Strain identifier

BacDive ID: 8583

Type strain: Yes

Species: Mycobacterium mantenii

Strain Designation: 04-1474, NLA000401474

Strain history: CIP <- 2008, J. Van Inge, RIVM, Bilthoven, The Netherlands: strain NLA000401474 <- E. J. Kuijper, Leiden Univ., Leiden, The Netherlands

NCBI tax ID(s): 560555 (species)

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General

@ref: 15933

BacDive-ID: 8583

DSM-Number: 45255

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

description: Mycobacterium mantenii 04-1474 is a mesophilic, rod-shaped bacterium that was isolated from lymph node biopsy of a child.

NCBI tax id

  • NCBI tax id: 560555
  • Matching level: species

strain history

@refhistory
15933<- J. van Ingen; NLA000401474 <- E. J. Kuijper
67770CIP 109863 <-- J. van Ingen NLA000401474 (=04-1474) <-- E. J. Kuijper.
120782CIP <- 2008, J. Van Inge, RIVM, Bilthoven, The Netherlands: strain NLA000401474 <- E. J. Kuijper, Leiden Univ., Leiden, The Netherlands

doi: 10.13145/bacdive8583.20250331.9.3

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

@ref: 15933

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium mantenii

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

strain designation: 04-1474, NLA000401474

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
29294rod-shaped
120782no
125439positive94

pigmentation

  • @ref: 29294
  • production: yes

multimedia

  • @ref: 15933
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45255.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15933MIDDLEBROOK 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
37864MEDIUM 55 - for Mycobacteriumyes
120782CIP Medium 750yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=750
120782CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
15933positivegrowth37
29294positivegrowth25-45
29294positiveoptimum36
37864positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99.6

spore formation

  • @ref: 29294
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12078217632nitrate-reduction
12078216301nitrite-reduction

metabolite production

  • @ref: 120782
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29294catalase+1.11.1.6
29294urease+3.5.1.5
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 lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
120782oxidase-
120782catalase+1.11.1.6
120782urease+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
120782-+-+-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15933lymph node biopsy of a childLeidenNetherlandsNLDEurope
67770Human, lymph node biopsy specimenLeidenNetherlandsNLDEurope
120782Human, Lymph node biopsyLeidenNetherlandsNLDEurope2004

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Biopsy
#Infection#Patient
#Host Body-Site#Organ#Lymph node
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_475.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_475&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: FJ042897
  • Sequence Identity:
  • Total samples: 2232
  • soil counts: 1602
  • aquatic counts: 300
  • animal counts: 128
  • plant counts: 202

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159332Risk group (German classification)
1207821Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15933Mycobacterium mantenii strain NLA000401474 16S ribosomal RNA gene, partial sequenceFJ0428971471nuccore560555
67770Mycobacterium mantenii strain NLA000401474 16S-23S ribosomal RNA intergenic spacer, partial sequenceFJ232522281nuccore560555

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium mantenii JCM 18113GCA_010731775completencbi560555
66792Mycobacterium mantenii strain DSM 45255560555.3wgspatric560555
66792Mycobacterium mantenii strain JCM 18113560555.10completepatric560555
67770Mycobacterium mantenii DSM 45255GCA_002086335contigncbi560555
66792Mycobacterium mantenii DSM 45255GCA_025822645scaffoldncbi560555

GC content

  • @ref: 67770
  • GC-content: 66.9
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.36no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.492no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.685no
125438spore-formingspore-formingAbility to form endo- or exosporesno63.986yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.3yes
125438motile2+flagellatedAbility to perform flagellated movementno86no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno65.8
125439BacteriaNetmotilityAbility to perform movementno77.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive94
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.6

External links

@ref: 15933

culture collection no.: DSM 45255, CIP 109863, JCM 18113

straininfo link

  • @ref: 77967
  • straininfo: 364721

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625425
  • title: Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species.
  • authors: van Ingen J, Lindeboom JA, Hartwig NG, de Zwaan R, Tortoli E, Dekhuijzen PN, Boeree MJ, van Soolingen D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010405-0
  • year: 2009
  • mesh: Aged, Aged, 80 and over, Bacterial Proteins/genetics, Child, Preschool, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Female, Humans, Infant, Lymph Nodes/microbiology, Male, Molecular Sequence Data, Mycobacterium/classification/*isolation & purification/metabolism/pathogenicity, Mycobacterium Infections/*microbiology, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15933Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45255)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45255
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
29294Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2571028776041
37864Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7655
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
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
77967Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364721.1StrainInfo: A central database for resolving microbial strain identifiers
120782Curators of the CIPCollection of Institut Pasteur (CIP 109863)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109863
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1