Strain identifier

BacDive ID: 24237

Type strain: Yes

Species: Mycobacterium arabiense

Strain history: S.-K. Tang YIM 121001.

NCBI tax ID(s): 1286181 (species)

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General

@ref: 20672

BacDive-ID: 24237

DSM-Number: 45768

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

description: Mycobacterium arabiense DSM 45768 is a mesophilic, Gram-positive, ovoid-shaped bacterium that was isolated from coastal sand.

NCBI tax id

  • NCBI tax id: 1286181
  • Matching level: species

strain history

@refhistory
20672<- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM 121001 <- J. Yi
67770S.-K. Tang YIM 121001.

doi: 10.13145/bacdive24237.20230509.8.1

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 arabiense
  • full scientific name: Mycobacterium arabiense Zhang et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium arabiense

@ref: 20672

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium arabiense

full scientific name: Mycobacterium arabiense Zhang et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31044positiveovoid-shapedno
69480no93.588
69480positive100

pigmentation

  • @ref: 31044
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20672
  • name: MIDDLEBROOK MEDIUM (DSMZ Medium 645)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/645
  • composition: Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water

culture temp

@refgrowthtypetemperaturerange
20672positivegrowth28mesophilic
31044positivegrowth05-37
31044positiveoptimum31mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31044positivegrowth6.0-8.0
31044positiveoptimum7

Physiology and metabolism

spore formation

@refspore formationconfidence
31044no
69481no100
69480no99.582

halophily

@refsaltgrowthtested relationconcentration
31044NaClpositivegrowth0-5 %
31044NaClpositiveoptimum1.5 %

enzymes

@refvalueactivityec
31044catalase+1.11.1.6
31044urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20672coastal sandDubai shoreUnited Arab EmiratesAREAsia
67770Coastal zone sandDubaiUnited Arab EmiratesAREAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_84092.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_2631;98_45656;99_84092&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: KC010491
  • Sequence Identity:
  • Total samples: 984
  • soil counts: 382
  • aquatic counts: 312
  • animal counts: 227
  • plant counts: 63

Safety information

risk assessment

  • @ref: 20672
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20672Mycobacterium arabiense strain YIM 121001 16S ribosomal RNA gene, partial sequenceKC0104911535ena1286181
67770Mycobacterium arabiense strain YIM 121001 16S-23S ribosomal RNA intergenic spacer, complete sequenceKC010493433ena1286181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium arabiense JCM 18538GCA_010731815completencbi1286181
66792Mycolicibacterium arabiense strain JCM 185381286181.8wgspatric1286181
66792Mycolicibacterium arabiense JCM 185382888232652completeimg1286181
66792Mycolicibacterium arabiense DSM 45768GCA_025823225contigncbi1286181

GC content

@refGC-contentmethod
2067262.8high performance liquid chromatography (HPLC)
3104462.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.224no
flagellatedno97.639yes
gram-positiveyes90.623no
anaerobicno99.471no
aerobicyes89.273no
halophileno93.837yes
spore-formingno82.859no
glucose-utilyes87.067no
thermophileno99.661no
glucose-fermentno90.765no

External links

@ref: 20672

culture collection no.: DSM 45768, JCM 18538, YIM 121001

straininfo link

  • @ref: 88180
  • straininfo: 406386

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23728378Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.050567-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Mycobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, United Arab EmiratesGenetics
Phylogeny35633692Mycolicibacterium lacusdiani sp. nov., an Attached Bacterium of Microcystis aeruginosa.Xiao Y, Chen J, Chen M, Deng SJ, Xiong ZQ, Tian BY, Zhang BHFront Microbiol10.3389/fmicb.2022.8612912022

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20672Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45768Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45768)
31044Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172737428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88180Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406386.1