Strain identifier

BacDive ID: 8470

Type strain: Yes

Species: Mycobacterium hiberniae

Strain Designation: Hi 11, 14 403 0001

Strain history: CIP <- 2002, DSMZ <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 403 0001 <- ATCC <- J. Kadza, Borstel, Germany: strain Hi 11

NCBI tax ID(s): 29314 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11616

BacDive-ID: 8470

DSM-Number: 44241

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

description: Mycobacterium hiberniae Hi 11 is a mesophilic bacterium that was isolated from moss .

NCBI tax id

  • NCBI tax id: 29314
  • Matching level: species

strain history

@refhistory
11616<- A.F. Yassin <- ATCC <- J. Kazda, IR 103 [Hi 11]
67770CIP 104537 <-- DSM 44241 <-- A. F. Yassin <-- ATCC 49874 <-- J. Kazda Hi 11.
119888CIP <- 2002, DSMZ <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 403 0001 <- ATCC <- J. Kadza, Borstel, Germany: strain Hi 11

doi: 10.13145/bacdive8470.20230509.8.1

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 hiberniae
  • full scientific name: Mycobacterium hiberniae Kazda et al. 1993
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacter hiberniae

@ref: 11616

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium hiberniae

full scientific name: Mycobacterium hiberniae Kazda et al. 1993 emend. Nouioui et al. 2018

strain designation: Hi 11, 14 403 0001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.311
69480100positive
119888norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19855Ivory10-14 days5006
19855Ivory10-14 daysMB7H10
19855Ivory10-14 daysMB7H11

multimedia

  • @ref: 11616
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44241.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11616MIDDLEBROOK 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
19855MB7H10yesName: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
19855MB7H11yesName: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
198555006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
36391MEDIUM 55 - for Mycobacteriumyes
119888CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19855positiveoptimum37mesophilic
11616positivegrowth37mesophilic
36391positivegrowth37mesophilic
67770positivegrowth37mesophilic
119888positivegrowth22-37
119888nogrowth10psychrophilic
119888nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.959

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
11988817632nitrate+reduction
11988816301nitrite-reduction
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119888oxidase-
119888catalase+1.11.1.6
68382esterase lipase (C 8)+
68382lipase (C 14)-
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
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19855++++-+---+-++++++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControlAcid phosphatase
19855+++---------------
119888+++-+----+-+--+----+
11616-+/-+------+/----+/------+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11616+/-----+/-+/--------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119888---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
11616moss (Ctenidium molluscum)Ctenidium molluscumIrelandIRLEurope
54691Moss (Ctenidium molluscum)IrelandIRLEurope
67770Moss (Ctenidium molluscum)Ctenidium molluscum
119888Environment, SoilIrelandIRLEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Moss

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116161Risk group (German classification)
198551Risk group (German classification)
1198881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium hiberniae strain ATCC 49874 16S ribosomal RNA gene, partial sequenceJN571173479ena29314
20218M.hiberniae 16S rRNAX670961419ena29314
20218Mycobacterium hiberniae 16S ribosomal RNA gene, partial sequenceAY438069556ena29314

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacter hiberniae JCM 13571GCA_010729485completencbi29314
66792Mycobacterium hiberniae strain ATCC 4987429314.3wgspatric29314
66792Mycolicibacter hiberniae strain JCM 1357129314.9completepatric29314
66792Mycolicibacter hiberniae ATCC 498742865376297draftimg29314
67770Mycolicibacter hiberniae ATCC 49874GCA_002101655contigncbi29314
66792Mycolicibacter hiberniae DSM 44241GCA_025821605scaffoldncbi29314

GC content

  • @ref: 67770
  • GC-content: 68.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.752no
flagellatedno98.752no
gram-positiveyes93.052no
anaerobicno99.514no
aerobicyes93.649no
halophileno91.319no
spore-formingno89.189no
glucose-utilyes56.327no
thermophileno98.468no
glucose-fermentno91.554yes

External links

@ref: 11616

culture collection no.: CCUG 39184, JCM 13571, DSM 44241, ATCC 49874, CIP 104537, KCTC 19638

straininfo link

  • @ref: 77865
  • straininfo: 42729

literature

  • topic: Phylogeny
  • Pubmed-ID: 7684243
  • title: Mycobacterium hiberniae sp. nov.
  • authors: Kazda J, Cooney R, Monaghan M, Quinn PJ, Stackebrandt E, Dorsch M, Daffe M, Muller K, Cook BR, Tarnok ZS
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-43-2-352
  • year: 1993
  • mesh: Bacterial Typing Techniques, Biological Evolution, Classification, Cluster Analysis, DNA, Bacterial/genetics, Ireland, Molecular Sequence Data, Mycobacterium/*classification/growth & development/isolation & purification, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Plants/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11616Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44241)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44241
19855Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44241.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
36391Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16457
54691Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39184)https://www.ccug.se/strain?id=39184
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/
68369Automatically annotated from API 20NE
68379Automatically annotated from API Coryne
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
77865Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42729.1StrainInfo: A central database for resolving microbial strain identifiers
119888Curators of the CIPCollection of Institut Pasteur (CIP 104537)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104537