Strain identifier

BacDive ID: 8550

Type strain: Yes

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)

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General

@ref: 12347

BacDive-ID: 8550

DSM-Number: 45105

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

description: Mycobacterium colombiense 10B is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from blood of an HIV positive patient.

NCBI tax id

NCBI tax idMatching level
1041522strain
339268species

strain history

@refhistory
12347<- E. Tortoli, Univ. Firenze; 10B
420612005, M. J. Garcia, Madrid, Spain: strain B10
67770CECT 3035 <-- M. J. Garcia 10B <-- M. I. Murcia.
118706CIP <- 2005, M.J. Garcia, Madrid Univ., Madrid, Spain: strain B10

doi: 10.13145/bacdive8550.20250331.9.3

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

@refcell shapemotilitygram stainconfidence
118706rod-shapedno
125439positive91.9

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

@refnamegrowthlinkcomposition
12347MIDDLEBROOK 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
42061MEDIUM 55 - for Mycobacteriumyes
118706CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
12347positivegrowth37
42061positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118706obligate aerobe
125439obligate aerobe99.5

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11870617632nitrate+reduction
11870616301nitrite-reduction

metabolite production

  • @ref: 118706
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
118706oxidase-
118706alcohol dehydrogenase-1.1.1.1
118706catalase+1.11.1.6
118706lysine decarboxylase-4.1.1.18
118706ornithine decarboxylase-4.1.1.17
118706urease+3.5.1.5
68382alpha-glucosidase+3.2.1.20
68382naphthol-AS-BI-phosphohydrolase+
68382leucine arylamidase+3.4.11.1
68382alkaline phosphatase-3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118706--++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
12347blood of an HIV positive patientColombiaCOLMiddle and South America
60679Human blood,AIDS patientColombiaCOLMiddle and South America1995Bogota
67770Blood of an HIV-positive patientColombiaCOLMiddle and South America
118706Blood cultureColombiaCOLMiddle and South AmericaBogota1995

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
123472Risk group (German classification)
1187061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium colombiense strain CIP108962 16S ribosomal RNA gene, partial sequenceGQ1532751495nuccore1041522
12347Mycobacterium colombiense partial 16S rRNA gene and ITS1, type strain:10BAM0627641807nuccore1041522
124043Mycobacterium colombiense CECT 3035 16S ribosomal RNA gene, partial sequence.OK539011833nuccore1041522

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium colombiense CECT 3035GCA_002105755completencbi1041522
66792Mycobacterium colombiense CECT 30351041522.3wgspatric1041522
66792Mycobacterium colombiense CECT 3035 strain CECT 30351041522.28completepatric1041522
66792Mycobacterium colombiense CECT 30352562617111draftimg1041522
67770Mycobacterium colombiense CECT 3035GCA_000222105contigncbi1041522

GC content

  • @ref: 67770
  • GC-content: 68.1
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive91.9
125439BacteriaNetmotilityAbility to perform movementno68.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesno76.9
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.304no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.066no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.163yes
125438spore-formingspore-formingAbility to form endo- or exosporesno64.118no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5yes
125438motile2+flagellatedAbility to perform flagellated movementno86.5no

External links

@ref: 12347

culture collection no.: DSM 45105, CECT 3035, CIP 108962, CCUG 55633, JCM 16228

straininfo link

  • @ref: 77934
  • straininfo: 297257

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957098Mycobacterium 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 MJInt J Syst Evol Microbiol10.1099/ijs.0.64190-02006Bacterial 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/geneticsPathogenicity
Genetics21952541Genome sequence of the Mycobacterium colombiense type strain, CECT 3035.Gonzalez-Perez M, Murcia MI, Landsman D, Jordan IK, Marino-Ramirez LJ Bacteriol10.1128/JB.05928-112011Base Sequence, *Genome, Bacterial, Humans, Molecular Sequence Data, Mycobacterium avium Complex/classification/*genetics/isolation & purification, Mycobacterium avium-intracellulare Infection/*microbiologyPathogenicity
Pathogenicity22967705Identification of potential biomarkers to distinguish Mycobacterium colombiense from other mycobacterial species.Leguizamon J, Hernandez J, Murcia MI, Soto CYMol Cell Probes10.1016/j.mcp.2012.08.0092012Amino 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, DNAGenetics
Biotechnology26180799Sliding Motility, Biofilm Formation, and Glycopeptidolipid Production in Mycobacterium colombiense Strains.Maya-Hoyos M, Leguizamon J, Marino-Ramirez L, Soto CYBiomed Res Int10.1155/2015/4195492015*Biofilms, Membrane Lipids/genetics/*metabolism, *Multigene Family, Mycobacterium/*physiologyLipids
35357597In 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 MJ Genet Eng Biotechnol10.1186/s43141-022-00331-62022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12347Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45105)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45105
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
42061Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6650
60679Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55633)https://www.ccug.se/strain?id=55633
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
77934Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297257.1StrainInfo: A central database for resolving microbial strain identifiers
118706Curators of the CIPCollection of Institut Pasteur (CIP 108962)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108962
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1