Strain identifier

BacDive ID: 24236

Type strain: Yes

Species: Mycobacterium sediminis

Strain history: <- S-K Tang, Yunnan Inst., China

NCBI tax ID(s): 1286180 (species)

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

@ref: 20671

BacDive-ID: 24236

DSM-Number: 45643

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

description: Mycobacterium sediminis DSM 45643 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1286180
  • Matching level: species

strain history

@refhistory
20671<- S.-K. Tang, YIM; YIM M13028 <- D.-F. Zhang
67770S.-K. Tang YIM M13028.
67771<- S-K Tang, Yunnan Inst., China

doi: 10.13145/bacdive24236.20230509.8.1

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 sediminis
  • full scientific name: Mycobacterium sediminis Zhang et al. 2013
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium sediminis

@ref: 20671

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium sediminis

full scientific name: Mycobacterium sediminis Zhang et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31044positiveovoid-shapedno
67771positive
69480no93.781
69480positive100

pigmentation

  • @ref: 31044
  • production: yes

multimedia

  • @ref: 20671
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45643.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20671GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
20671MIDDLEBROOK 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

culture temp

@refgrowthtypetemperaturerange
20671positivegrowth28mesophilic
31044positivegrowth05-37
31044positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
31044positivegrowth6.0-8.0
31044positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31044no
69481no100
69480no99.876

halophily

@refsaltgrowthtested relationconcentration
31044NaClpositivegrowth0-4 %
31044NaClpositiveoptimum1 %

enzymes

@refvalueactivityec
31044catalase+1.11.1.6
31044urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20671marine sedimentYunnan, South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 mChinaCHNAsia19.5044111.004
67770Sediment sample from the South China Sea at a depth of 42 m
67771From marine sedimentSouthe China SeaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_13681.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_2631;98_10349;99_13681&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: KC010490
  • Sequence Identity:
  • Total samples: 4459
  • soil counts: 1808
  • aquatic counts: 648
  • animal counts: 1323
  • plant counts: 680

Safety information

risk assessment

  • @ref: 20671
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20671Mycobacterium sediminis strain YIM M13028 16S ribosomal RNA gene, partial sequenceKC0104901515ena1286180
67770Mycobacterium sediminis strain YIM M13028 16S-23S ribosomal RNA intergenic spacer, complete sequenceKC010492490ena1286180

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium sediminis JCM 17899GCA_010731735completencbi1286180
66792Mycolicibacterium sediminis strain JCM 178991286180.8completepatric1286180
66792Mycolicibacterium sediminis JCM 178992888243993completeimg1286180
66792Mycolicibacterium sediminis DSM 45643GCA_025822985scaffoldncbi1286180

GC content

@refGC-contentmethod
2067164.1high performance liquid chromatography (HPLC)
3104464.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.076yes
flagellatedno97.857yes
gram-positiveyes90.78yes
anaerobicno99.277no
aerobicyes92.421no
halophileno93.931yes
spore-formingno83.703yes
glucose-utilyes89.249no
thermophileno99.602yes
glucose-fermentno90.777no

External links

@ref: 20671

culture collection no.: DSM 45643, KCTC 19999, YIM M13028, JCM 17899

straininfo link

  • @ref: 88179
  • straininfo: 407834

literature

  • topic: Phylogeny
  • Pubmed-ID: 23728378
  • title: Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.
  • authors: Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.050567-0
  • year: 2013
  • mesh: Bacterial 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 Emirates
  • topic2: Genetics

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
20671Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45643Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45643)
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
88179Reimer, 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-ID407834.1