Strain identifier

BacDive ID: 8519

Type strain: Yes

Species: Mycobacterium boenickei

Strain Designation: MF-657, W5998

Strain history: CIP <- 2003, G. Goolsby, CDC, Atlanta, USA: strain W5998 <- R.J. Wallace <- J.R. Roche, Biomedical, Labs

NCBI tax ID(s): 146017 (species)

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

@ref: 11974

BacDive-ID: 8519

DSM-Number: 44677

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

description: Mycobacterium boenickei MF-657 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from leg wound.

NCBI tax id

  • NCBI tax id: 146017
  • Matching level: species

strain history

@refhistory
11974<- J. M. Brown, CDC; W5998 <- R. J. Wallace <- Roche Biochemical Labs.
67770CIP 107829 <-- G. Goolsby W5998 <-- R. J. Wallace Mf-657 <-- J. R. Roche.
116828CIP <- 2003, G. Goolsby, CDC, Atlanta, USA: strain W5998 <- R.J. Wallace <- J.R. Roche, Biomedical, Labs

doi: 10.13145/bacdive8519.20230509.8.1

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 boenickei
  • full scientific name: Mycobacterium boenickei Schinsky et al. 2004
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium boenickei

@ref: 11974

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium boenickei

full scientific name: Mycobacterium boenickei Schinsky et al. 2004 emend. Nouioui et al. 2018

strain designation: MF-657, W5998

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
29958positive
69480no92.29
69480positive100
116828norod-shaped

colony morphology

  • @ref: 57763
  • incubation period: 2 days

multimedia

  • @ref: 11974
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44677.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11974MIDDLEBROOK 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
36377MEDIUM 55 - for Mycobacteriumyes
116828CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116828CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11974positivegrowth37mesophilic
29958positivegrowth28-35mesophilic
29958positiveoptimum31.5mesophilic
36377positivegrowth37mesophilic
57763positivegrowth37mesophilic
67770positivegrowth37mesophilic
116828positivegrowth22-41
116828nogrowth10psychrophilic
116828nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57763aerobe
116828obligate aerobe

spore formation

@refspore formationconfidence
29958no
69481no100
69480no99.806

halophily

  • @ref: 29958
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2995828757fructose+carbon source
2995817234glucose+carbon source
2995829864mannitol+carbon source
2995837684mannose+carbon source
2995817268myo-inositol+carbon source
2995817814salicin+carbon source
2995827082trehalose+carbon source
2995817632nitrate+reduction
116828606565hippurate-hydrolysis
11682817632nitrate+reduction
11682816301nitrite-reduction
11682817632nitrate-respiration

metabolite production

  • @ref: 116828
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29958arylsulfatase+3.1.6.1
29958catalase+1.11.1.6
29958urease+3.5.1.5
116828oxidase-
116828beta-galactosidase-3.2.1.23
116828gelatinase-
116828amylase-
116828DNase-
116828caseinase-3.4.21.50
116828catalase+1.11.1.6
116828tween esterase+
116828gamma-glutamyltransferase+2.3.2.2
116828lecithinase-
116828lipase-
116828protease-
116828urease-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
116828--++-+----++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116828-+-----------------------------+++---------------+----------+-----------++------+-+++-+-+---+++++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11974leg woundUSAUSANorth America
57763Human wound,legUSAUSANorth America
67770Leg woundUSAUSANorth America
116828Leg woundUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Limb#Leg
#Host Body-Site#Other#Wound

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: AY012573
  • 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
119742Risk group (German classification)
1168281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11974
  • description: Mycobacterium bonickei strain W5998 16S ribosomal RNA gene, partial sequence
  • accession: AY012573
  • length: 1498
  • database: ena
  • NCBI tax ID: 146017

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium boenickei JCM 15653GCA_010731295completencbi146017
66792Mycolicibacterium boenickei CCUG47580GCA_002553535contigncbi146017
66792Mycobacterium boenickei strain CCUG47580146017.6wgspatric146017
66792Mycobacterium boenickei strain CIP107829146017.5wgspatric146017
66792Mycolicibacterium boenickei strain JCM 15653146017.12wgspatric146017
66792Mycobacterium boenickei CCUG 475802865743993draftimg146017
66792Mycolicibacterium boenickei CIP1078292856275449draftimg146017
67770Mycolicibacterium boenickei CIP107829GCA_900166915contigncbi146017
66792Mycolicibacterium boenickei DSM 44677GCA_022558525completencbi146017

GC content

@refGC-contentmethod
2995864
6777064thermal denaturation, midpoint method (Tm)
6777066.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.988no
flagellatedno98.099no
gram-positiveyes90.57yes
anaerobicno99.645yes
aerobicyes90.176no
halophileno92.101no
spore-formingno84.277no
glucose-utilyes88.994yes
thermophileno99.487yes
glucose-fermentno90.417no

External links

@ref: 11974

culture collection no.: DSM 44677, ATCC 49935, CCUG 47580, CIP 107829, JCM 15653

straininfo link

  • @ref: 77908
  • straininfo: 45257

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388725Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates.Schinsky MF, Morey RE, Steigerwalt AG, Douglas MP, Wilson RW, Floyd MM, Butler WR, Daneshvar MI, Brown-Elliott BA, Wallace RJ, McNeil MM, Brenner DJ, Brown JMInt J Syst Evol Microbiol10.1099/ijs.0.02743-02004Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA/genetics, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Mycobacterium Infections, Nontuberculous/*microbiology, Mycobacterium fortuitum/*classification/genetics/isolation & purification/physiology, Mycolic Acids/analysis, Nontuberculous Mycobacteria/*classification/genetics/isolation & purification/physiology, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNAEnzymology
Genetics28473389Draft Genome Sequence of Mycobacterium boenickei CIP 107829.Bouam A, Robert C, Croce O, Levasseur A, Drancourt MGenome Announc10.1128/genomeA.00292-172017

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11974Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44677)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44677
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
29958Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2632728776041
36377Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5383
57763Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47580)https://www.ccug.se/strain?id=47580
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77908Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45257.1StrainInfo: A central database for resolving microbial strain identifiers
116828Curators of the CIPCollection of Institut Pasteur (CIP 107829)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107829