Strain identifier
BacDive ID: 8551
Type strain: 
Species: Mycobacterium conceptionense
Strain Designation: D16
Strain history: CCUG 50187 <-- M. Drancourt D16.
NCBI tax ID(s): 451644 (species)
version 9.3 (current version)
General
@ref: 12344
BacDive-ID: 8551
DSM-Number: 45102
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Mycobacterium conceptionense D16 is an aerobe, mesophilic bacterium that was isolated from human bone tissue biospy, wound liquid outflow.
NCBI tax id
- NCBI tax id: 451644
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12344 | <- CCUG <- M. Drancourt, Timone, Marseille, France |
| 36345 | 2004, M. Drancourt, La Timone Hosp., Marseille, France: strain D16 |
| 67770 | CCUG 50187 <-- M. Drancourt D16. |
doi: 10.13145/bacdive8551.20250331.9.3
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 conceptionense
- full scientific name: Mycobacterium conceptionense Adékambi et al. 2006
synonyms
- @ref: 20215
- synonym: Mycolicibacterium conceptionense
@ref: 12344
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium conceptionense
full scientific name: Mycobacterium conceptionense Adékambi et al. 2006 emend. Nouioui et al. 2018
strain designation: D16
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | positive | 94.3 | |
| 125438 | 90 | no | |
| 125438 | positive | 91.55 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 12344 | 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 |
| 12344 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| 36345 | MEDIUM 55 - for Mycobacterium | yes |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 12344 | positive | growth | 37 |
| 36345 | positive | growth | 30 |
| 58777 | positive | growth | 30-37 |
| 67770 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 58777 | aerobe | |
| 125439 | obligate aerobe | 95.2 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | sampling date | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 12344 | human bone tissue biospy, wound liquid outflow | Reunion Island, Indian Ocean | ||||
| 58777 | Human bone tissue biopsy,wound liquid outflow | 2002-09-01 | Reunion | FRA | Africa | |
| 67770 | Wound liquid | Reunion Island | French Overseas | FRA |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | #Biopsy |
| #Host | #Human | |
| #Host Body-Site | #Other | #Bone |
| #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: AY859684
- Sequence Identity:
- Total samples: 496
- soil counts: 45
- aquatic counts: 64
- animal counts: 50
- plant counts: 337
Safety information
risk assessment
- @ref: 12344
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Mycobacterium conceptionense partial 16S rRNA gene, type strain CIP 108544T | AM884281 | 551 | nuccore | 451644 |
| 20218 | Mycolicibacterium conceptionense strain CIP 108544 16S ribosomal RNA gene, partial sequence | AY859684 | 1483 | nuccore | 451644 |
| 20218 | Mycobacterium conceptionense strain CIP 108544 16S ribosomal RNA gene, partial sequence | EU191913 | 457 | nuccore | 451644 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium conceptionense strain CCUG 50187 | 451644.16 | wgs | patric | 451644 |
| 67770 | Mycolicibacterium conceptionense D16 | GCA_001052995 | scaffold | ncbi | 451644 |
| 67770 | Mycolicibacterium conceptionense CCUG 50187 | GCA_002102065 | contig | ncbi | 451644 |
| 66792 | Mycolicibacterium conceptionense DSM 45102 | GCA_025823065 | scaffold | ncbi | 451644 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12344 | 64 | |
| 67770 | 62-66 | high performance liquid chromatography (HPLC) |
| 67770 | 66.3 | genome sequence analysis |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 91.55 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.085 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 61.255 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.456 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 90 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 55.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 74.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 94.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 95.2 |
External links
@ref: 12344
culture collection no.: JCM 15299, DSM 45102, CCUG 50187, CIP 108544
straininfo link
- @ref: 77935
- straininfo: 289773
literature
- topic: Phylogeny
- Pubmed-ID: 16597850
- title: Description of Mycobacterium conceptionense sp. nov., a Mycobacterium fortuitum group organism isolated from a posttraumatic osteitis inflammation.
- authors: Adekambi T, Stein A, Carvajal J, Raoult D, Drancourt M
- journal: J Clin Microbiol
- DOI: 10.1128/JCM.44.4.1268-1273.2006
- year: 2006
- mesh: Adult, Bacterial Proteins/*genetics, Chaperonin 60, Chaperonins/*genetics, DNA, Bacterial/analysis/chemistry/isolation & purification, Female, Humans, Inflammation/microbiology, Mycobacterium/classification/genetics/growth & development/*isolation & purification, Mycobacterium Infections/microbiology, Mycobacterium fortuitum/classification/genetics, Osteitis/*microbiology, Phylogeny, Staining and Labeling, Tibia, Wound Infection/microbiology
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 12344 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45102) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45102 | |||
| 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 | |
| 36345 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6178 | ||||
| 58777 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50187) | https://www.ccug.se/strain?id=50187 | |||
| 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/ | ||||
| 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 | |||
| 77935 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID289773.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |