Strain identifier

BacDive ID: 8488

Type strain: Yes

Species: Mycobacterium holsaticum

Strain Designation: 1406

Strain history: CIP <- 2002, CCUG <- E. Richter, Borstel, Germany: strain 1406

NCBI tax ID(s): 1226752 (strain), 152142 (species)

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General

@ref: 11804

BacDive-ID: 8488

DSM-Number: 44478

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Mycobacterium holsaticum 1406 is an aerobe, mesophilic human pathogen that was isolated from human sputum.

NCBI tax id

NCBI tax idMatching level
152142species
1226752strain

strain history

@refhistory
11804<- E. Richter, Research Center, Borstel; 1406
67770CCUG 46266 <-- E. Richter 1406.
119933CIP <- 2002, CCUG <- E. Richter, Borstel, Germany: strain 1406

doi: 10.13145/bacdive8488.20230509.8.1

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 holsaticum
  • full scientific name: Mycobacterium holsaticum Richter et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium holsaticum

@ref: 11804

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium holsaticum

full scientific name: Mycobacterium holsaticum Richter et al. 2002

strain designation: 1406

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.562
69480100positive
119933norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20061Rapeseed yellow (1021)10-14 days5006
20061Rapeseed yellow (1021)10-14 daysMB7H10
20061Rapeseed yellow (1021)10-14 daysMB7H11
57133>3 days

multimedia

  • @ref: 11804
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44478.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11804MIDDLEBROOK 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
20061MB7H10yesName: 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
20061MB7H11yesName: 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
200615006yesMedium: 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
36333MEDIUM 55 - for Mycobacteriumyes
119933CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20061positiveoptimum37mesophilic
11804positivegrowth37mesophilic
36333positivegrowth30mesophilic
57133positivegrowth31mesophilic
67770positivegrowth37mesophilic
119933positivegrowth22-37
119933nogrowth10psychrophilic
119933nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57133aerobe
119933obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.98

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119933606565hippurate+hydrolysis
11993317632nitrate+reduction
11993316301nitrite-reduction
11993317632nitrate-respiration
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: 119933
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
119933oxidase-
119933beta-galactosidase+3.2.1.23
119933gelatinase-
119933amylase-
119933DNase-
119933caseinase-3.4.21.50
119933catalase+1.11.1.6
119933tween esterase-
119933gamma-glutamyltransferase-2.3.2.2
119933lecithinase+
119933lipase-
119933protease+
119933urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20061++-+--+--+-++++++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20061-++++++++++---+----
119933-++-+----++---+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
11804human sputumGermanyDEUEurope
57133Human sputumGermanyDEUEurope1998Borstel
67770SputumGermanyDEUEurope
119933Human, SputumGermanyDEUEurope1998

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11804yes, in single cases1Risk group (German classification)
200611German classification
1199331Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium holsaticum 16S ribosomal RNA gene, partial sequenceAY438070542ena1226752
11804Mycobacterium holsaticum 16S rRNA gene, strain 1406AJ3104671526ena152142

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium holsaticum DSM 44478 = JCM 12374GCA_019645835completencbi1226752
66792Mycolicibacterium holsaticum strain JCM 12374152142.10completepatric152142
66792Mycolicibacterium holsaticum DSM 44478 = JCM 12374GCA_022558565completencbi1226752
66792Mycolicibacterium holsaticum DSM 44478 = JCM 12374GCA_027886245contigncbi1226752

GC content

@refGC-contentmethod
1180468.4
6777068.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno85no
flagellatedno99.007no
gram-positiveyes90.575no
anaerobicno99.499no
aerobicyes91.496yes
halophileno81.762no
spore-formingno81.492no
motileno93.817no
glucose-fermentno88.772yes
thermophileno97.738yes
glucose-utilyes83.315no

External links

@ref: 11804

culture collection no.: DSM 44478, CCUG 46266, CIP 107726, ATCC BAA 771, JCM 12374, CIP 107786

straininfo link

  • @ref: 77882
  • straininfo: 100512

literature

  • topic: Phylogeny
  • Pubmed-ID: 12508858
  • title: Mycobacterium holsaticum sp. nov.
  • authors: Richter E, Niemann S, Gloeckner FO, Pfyffer GE, Rusch-Gerdes S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-6-1991
  • year: 2002
  • mesh: *Bacterial Proteins, Base Composition, Base Sequence, Chaperonin 60, Chaperonins/genetics, DNA, Bacterial/chemistry/genetics, DNA, Intergenic/genetics, DNA, Ribosomal/genetics, Genes, Bacterial, Humans, Lipids/analysis, Molecular Sequence Data, Mycobacterium/*classification/genetics/*isolation & purification/metabolism, Mycobacterium tuberculosis/classification/genetics, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11804Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44478)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44478
20061Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44478.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
36333Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5259
57133Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46266)https://www.ccug.se/strain?id=46266
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
77882Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100512.1StrainInfo: A central database for resolving microbial strain identifiers
119933Curators of the CIPCollection of Institut Pasteur (CIP 107786)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107786