Strain identifier

BacDive ID: 8407

Type strain: Yes

Species: Mycobacterium gastri

Strain Designation: W-417, 14 034 0001

Strain history: CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 034 0001 <- ATCC <- L.G. Wayne: strain W-417

NCBI tax ID(s): 1777 (species)

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General

@ref: 11094

BacDive-ID: 8407

DSM-Number: 43505

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

description: Mycobacterium gastri W-417 is an obligate aerobe, mesophilic bacterium that was isolated from gastric lavage.

NCBI tax id

  • NCBI tax id: 1777
  • Matching level: species

strain history

@refhistory
11094<- I. Tarnok, SN 583 <- L.G. Wayne, W-417
67770CIP 104530 <-- V. Vincent <-- ATCC 15754 <-- L. G. Wayne W-417.
119556CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 034 0001 <- ATCC <- L.G. Wayne: strain W-417

doi: 10.13145/bacdive8407.20230509.8.1

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 gastri
  • full scientific name: Mycobacterium gastri Wayne 1966 (Approved Lists 1980)

@ref: 11094

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium gastri

full scientific name: Mycobacterium gastri Wayne 1966

strain designation: W-417, 14 034 0001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.956
69480100positive
119556norod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11094LÖWENSTEIN-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
39727MEDIUM 55 - for Mycobacteriumyes
119556CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11094positivegrowth37mesophilic
39727positivegrowth37mesophilic
67770positivegrowth37mesophilic
119556positivegrowth37mesophilic
119556nogrowth10psychrophilic
119556nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119556
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.867

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1195564853esculin-hydrolysis
11955617632nitrate+reduction
11955616301nitrite-reduction

metabolite production

  • @ref: 119556
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119556oxidase-
119556beta-galactosidase+3.2.1.23
119556catalase+1.11.1.6
119556urease+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
119556-+++-+-+--+--------+

Isolation, sampling and environmental information

isolation

@refsample type
11094gastric lavage
67770Gastric lavage
119556Human, Gastric lavage

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Gastrointestinal tract
  • Cat3: #Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_75.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_75&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: X52919
  • Sequence Identity:
  • Total samples: 1520
  • soil counts: 881
  • aquatic counts: 382
  • animal counts: 203
  • plant counts: 54

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
110942Risk group (German classification)
1195561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium gastri 16S ribosomal RNA gene, partial sequenceAF4806021469ena1777
20218M.gastri 16S ribosomal RNA geneM59266145ena1777
20218Mycobacterium gastri 16S rRNA geneX529191460ena1777
20218M.gastri DNA for internal transcribed spacer between 16S rRNA and 23S rRNA genesX97633285ena1777
20218Mycobacterium gastri strain CIP 104530 16S ribosomal RNA gene, partial sequenceAF547927554ena1777
20218Mycobacterium gastri DNA for 16S rRNA, internal transcribed spacer, 23S rRNAAB026697443ena1777

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium gastri strain DSM 435051777.3wgspatric1777
67770Mycobacterium gastri 'Wayne'GCA_000521195contigncbi1436723
67770Mycobacterium gastri DSM 43505GCA_002102175contigncbi1777

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileno96.072no
gram-positiveyes89.083no
anaerobicno98.11no
aerobicyes87.077no
halophileno94.06no
spore-formingno85.052no
thermophileno96.901yes
glucose-utilyes66.726no
flagellatedno99.064no
glucose-fermentno90.024no

External links

@ref: 11094

culture collection no.: DSM 43505, ATCC 15754, ATCC 15980, IMET 10662, TMC 1456, SN 583, JCM 12407, CCUG 20995, CCUG 29062, CCUG 47488, CIP 104530, DSM 43506

straininfo link

  • @ref: 77806
  • straininfo: 36475

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43505
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
39727Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16449
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)
77806Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36475.1StrainInfo: A central database for resolving microbial strain identifiers
119556Curators of the CIPCollection of Institut Pasteur (CIP 104530)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104530