Strain identifier

BacDive ID: 8402

Type strain: Yes

Species: Mycobacterium gilvum

Strain Designation: SM35, SM 35, 14 119 0001

Variant: Isotype of BacDive ID 8500

Strain history: CIP <- 2000, V. Vincent, Inst. Pasteur, Paris, France: strain 14 119 0001 <- J.L. Stanford: strain SM 35 <- A. Beck

NCBI tax ID(s): 1804 (species)

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General

@ref: 16412

BacDive-ID: 8402

DSM-Number: 45363

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

description: Mycobacterium gilvum SM35 is an obligate aerobe, mesophilic bacterium that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 1804
  • Matching level: species

strain history

@refhistory
16412<- CCUG; CCUG 57112 <- M. Sakamoto, JCM/RIKEN <- NCTC; NCTC 10742 <- J. L. Stanford; SM35 <- A. Beck
67770NCTC 10742 <-- J. L. Stanford SM 35 <-- A. Beck.
119619CIP <- 2000, V. Vincent, Inst. Pasteur, Paris, France: strain 14 119 0001 <- J.L. Stanford: strain SM 35 <- A. Beck

doi: 10.13145/bacdive8402.20230509.8.1

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 gilvum
  • full scientific name: Mycobacterium gilvum Stanford and Gunthorpe 1971 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium gilvum

@ref: 16412

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium gilvum

full scientific name: Mycobacterium gilvum Stanford and Gunthorpe 1971

strain designation: SM35, SM 35, 14 119 0001

variant: Isotype of BacDive ID 8500

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.346
69480100positive
119619norod-shaped

multimedia

  • @ref: 16412
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45363.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16412MIDDLEBROOK 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
36382MEDIUM 55 - for Mycobacteriumyes
119619CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
16412positivegrowth37mesophilic
36382positivegrowth37mesophilic
67770positivegrowth37mesophilic
119619positivegrowth22-37
119619nogrowth10psychrophilic
119619nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119619
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.896

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119619606565hippurate-hydrolysis
11961917632nitrate+reduction
11961916301nitrite-reduction
11961917632nitrate-respiration

metabolite production

  • @ref: 119619
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119619oxidase-
119619beta-galactosidase-3.2.1.23
119619catalase+1.11.1.6
119619gamma-glutamyltransferase+2.3.2.2
119619urease-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
119619--++-+--+-++---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
16412human sputumUnited KingdomGBREurope
67770Sputum
119619SputumUnited KingdomGBREuropeEngland

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164121Risk group (German classification)
1196191Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218M.gilvum 16S ribosomal RNA, partX555991458ena1804
20218M.gilvum 16S rRNA geneX819961428ena1804
20218Mycobacterium gilvum strain DSM 44503 16S ribosomal RNA gene, partial sequenceAF547929540ena1804

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium gilvum strain NCTC107421804.5wgspatric1804
66792Mycolicibacterium gilvum NCTC 107422871780381draftimg1804
67770Mycolicibacterium gilvum NCTC10742GCA_900454025contigncbi1804
66792Mycolicibacterium gilvum DSM 45363GCA_025821885scaffoldncbi1804

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno74no
motileno91.33no
gram-positiveyes89.878no
anaerobicno99.228no
aerobicyes87.841no
halophileno84.591no
spore-formingno81.687no
glucose-utilyes87.744no
flagellatedno98.267no
thermophileno99.475yes
glucose-fermentno90.976no

External links

@ref: 16412

culture collection no.: DSM 45363, ATCC 43909, CCUG 57112, CIP 106743, JCM 15464, NCTC 10742, JCM 6395, KCTC 19423

straininfo link

  • @ref: 77801
  • straininfo: 42119

literature

  • topic: Metabolism
  • Pubmed-ID: 17496960
  • title: Acetylation and nitrosation of ciprofloxacin by environmental strains of mycobacteria.
  • authors: Adjei MD, Heinze TM, Deck J, Freeman JP, Williams AJ, Sutherland JB
  • journal: Can J Microbiol
  • DOI: 10.1139/w06-101
  • year: 2007
  • mesh: Acetylation, Anti-Infective Agents/*metabolism, Chromatography, High Pressure Liquid, Ciprofloxacin/*metabolism, Drug Resistance, Bacterial/physiology, Fluoroquinolones/*metabolism, Magnetic Resonance Spectroscopy, Nitrosation, Nontuberculous Mycobacteria/*drug effects/metabolism
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16412Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45363)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45363
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
36382Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18907
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
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)
77801Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42119.1StrainInfo: A central database for resolving microbial strain identifiers
119619Curators of the CIPCollection of Institut Pasteur (CIP 106743)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106743