Strain identifier

BacDive ID: 8578

Type strain: Yes

Species: Mycobacterium noviomagense

Strain Designation: NLA000500338

Strain history: CIP <- 2007, J. van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000500338 <- Laurentius Hosp., Roermond, The Netherlands

NCBI tax ID(s): 459858 (species)

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General

@ref: 15422

BacDive-ID: 8578

DSM-Number: 45145

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped

description: Mycobacterium noviomagense NLA000500338 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from sputum.

NCBI tax id

  • NCBI tax id: 459858
  • Matching level: species

strain history

@refhistory
15422<- J. van Ingen; NLA000500338 <- Laurentius Hospital Roermond
67770CIP 109766 <-- J. van Ingen NLA000500338 <-- Laurentius Hosp., Roermond, Netherlands.
121365CIP <- 2007, J. van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000500338 <- Laurentius Hosp., Roermond, The Netherlands

doi: 10.13145/bacdive8578.20241212.9.2

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 noviomagense
  • full scientific name: Mycobacterium noviomagense van Ingen et al. 2009

@ref: 15422

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium noviomagense

full scientific name: Mycobacterium noviomagense van Ingen et al. 2009 emend. Nouioui et al. 2018

strain designation: NLA000500338

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
28917positiverod-shaped
121365no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15422MIDDLEBROOK 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
36086MEDIUM 55 - for Mycobacteriumyes
121365CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
15422positivegrowth37
36086positivegrowth30
67770positivegrowth37

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12136517632nitrate-reduction
12136516301nitrite-reduction

metabolite production

  • @ref: 121365
  • 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-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
121365oxidase-
121365catalase+1.11.1.6
121365urease-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
121365--++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15422sputumWeertNetherlandsNLDEurope
67770SputumNetherlandsNLDEurope
121365Human, SputumWeert, LimburgNetherlandsNLDEurope2005

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
15422yes, in single cases1Risk group (German classification)
1213651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15422
  • description: Mycobacterium noviomagense strain NLA000500338 16S ribosomal RNA gene, partial sequence
  • accession: EU239955
  • length: 1478
  • database: nuccore
  • NCBI tax ID: 459858

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium noviomagense JCM 16367GCA_010731635completencbi459858
66792Mycobacterium noviomagense strain DSM 45145459858.3wgspatric459858
66792Mycobacterium noviomagense strain JCM 16367459858.9completepatric459858
66792Mycobacterium noviomagense DSM 451452865568667draftimg459858
67770Mycobacterium noviomagense DSM 45145GCA_002086415contigncbi459858
66792Mycobacterium noviomagense DSM 45145GCA_025821305contigncbi459858

GC content

  • @ref: 67770
  • GC-content: 65.8
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.034no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.039no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes74.543no
69480spore-formingspore-formingAbility to form endo- or exosporesno64.42no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.285no
69480flagellatedmotile2+Ability to perform flagellated movementno88no

External links

@ref: 15422

culture collection no.: DSM 45145, CIP 109766, JCM 16367

straininfo link

  • @ref: 77962
  • straininfo: 362318

literature

  • topic: Phylogeny
  • Pubmed-ID: 19329618
  • title: Mycobacterium noviomagense sp. nov.; clinical relevance evaluated in 17 patients.
  • authors: van Ingen J, Boeree MJ, de Lange WC, de Haas PE, van der Zanden AG, Mijs W, Rigouts L, Dekhuijzen PN, van Soolingen D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.001511-0
  • year: 2009
  • mesh: Bacterial Proteins/genetics, Bacterial Typing Techniques, Chaperonin 60, Chaperonins/genetics, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Genotype, Humans, Molecular Sequence Data, Mycobacterium/*classification/genetics/*isolation & purification/physiology, Mycobacterium Infections/*microbiology, Netherlands, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15422Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45145)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45145
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
28917Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2535628776041
36086Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7545
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
77962Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362318.1StrainInfo: A central database for resolving microbial strain identifiers
121365Curators of the CIPCollection of Institut Pasteur (CIP 109766)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109766