Strain identifier

BacDive ID: 8551

Type strain: Yes

Species: Mycobacterium conceptionense

Strain Designation: D16

Strain history: CCUG 50187 <-- M. Drancourt D16.

NCBI tax ID(s): 451644 (species)

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General

@ref: 12344

BacDive-ID: 8551

DSM-Number: 45102

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Mycobacterium conceptionense D16 is an aerobe, mesophilic human pathogen that was isolated from human bone tissue biospy, wound liquid outflow.

NCBI tax id

  • NCBI tax id: 451644
  • Matching level: species

strain history

@refhistory
12344<- CCUG <- M. Drancourt, Timone, Marseille, France
363452004, M. Drancourt, La Timone Hosp., Marseille, France: strain D16
67770CCUG 50187 <-- M. Drancourt D16.

doi: 10.13145/bacdive8551.20230509.8.1

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 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

@refmotilityconfidencegram stain
69480no95.947
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12344MIDDLEBROOK 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
12344COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
36345MEDIUM 55 - for Mycobacteriumyes

culture temp

@refgrowthtypetemperaturerange
12344positivegrowth37mesophilic
36345positivegrowth30mesophilic
58777positivegrowth30-37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 58777
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.947

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountryorigin.countrycontinent
12344human bone tissue biospy, wound liquid outflowReunion Island, Indian Ocean
58777Human bone tissue biopsy,wound liquid outflow2002-09-01ReunionFRAAfrica
67770Wound liquidReunion IslandFrench OverseasFRA

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium conceptionense partial 16S rRNA gene, type strain CIP 108544TAM884281551ena451644
20218Mycobacterium conceptionense CIP 108544 16S ribosomal RNA gene, partial sequenceAY8596841483ena451644
20218Mycobacterium conceptionense strain CIP 108544 16S ribosomal RNA gene, partial sequenceEU191913457ena451644

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium conceptionense strain CCUG 50187451644.16wgspatric451644
67770Mycolicibacterium conceptionense D16GCA_001052995scaffoldncbi451644
67770Mycolicibacterium conceptionense CCUG 50187GCA_002102065contigncbi451644
66792Mycolicibacterium conceptionense DSM 45102GCA_025823065scaffoldncbi451644

GC content

@refGC-contentmethod
1234464
6777062-66high performance liquid chromatography (HPLC)
6777066.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveyes90.649no
anaerobicno99.143no
halophileno94.051no
spore-formingno85.925no
glucose-utilyes86.249no
aerobicyes87.291no
flagellatedno97.956no
motileno93.924no
thermophileno99.707yes
glucose-fermentno90.929no

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

@idauthorscataloguedoi/urltitlejournalpubmed
12344Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45102)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45102
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
36345Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6178
58777Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50187)https://www.ccug.se/strain?id=50187
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/
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
77935Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289773.1StrainInfo: A central database for resolving microbial strain identifiers