Strain identifier

BacDive ID: 8553

Type strain: Yes

Species: Mycobacterium setense

Strain Designation: ABO-M06, MBS-1, AB0-M06

Strain history: CIP <- 2006, B. Lamy, Bassin de Thau Hosp., Sète, France: strain AB0-M06

NCBI tax ID(s): 431269 (species)

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General

@ref: 12313

BacDive-ID: 8553

DSM-Number: 45070

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

description: Mycobacterium setense ABO-M06 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from chronic cutaneous abcess associated with osteitis.

NCBI tax id

  • NCBI tax id: 431269
  • Matching level: species

strain history

@refhistory
12313<- B. Lamy; MBS-1
67770CIP 109395 <-- B. Lamy ABO-M06.
122574CIP <- 2006, B. Lamy, Bassin de Thau Hosp., Sète, France: strain AB0-M06

doi: 10.13145/bacdive8553.20230509.8.1

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 setense
  • full scientific name: Mycobacterium setense Lamy et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium setense

@ref: 12313

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium setense

full scientific name: Mycobacterium setense Lamy et al. 2008 emend. Nouioui et al. 2018

strain designation: ABO-M06, MBS-1, AB0-M06

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
32264positiverod-shaped
122574positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19908Zinc yellow10-14 daysISP 2
19908Zinc yellow10-14 daysISP 3
19908Zinc yellow10-14 daysISP 4
19908Zinc yellow10-14 daysISP 5
19908Zinc yellow10-14 daysISP 6
19908Zinc yellow10-14 daysISP 7
608113 days

multicellular morphology

@refforms multicellular complexmedium name
19908noISP 2
19908noISP 3
19908noISP 4
19908noISP 5
19908noISP 6
19908noISP 7

pigmentation

  • @ref: 32264
  • production: no

multimedia

  • @ref: 12313
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45070.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12313MIDDLEBROOK 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
19908ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19908ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19908ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19908ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19908ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19908ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
122574CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
12313positivegrowth37mesophilic
19908positiveoptimum37mesophilic
32264positivegrowth25-37mesophilic
32264positiveoptimum30mesophilic
60811positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60811
  • oxygen tolerance: aerobe

halophily

  • @ref: 32264
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3226417234glucose+carbon source
3226429864mannitol+carbon source
3226417632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

enzymes

@refvalueactivityec
32264alkaline phosphatase+3.1.3.1
32264arylsulfatase+3.1.6.1
32264catalase+1.11.1.6
32264gelatinase+
32264pyrazinamidase+3.5.1.B15
32264urease+3.5.1.5
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
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 coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19908+++--+--++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19908+++-+-++-+++-+++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
12313chronic cutaneous abcess associated with osteitisHérault, SèteFranceFRAEurope
60811Human soft tissue infection and osteitisHérault,SèteFranceFRAEurope2005
67770Excised skin and soft tissue specimenSèteFranceFRAEurope
122574Human, AbscessSèteFranceFRAEurope2005

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host Body-Site#Other#Abscess
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_515.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_515&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: EU371504
  • Sequence Identity:
  • Total samples: 496
  • soil counts: 45
  • aquatic counts: 64
  • animal counts: 50
  • plant counts: 337

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123132Risk group (German classification)
199082Risk group (German classification)
1225741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium setense strain CIP109395 16S ribosomal RNA gene, partial sequenceEU3715041442ena431269
12313Mycobacterium setense strain ABO-M06 16S ribosomal RNA gene, partial sequenceEF1388181336ena431269

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium setense DSM 45070431269.3wgspatric431269
66792Mycolicibacterium setense DSM 450702648501822draftimg431269
67770Mycolicibacterium setense DSM 45070GCA_000805385contigncbi431269
66792Mycolicibacterium setense DSM 45070GCA_025821545contigncbi431269

GC content

  • @ref: 67770
  • GC-content: 66.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes92.439no
anaerobicno99.47yes
halophileno91.351no
spore-formingno82.097no
glucose-utilyes87.608yes
aerobicyes87.614no
flagellatedno98.041no
thermophileno99.694no
motileno93.59no
glucose-fermentno91.968no

External links

@ref: 12313

culture collection no.: DSM 45070, CIP 109395, CCUG 55975, CIP 139395, JCM 15660

straininfo link

  • @ref: 77936
  • straininfo: 323982

literature

  • topic: Phylogeny
  • Pubmed-ID: 18218954
  • title: Mycobacterium setense sp. nov., a Mycobacterium fortuitum-group organism isolated from a patient with soft tissue infection and osteitis.
  • authors: Lamy B, Marchandin H, Hamitouche K, Laurent F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65222-0
  • year: 2008
  • mesh: Bacterial Proteins/genetics, Cell Wall/chemistry, DNA, Bacterial/analysis, Fatty Acids/analysis, *Foot Bones, Genes, rRNA, Genotype, Humans, Male, Middle Aged, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/*isolation & purification, Mycobacterium Infections/*microbiology, Osteitis/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soft Tissue Infections/*microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12313Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45070)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45070
19908Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45070.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
32264Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128505
60811Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55975)https://www.ccug.se/strain?id=55975
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/
68379Automatically annotated from API Coryne
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
77936Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323982.1StrainInfo: A central database for resolving microbial strain identifiers
122574Curators of the CIPCollection of Institut Pasteur (CIP 109395)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109395