Strain identifier
BacDive ID: 8519
Type strain:
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)
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
@ref | history |
---|---|
11974 | <- J. M. Brown, CDC; W5998 <- R. J. Wallace <- Roche Biochemical Labs. |
67770 | CIP 107829 <-- G. Goolsby W5998 <-- R. J. Wallace Mf-657 <-- J. R. Roche. |
116828 | CIP <- 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
@ref | gram stain | motility | confidence | cell shape |
---|---|---|---|---|
29958 | positive | |||
69480 | no | 92.29 | ||
69480 | positive | 100 | ||
116828 | no | rod-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
@ref | name | growth | link | composition |
---|---|---|---|---|
11974 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
36377 | MEDIUM 55 - for Mycobacterium | yes | ||
116828 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
116828 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11974 | positive | growth | 37 | mesophilic |
29958 | positive | growth | 28-35 | mesophilic |
29958 | positive | optimum | 31.5 | mesophilic |
36377 | positive | growth | 37 | mesophilic |
57763 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
116828 | positive | growth | 22-41 | |
116828 | no | growth | 10 | psychrophilic |
116828 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
57763 | aerobe |
116828 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29958 | no | |
69481 | no | 100 |
69480 | no | 99.806 |
halophily
- @ref: 29958
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29958 | 28757 | fructose | + | carbon source |
29958 | 17234 | glucose | + | carbon source |
29958 | 29864 | mannitol | + | carbon source |
29958 | 37684 | mannose | + | carbon source |
29958 | 17268 | myo-inositol | + | carbon source |
29958 | 17814 | salicin | + | carbon source |
29958 | 27082 | trehalose | + | carbon source |
29958 | 17632 | nitrate | + | reduction |
116828 | 606565 | hippurate | - | hydrolysis |
116828 | 17632 | nitrate | + | reduction |
116828 | 16301 | nitrite | - | reduction |
116828 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 116828
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29958 | arylsulfatase | + | 3.1.6.1 |
29958 | catalase | + | 1.11.1.6 |
29958 | urease | + | 3.5.1.5 |
116828 | oxidase | - | |
116828 | beta-galactosidase | - | 3.2.1.23 |
116828 | gelatinase | - | |
116828 | amylase | - | |
116828 | DNase | - | |
116828 | caseinase | - | 3.4.21.50 |
116828 | catalase | + | 1.11.1.6 |
116828 | tween esterase | + | |
116828 | gamma-glutamyltransferase | + | 2.3.2.2 |
116828 | lecithinase | - | |
116828 | lipase | - | |
116828 | protease | - | |
116828 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116828 | - | - | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116828 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | + | - | + | + | + | - | + | - | + | - | - | - | + | + | + | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
11974 | leg wound | USA | USA | North America |
57763 | Human wound,leg | USA | USA | North America |
67770 | Leg wound | USA | USA | North America |
116828 | Leg wound | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
11974 | 2 | Risk group (German classification) |
116828 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacterium boenickei JCM 15653 | GCA_010731295 | complete | ncbi | 146017 |
66792 | Mycolicibacterium boenickei CCUG47580 | GCA_002553535 | contig | ncbi | 146017 |
66792 | Mycobacterium boenickei strain CCUG47580 | 146017.6 | wgs | patric | 146017 |
66792 | Mycobacterium boenickei strain CIP107829 | 146017.5 | wgs | patric | 146017 |
66792 | Mycolicibacterium boenickei strain JCM 15653 | 146017.12 | wgs | patric | 146017 |
66792 | Mycobacterium boenickei CCUG 47580 | 2865743993 | draft | img | 146017 |
66792 | Mycolicibacterium boenickei CIP107829 | 2856275449 | draft | img | 146017 |
67770 | Mycolicibacterium boenickei CIP107829 | GCA_900166915 | contig | ncbi | 146017 |
66792 | Mycolicibacterium boenickei DSM 44677 | GCA_022558525 | complete | ncbi | 146017 |
GC content
@ref | GC-content | method |
---|---|---|
29958 | 64 | |
67770 | 64 | thermal denaturation, midpoint method (Tm) |
67770 | 66.8 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 94.988 | no |
flagellated | no | 98.099 | no |
gram-positive | yes | 90.57 | yes |
anaerobic | no | 99.645 | yes |
aerobic | yes | 90.176 | no |
halophile | no | 92.101 | no |
spore-forming | no | 84.277 | no |
glucose-util | yes | 88.994 | yes |
thermophile | no | 99.487 | yes |
glucose-ferment | no | 90.417 | no |
External links
@ref: 11974
culture collection no.: DSM 44677, ATCC 49935, CCUG 47580, CIP 107829, JCM 15653
straininfo link
- @ref: 77908
- straininfo: 45257
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15388725 | Taxonomic 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 JM | Int J Syst Evol Microbiol | 10.1099/ijs.0.02743-0 | 2004 | Anti-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, DNA | Enzymology |
Genetics | 28473389 | Draft Genome Sequence of Mycobacterium boenickei CIP 107829. | Bouam A, Robert C, Croce O, Levasseur A, Drancourt M | Genome Announc | 10.1128/genomeA.00292-17 | 2017 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
11974 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44677) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44677 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
29958 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26327 | 28776041 | |
36377 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5383 | ||||
57763 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 47580) | https://www.ccug.se/strain?id=47580 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
77908 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45257.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116828 | Curators of the CIP | Collection of Institut Pasteur (CIP 107829) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107829 |