374875completencbi318424
66792Mycolicibacterium rufum DSM 45406GCA_025821255scaffoldncbi318424

GC content

  • @ref: 67770
  • GC-content: 69.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
flagellatedno98.378yes
flagellatedno98.378yes
flagellatedno98.378yes
gram-positiveyes90.96yes
gram-positiveyes90.96yes
gram-positiveyes90.96yes
anaerobicno99.488yes
anaerobicno99.488yes
anaerobicno99.488yes
aerobicyes92.436no
aerobicyes92.436no
aerobicyes92.436no
halophileno93.669no
halophileno93.669no
halophileno93.669no
spore-formingno86.048no
spore-formingno86.048no
spore-formingno86.048no
motileno91.886no
motileno91.886no
motileno91.886no
glucose-fermentno90.923no
glucose-fermentno90.923no
glucose-fermentno90.923no
thermophileno99.326yes
thermophileno99.326yes
thermophileno99.326yes
glucose-utilyes88.332yes
glucose-utilyes88.332yes
glucose-utilyes88.332yes

External links

@ref: 16675

culture collection no.: DSM 45406, ATCC BAA 1377, CIP 109273, JCM 16372

straininfo link

  • @ref: 77960
  • straininfo: 300731

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19196782Polycyclic 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.Hennessee CT, Seo JS, Alvarez AM, Li QXInt J Syst Evol Microbiol10.1099/ijs.0.65827-02009Genes, Bacterial/genetics, Hawaii, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/metabolism, Phenotype, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Genetics27486485Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii.Kwak Y, Li QX, Shin JHStand Genomic Sci10.1186/s40793-016-0167-52016

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16675Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45406)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45406
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
37496Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6996
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
77960Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID300731.1StrainInfo: A central database for resolving microbial strain identifiers
122303Curators of the CIPCollection of Institut Pasteur (CIP 109273)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109273