Strain identifier

BacDive ID: 8442

Type strain: Yes

Species: Mycobacterium shimoidei

Strain Designation: E4796

Strain history: CCUG 37517 <-- DSM 44152 <-- ATCC 27962 <-- M. Tsukamura E4796.

NCBI tax ID(s): 29313 (species)

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General

@ref: 11552

BacDive-ID: 8442

DSM-Number: 44152

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Mycobacterium shimoidei E4796 is a mesophilic bacterium that was isolated from sputum of patient with tuberculosis-like disease.

NCBI tax id

  • NCBI tax id: 29313
  • Matching level: species

strain history

@refhistory
11552<- ATCC <- M. Tsukamura, 4796
67770CCUG 37517 <-- DSM 44152 <-- ATCC 27962 <-- M. Tsukamura E4796.

doi: 10.13145/bacdive8442.20230509.8.1

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 shimoidei
  • full scientific name: Mycobacterium shimoidei (ex Tsukamura et al. 1975) Tsukamura 1982

@ref: 11552

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium shimoidei

full scientific name: Mycobacterium shimoidei (ex Tsukamura et al. 1975) Tsukamura 1982 emend. Nouioui et al. 2018

strain designation: E4796

type strain: yes

Morphology

colony morphology

  • @ref: 53711
  • incubation period: 10 days

multimedia

  • @ref: 11552
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44152.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11552LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
11552MIDDLEBROOK 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
11552positivegrowth37mesophilic
53711positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    53711C14:0114
    53711C15:00.315
    53711C16:03016
    53711C17:00.317
    53711C18:03.818
    53711C16:0 2OH0.317.233
    53711C16:1 ω7c2.915.819
    53711C16:1 ω9c1.615.774
    53711C18:1 ω7c /12t/9t2.317.824
    53711C18:1 ω9c39.717.769
    53711C18:2 ω6,9c/C18:0 ANTE12.117.724
    53711C20:0 alcohol (C20:0 2OH alc)218.835
    53711C20:4 ω6,9,12,15c1.319.395
    53711TBSA 10Me18:02.218.392
    53711Unidentified0.316.904
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample type
11552sputum of patient with tuberculosis-like disease
53711Human sputum,patient w/tuberculosis-like disease
67770Sputum of a patient

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_7114.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_3466;98_5232;99_7114&stattab=map
  • Last taxonomy: Mycobacterium shimoidei subclade
  • 16S sequence: X82459
  • Sequence Identity:
  • Total samples: 3932
  • soil counts: 3022
  • aquatic counts: 394
  • animal counts: 297
  • plant counts: 219

Safety information

risk assessment

  • @ref: 11552
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium shimoidei 16S rRNA gene and internal transcribed spacerAJ0050051805ena29313
20218M.shimoidei 16S rRNA geneX824591428ena29313
20218M.shimoidei internal transcribed spacer between 16S and 23S rRNA, genomic sequenceX99219274ena29313
20218Mycobacterium shimoidei strain DSM 44152 16S ribosomal RNA gene, partial sequenceAF547965556ena29313

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium shimoidei strain DSM 4415229313.4wgspatric29313
67770Mycobacterium shimoidei DSM 44152GCA_002101905contigncbi29313
66792Mycobacterium shimoidei DSM 44152GCA_025822885scaffoldncbi29313

GC content

  • @ref: 67770
  • GC-content: 65.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes90.245no
anaerobicno98.682no
halophileno90.65no
spore-formingno89.775no
thermophileno94.706yes
glucose-utilyes64.418no
motileno95.025no
flagellatedno99.088no
aerobicyes89.344no
glucose-fermentno93.274no

External links

@ref: 11552

culture collection no.: CCUG 37517, JCM 12376, DSM 44152, ATCC 27962

straininfo link

  • @ref: 77841
  • straininfo: 44801

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11552Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44152)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44152
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
53711Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37517)https://www.ccug.se/strain?id=37517
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/
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
77841Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44801.1StrainInfo: A central database for resolving microbial strain identifiers