Strain identifier
BacDive ID: 8550
Type strain:
Species: Mycobacterium colombiense
Strain Designation: 10B, B10
Strain history: CIP <- 2005, M.J. Garcia, Madrid Univ., Madrid, Spain: strain B10
NCBI tax ID(s): 1041522 (strain), 339268 (species)
General
@ref: 12347
BacDive-ID: 8550
DSM-Number: 45105
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic
description: Mycobacterium colombiense 10B is an obligate aerobe, mesophilic bacterium that was isolated from blood of an HIV positive patient.
NCBI tax id
NCBI tax id | Matching level |
---|---|
339268 | species |
1041522 | strain |
strain history
@ref | history |
---|---|
12347 | <- E. Tortoli, Univ. Firenze; 10B |
42061 | 2005, M. J. Garcia, Madrid, Spain: strain B10 |
67770 | CECT 3035 <-- M. J. Garcia 10B <-- M. I. Murcia. |
118706 | CIP <- 2005, M.J. Garcia, Madrid Univ., Madrid, Spain: strain B10 |
doi: 10.13145/bacdive8550.20230509.8.1
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 colombiense
- full scientific name: Mycobacterium colombiense Murcia et al. 2006
@ref: 12347
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium colombiense
full scientific name: Mycobacterium colombiense Murcia et al. 2006 emend. Nouioui et al. 2018
strain designation: 10B, B10
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 95.856 | ||
69480 | 100 | positive | ||
118706 | no | rod-shaped |
colony morphology
- @ref: 118706
multimedia
- @ref: 12347
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45105.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12347 | 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 |
42061 | MEDIUM 55 - for Mycobacterium | yes | ||
118706 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
12347 | positive | growth | 37 | mesophilic |
42061 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118706
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 97 |
69480 | no | 99.956 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118706 | 17632 | nitrate | + | reduction |
118706 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118706
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
118706 | oxidase | - | |
118706 | alcohol dehydrogenase | - | 1.1.1.1 |
118706 | catalase | + | 1.11.1.6 |
118706 | lysine decarboxylase | - | 4.1.1.18 |
118706 | ornithine decarboxylase | - | 4.1.1.17 |
118706 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118706 | - | - | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | geographic location | isolation date |
---|---|---|---|---|---|---|---|
12347 | blood of an HIV positive patient | Colombia | COL | Middle and South America | |||
60679 | Human blood,AIDS patient | Colombia | COL | Middle and South America | 1995 | Bogota | |
67770 | Blood of an HIV-positive patient | Colombia | COL | Middle and South America | |||
118706 | Blood culture | Colombia | COL | Middle and South America | Bogota | 1995 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host Body Product | #Fluids | #Blood |
taxonmaps
- @ref: 69479
- File name: preview.99_402.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_402&stattab=map
- Last taxonomy: Mycobacterium
- 16S sequence: GQ153275
- Sequence Identity:
- Total samples: 24078
- soil counts: 12779
- aquatic counts: 4789
- animal counts: 3677
- plant counts: 2833
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12347 | 2 | Risk group (German classification) |
118706 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium colombiense strain CIP108962 16S ribosomal RNA gene, partial sequence | GQ153275 | 1495 | ena | 1041522 |
12347 | Mycobacterium colombiense partial 16S rRNA gene and ITS1, type strain:10B | AM062764 | 1807 | ena | 1041522 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium colombiense CECT 3035 | GCA_002105755 | complete | ncbi | 1041522 |
66792 | Mycobacterium colombiense CECT 3035 | 1041522.3 | wgs | patric | 1041522 |
66792 | Mycobacterium colombiense CECT 3035 strain CECT 3035 | 1041522.28 | complete | patric | 1041522 |
66792 | Mycobacterium colombiense CECT 3035 | 2562617111 | draft | img | 1041522 |
67770 | Mycobacterium colombiense CECT 3035 | GCA_000222105 | contig | ncbi | 1041522 |
GC content
- @ref: 67770
- GC-content: 68.1
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 97 | no |
flagellated | no | 98.872 | no |
gram-positive | yes | 88.148 | no |
anaerobic | no | 99.288 | no |
aerobic | yes | 89.554 | no |
halophile | no | 93.054 | no |
spore-forming | no | 87.919 | no |
glucose-util | yes | 66.852 | no |
thermophile | no | 97.9 | no |
glucose-ferment | no | 90.991 | no |
motile | no | 95.68 | no |
External links
@ref: 12347
culture collection no.: DSM 45105, CECT 3035, CIP 108962, CCUG 55633, JCM 16228
straininfo link
- @ref: 77934
- straininfo: 297257
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16957098 | Mycobacterium colombiense sp. nov., a novel member of the Mycobacterium avium complex and description of MAC-X as a new ITS genetic variant. | Murcia MI, Tortoli E, Menendez MC, Palenque E, Garcia MJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64190-0 | 2006 | Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Intergenic/analysis, DNA, Ribosomal Spacer/*analysis, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*classification/genetics, RNA, Ribosomal, 16S/*analysis/genetics | Pathogenicity |
Genetics | 21952541 | Genome sequence of the Mycobacterium colombiense type strain, CECT 3035. | Gonzalez-Perez M, Murcia MI, Landsman D, Jordan IK, Marino-Ramirez L | J Bacteriol | 10.1128/JB.05928-11 | 2011 | Base Sequence, *Genome, Bacterial, Humans, Molecular Sequence Data, Mycobacterium avium Complex/classification/*genetics/isolation & purification, Mycobacterium avium-intracellulare Infection/*microbiology | Pathogenicity |
Pathogenicity | 22967705 | Identification of potential biomarkers to distinguish Mycobacterium colombiense from other mycobacterial species. | Leguizamon J, Hernandez J, Murcia MI, Soto CY | Mol Cell Probes | 10.1016/j.mcp.2012.08.009 | 2012 | Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics, Bacterial Typing Techniques, Base Sequence, Biomarkers, Chromatography, Thin Layer, DNA Primers/genetics, DNA, Bacterial/*genetics, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*classification/*genetics, Mycobacterium avium-intracellulare Infection/diagnosis, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNA | Genetics |
Biotechnology | 26180799 | Sliding Motility, Biofilm Formation, and Glycopeptidolipid Production in Mycobacterium colombiense Strains. | Maya-Hoyos M, Leguizamon J, Marino-Ramirez L, Soto CY | Biomed Res Int | 10.1155/2015/419549 | 2015 | *Biofilms, Membrane Lipids/genetics/*metabolism, *Multigene Family, Mycobacterium/*physiology | Lipids |
35357597 | In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035. | Hamde F, Dinka H, Naimuddin M | J Genet Eng Biotechnol | 10.1186/s43141-022-00331-6 | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
12347 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45105) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45105 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
42061 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6650 | ||||
60679 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55633) | https://www.ccug.se/strain?id=55633 | |||
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 | |||
77934 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297257.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118706 | Curators of the CIP | Collection of Institut Pasteur (CIP 108962) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108962 |