Strain identifier

BacDive ID: 8535

Type strain: Yes

Species: Mycobacterium pyrenivorans

Strain Designation: 17A3, ID 705-01

Strain history: CIP <- 2004, DSMZ <- I. Schuphan, RWTH, Aachen, Germany: strain 17A3

NCBI tax ID(s): 1305860 (strain), 187102 (species)

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General

@ref: 11920

BacDive-ID: 8535

DSM-Number: 44605

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

description: Mycobacterium pyrenivorans 17A3 is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1305860strain
187102species

strain history

@refhistory
11920<- I. Schuphan, RWTH, Aachen; 17A3
67770NRRL B-24349 <-- DSM 44605 <-- I. Schuphan 17A3.
122087CIP <- 2004, DSMZ <- I. Schuphan, RWTH, Aachen, Germany: strain 17A3

doi: 10.13145/bacdive8535.20241212.9.2

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 pyrenivorans
  • full scientific name: Mycobacterium pyrenivorans Derz et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium pyrenivorans

@ref: 11920

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium pyrenivorans

full scientific name: Mycobacterium pyrenivorans Derz et al. 2004

strain designation: 17A3, ID 705-01

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidence
122087rod-shapedno
69480no94.5

multimedia

  • @ref: 11920
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44605.jpg
  • caption: Medium 645 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11920MIDDLEBROOK 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
36343MEDIUM 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)
122087CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperature
11920positivegrowth28
36343positivegrowth30
67770positivegrowth28
122087positivegrowth22-30
122087nogrowth10
122087nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 122087
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
122087606565hippurate-hydrolysis
12208717632nitrate+reduction
12208716301nitrite-reduction
12208717632nitrate-respiration

antibiotic resistance

  • @ref: 122087
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122087
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122087oxidase-
122087beta-galactosidase-3.2.1.23
122087gelatinase-
122087amylase+
122087DNase-
122087caseinase-3.4.21.50
122087catalase+1.11.1.6
122087tween esterase+
122087gamma-glutamyltransferase+2.3.2.2
122087lecithinase-
122087lipase-
122087protease+
122087urease+3.5.1.5
68382alpha-chymotrypsin-3.4.21.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122087-+++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122087-+-----+------------------------++---------------+----------+-------------------+---+---+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11920soilÜbach-PalenbergGermanyDEUEurope
67770Contaminated soil of a former coking plantÜbach-PalenbergGermanyDEUEurope
122087Environment, SoilGermanyDEUEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119201Risk group (German classification)
1220871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium pyrenivorans strain DSM 44605 16S ribosomal RNA gene, partial sequenceDQ124113536nuccore187102
11920Mycobacterium sp. DSM 44605 16S rRNA gene, strain DSM 44605AJ4313711481nuccore187102

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium pyrenivorans JCM 15927GCA_001314105contigncbi1305860
66792Mycolicibacterium pyrenivorans JCM 159271305860.4wgspatric1305860
66792Mycolicibacterium pyrenivorans JCM 159272734481971draftimg1305860
66792Mycolicibacterium pyrenivorans DSM 44605GCA_025821625scaffoldncbi187102

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno80no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes79.606no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.006yes
69480spore-formingspore-formingAbility to form endo- or exosporesno71.137no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.66yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.742yes
69480flagellatedmotile2+Ability to perform flagellated movementno94.5no

External links

@ref: 11920

culture collection no.: DSM 44605, CIP 108596, NRRL B-24349, JCM 15927, NRRL B-24244

straininfo link

  • @ref: 77921
  • straininfo: 362273

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545477Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species.Derz K, Klinner U, Schuphan I, Stackebrandt E, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/ijs.0.03003-02004Bacterial Typing Techniques, Biodegradation, Environmental, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, DNA, Ribosomal Spacer/analysis, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Germany, Molecular Sequence Data, Mycobacterium/*classification/genetics/*isolation & purification/metabolism, Mycolic Acids/analysis/isolation & purification, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology
Phylogeny34878372Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species.Cheng Y, Lei W, Wang X, Tian Z, Liu H, Yang J, Lu S, Lai XH, Pu J, Huang Y, Zhang S, Yang C, Lian X, Bai Y, Wan K, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0050192021Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Feces/microbiology, Mycobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11920Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44605)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44605
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
36343Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6243
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
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
77921Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362273.1StrainInfo: A central database for resolving microbial strain identifiers
122087Curators of the CIPCollection of Institut Pasteur (CIP 108596)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108596