Strain identifier

BacDive ID: 8573

Type strain: Yes

Species: Mycobacterium aromaticivorans

Strain Designation: JS19b1

Strain history: CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS19b1, "Mycobacterium aromativorans"

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16676

BacDive-ID: 8573

DSM-Number: 45407

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

description: Mycobacterium aromaticivorans JS19b1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
318425species
1440774strain

strain history

@refhistory
16676<- CIP <- Q. X. Li, Honolulu, Hawai, USA; JS19b1
67770CIP 109274 <-- Q. X. Li JS19b1.
116500CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS19b1, "Mycobacterium aromativorans"

doi: 10.13145/bacdive8573.20230509.8.1

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

    • @ref: 20215
    • synonym: Mycolicibacterium aromaticivorans

@ref: 16676

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium aromaticivorans

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

strain designation: JS19b1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32638positiverod-shapedno
116500rod-shapedno

multimedia

  • @ref: 16676
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45407.jpg
  • caption: Medium 250 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16676MIDDLEBROOK 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
116500CIP Medium 267yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=267

culture temp

@refgrowthtypetemperaturerange
16676positivegrowth28mesophilic
32638positivegrowth28-37mesophilic
32638positiveoptimum32.5mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32638aerobe
116500obligate aerobe

halophily

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

observation

  • @ref: 32638
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3263828757fructose+carbon source
3263817234glucose+carbon source
3263829864mannitol+carbon source
3263837684mannose+carbon source
3263830031succinate+carbon source
3263827082trehalose+carbon source
11650017632nitrate-reduction
11650016301nitrite-reduction

metabolite production

  • @ref: 116500
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32638alkaline phosphatase+3.1.3.1
32638catalase+1.11.1.6
116500oxidase-
116500catalase+1.11.1.6
116500urease+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
116500-+++-+-+--++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16676soilHawai, HiloUSAUSANorth America
67770Polycyclic aromatic hydrocarbon-contaminated soil of a former oil-gasification company siteHilo, HIUSAUSANorth America
116500Environment, SoilHilo, HawaiiUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_2774&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: AY943386
  • Sequence Identity:
  • Total samples: 372
  • soil counts: 136
  • aquatic counts: 31
  • animal counts: 53
  • plant counts: 152

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166761Risk group (German classification)
1165001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16676
  • description: Mycobacterium aromaticivorans strain JS19b1 16S ribosomal RNA gene, partial sequence
  • accession: AY943386
  • length: 1331
  • database: ena
  • NCBI tax ID: 318425

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium aromaticivorans JS19b1 = JCM 16368GCA_001314125contigncbi1440774
66792Mycobacterium aromaticivorans JS19b11440774.4wgspatric1440774
66792Mycobacterium aromaticivorans JS19b1 = JCM 163681440774.6wgspatric1440774
67770Mycolicibacterium aromaticivorans JS19b1 = JCM 16368GCA_000559085contigncbi1440774

GC content

  • @ref: 67770
  • GC-content: 66.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.291yes
gram-positiveyes90.555yes
anaerobicno99.487no
halophileno95.447no
spore-formingno87.487no
glucose-utilyes83.741no
thermophileno99.621no
aerobicyes92.119yes
flagellatedno98.617yes
glucose-fermentno91.37no

External links

@ref: 16676

culture collection no.: DSM 45407, ATCC BAA 1378, CIP 109274, JCM 16368

straininfo link

  • @ref: 77957
  • straininfo: 298325

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
Genetics25019926Genome sequence of Mycobacterium aromaticivorans JS19b1(T), a novel isolate from Hawaiian soil.Kwak Y, Park GS, Lee SE, Li QX, Shin JHJ Biotechnol10.1016/j.jbiotec.2014.06.0342014DNA, Bacterial/analysis, Genome, Bacterial/*genetics, Hawaii, Mycobacterium/*genetics/metabolism, Polycyclic Aromatic Hydrocarbons/metabolism, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16676Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45407)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45407
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
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
77957Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID298325.1StrainInfo: A central database for resolving microbial strain identifiers
116500Curators of the CIPCollection of Institut Pasteur (CIP 109274)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109274