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BacDive ID 24234
Type strain
Strain Designation 4355387
Culture col. no. DSM 45439 CCUG 56331 CIP 109827 CSUR P34 JCM 17323 4355387 1 more
NCBI tax ID(s) 701041
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 20669

BacDive-ID: 24234

DSM-Number: 45439

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, human pathogen

description: Mycobacterium avium 4355387 is a mesophilic, Gram-positive human pathogen that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 701041
  • Matching level: species

strain history

@refhistory
20669<- CIP; CIP 109827 <- I. Ben Salah and M. Drancourt, IRD, Marseille; 4355387
412202008, M. Drancourt, La Timone Hosp, Marseille, France: strain 4355387

doi: 10.13145/bacdive24234.20250331.9.3

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 avium
  • full scientific name: Mycobacterium avium Chester 1901 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Mycobacterium bouchedurhonense

@ref: 20669

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium avium

full scientific name: Mycobacterium avium Chester 1901 emend. Thorel et al. 1990

strain designation: 4355387

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthconfidence
29309positive0.87 µm0.49 µm
125439positive97.4

pigmentation

  • @ref: 29309
  • production: no

multimedia

@refmultimedia contentintellectual property rightscaption
20669https://www.dsmz.de/microorganisms/photos/DSM_45439-1.jpg© Leibniz-Institut DSMZ
20669https://www.dsmz.de/microorganisms/photos/DSM_45439.jpg© Leibniz-Institut DSMZMedium 645 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20669MIDDLEBROOK 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
41220MEDIUM 93 - for Mycobacterium avium subsp. sylvaticumyesDistilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)

culture temp

@refgrowthtypetemperature
20669positivegrowth30
41220positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 97.9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2930916947citrate+carbon source
2930933942ribose+carbon source
293094853esculin+hydrolysis
6837928087glycogen-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis

enzymes

@refvalueactivityec
29309acid phosphatase+3.1.3.2
29309alkaline phosphatase+3.1.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382naphthol-AS-BI-phosphohydrolase-
68382esterase lipase (C 8)+
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase-3.2.1.20
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
20669--------------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20669---+-+/---------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
20669human sputumMarseilleFranceFRAEurope
60921Human sputumMarseilleFranceFRAEurope2000

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

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: EF591053
  • Sequence Identity:
  • Total samples: 24078
  • soil counts: 12779
  • aquatic counts: 4789
  • animal counts: 3677
  • plant counts: 2833

Safety information

risk assessment

  • @ref: 20669
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20669
  • description: Mycobacterium bouchedurhonense strain 4355387 16S ribosomal RNA gene, partial sequence
  • accession: EF591053
  • length: 1498
  • database: nuccore
  • NCBI tax ID: 701041

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium bouchedurhonense DSM 45439GCA_002086165contigncbi701041
66792Mycobacterium bouchedurhonense strain DSM 45439701041.3wgspatric701041
66792Mycobacterium bouchedurhonense DSM 45439GCA_025822125scaffoldncbi701041

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.216no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.993no
125438spore-formingspore-formingAbility to form endo- or exosporesno59.603no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.521no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementno86.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno55.1
125439BacteriaNetmotilityAbility to perform movementno76
125439BacteriaNetgram_stainReaction to gram-stainingpositive97.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.9

External links

@ref: 20669

culture collection no.: DSM 45439, CCUG 56331, CIP 109827, CSUR P34, JCM 17323

literature

  • topic: Phylogeny
  • Pubmed-ID: 19628609
  • title: Mycobacterium marseillense sp. nov., Mycobacterium timonense sp. nov. and Mycobacterium bouchedurhonense sp. nov., members of the Mycobacterium avium complex.
  • authors: Ben Salah I, Cayrou C, Raoult D, Drancourt M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010637-0
  • year: 2009
  • mesh: Bacterial Proteins/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*classification/enzymology/genetics/*isolation & purification, Mycobacterium avium-intracellulare Infection/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Respiratory System/microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20669Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45439Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45439)
29309Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172572228776041
41220Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7613
60921Curators of the CCUGhttps://www.ccug.se/strain?id=56331Culture Collection University of Gothenburg (CCUG) (CCUG 56331)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68379Automatically annotated from API Coryne
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG

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