Strain identifier

BacDive ID: 8485

Type strain: Yes

Species: Mycobacterium heidelbergense

Strain Designation: 2554/91

Strain history: CIP <- 1998, ATCC <- W.H. Haas: strain 2554/91

NCBI tax ID(s): 53376 (species)

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General

@ref: 11797

BacDive-ID: 8485

DSM-Number: 44471

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Mycobacterium heidelbergense 2554/91 is a facultative anaerobe, mesophilic bacterium that was isolated from child .

NCBI tax id

  • NCBI tax id: 53376
  • Matching level: species

strain history

@refhistory
11797<- W. H. Haas, Univ. Heidelberg; 2554/91
67770CIP 105424 <-- ATCC 51253 <-- W. H. Haas 2554/91.
119856CIP <- 1998, ATCC <- W.H. Haas: strain 2554/91

doi: 10.13145/bacdive8485.20230509.8.1

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 heidelbergense
  • full scientific name: Mycobacterium heidelbergense Haas et al. 1998

@ref: 11797

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium heidelbergense

full scientific name: Mycobacterium heidelbergense Haas et al. 1998 emend. Nouioui et al. 2018

strain designation: 2554/91

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.054
69480100positive
119856norod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11797MIDDLEBROOK 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
11797LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
36315MEDIUM 55 - for Mycobacteriumyes
119856CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
11797positivegrowth37mesophilic
36315positivegrowth37mesophilic
67770positivegrowth37mesophilic
119856positivegrowth30-37mesophilic
119856nogrowth10psychrophilic
119856nogrowth22psychrophilic
119856nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119856
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.731

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119856606565hippurate-hydrolysis
11985617632nitrate-reduction
11985616301nitrite-reduction
11985617632nitrate+respiration

metabolite production

  • @ref: 119856
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119856oxidase-
119856beta-galactosidase-3.2.1.23
119856gelatinase-
119856catalase-1.11.1.6
119856gamma-glutamyltransferase-2.3.2.2
119856urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119856--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11797child (lymph node)GermanyDEUEurope
67770Cervical lymph nodeGermanyDEUEuropeHeidelberg
119856Human, Lymph node (child)GermanyDEUEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117972Risk group (German classification)
1198561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium heidelbergense 16S rRNA geneAJ0006841445ena53376
20218M.heidelbergense 16S rRNAX709601446ena53376
20218Mycobacterium heidelbergense strain CIP 105424 16S ribosomal RNA gene, partial sequenceAF547935542ena53376
20218Mycobacterium heidelbergense strain DSM 44471 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM022203283ena53376

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium heidelbergense JCM 14842GCA_010730745completencbi53376
66792Mycobacterium heidelbergense strain DSM 4447153376.3wgspatric53376
66792Mycobacterium heidelbergense strain JCM 1484253376.9completepatric53376
66792Mycobacterium heidelbergense DSM 444712865543863draftimg53376
67770Mycobacterium heidelbergense DSM 44471GCA_002086215contigncbi53376
66792Mycobacterium heidelbergense DSM 44471GCA_025821945scaffoldncbi53376

GC content

  • @ref: 67770
  • GC-content: 68
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileno95.299no
flagellatedno98.795no
gram-positiveyes86.435no
anaerobicno99.149no
aerobicyes82.791no
halophileno92.624no
spore-formingno86.508no
glucose-utilyes63.349no
thermophileno96.283yes
glucose-fermentno89.492no

External links

@ref: 11797

culture collection no.: DSM 44471, ATCC 51253, CIP 105424, JCM 14842

straininfo link

  • @ref: 77879
  • straininfo: 42879

literature

  • topic: Phylogeny
  • Pubmed-ID: 9399520
  • title: A new agent of mycobacterial lymphadenitis in children: Mycobacterium heidelbergense sp. nov.
  • authors: Haas WH, Butler WR, Kirschner P, Plikaytis BB, Coyle MB, Amthor B, Steigerwalt AG, Brenner DJ, Salfinger M, Crawford JT, Bottger EC, Bremer HJ
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.35.12.3203-3209.1997
  • year: 1997
  • mesh: Antitubercular Agents/pharmacology, Base Sequence, Child, Child, Preschool, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Drug Resistance, Microbial, Genes, Bacterial, Humans, Isoniazid/pharmacology, Lymphadenitis/*etiology/*microbiology, Molecular Sequence Data, Mycobacterium/classification/genetics/*pathogenicity, Mycobacterium Infections/*etiology/*microbiology, Neck, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11797Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44471)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44471
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
36315Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17442
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
77879Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42879.1StrainInfo: A central database for resolving microbial strain identifiers
119856Curators of the CIPCollection of Institut Pasteur (CIP 105424)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105424