Strain identifier

BacDive ID: 8522

Type strain: Yes

Species: Mycobacterium psychrotolerans

Strain history: CIP <- 2004, M. E. Trujillo, Salamanca Univ., Salamanca, Spain: strain WA101

NCBI tax ID(s): 216929 (species)

« back to strain detail view
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: 11888

BacDive-ID: 8522

DSM-Number: 44697

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

description: Mycobacterium psychrotolerans DSM 44697 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from water pond near an uranium mine.

NCBI tax id

  • NCBI tax id: 216929
  • Matching level: species

strain history

@refhistory
11888<- M. E. Trujillo; WA101
363422004, M. E. Trujillo, Salamanca Univ., Salamanca, Spain: strain WA101
67770LMG 21953 <-- M. E. Trujillo WA101.
122036CIP <- 2004, M. E. Trujillo, Salamanca Univ., Salamanca, Spain: strain WA101

doi: 10.13145/bacdive8522.20230509.8.1

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 psychrotolerans
  • full scientific name: Mycobacterium psychrotolerans Trujillo et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium psychrotolerans

@ref: 11888

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium psychrotolerans

full scientific name: Mycobacterium psychrotolerans Trujillo et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30098positiverod-shapedno
69480positive100
122036rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20096Yellow orange (2000)10-14 days5006
20096Yellow orange (2000)10-14 daysMB7H10
20096Yellow orange (2000)10-14 daysMB7H11

pigmentation

  • @ref: 30098
  • production: yes

multimedia

  • @ref: 11888
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44697.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11888MIDDLEBROOK 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
20096MB7H10yesName: 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
20096MB7H11yesName: 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
200965006yesMedium: 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
36342MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
122036CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
20096positiveoptimum37mesophilic
11888positivegrowth37mesophilic
30098positivegrowth04-37
36342positivegrowth30mesophilic
67770positivegrowth28mesophilic
122036positivegrowth22-30
122036nogrowth10psychrophilic
122036nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122036
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
30098no
69481no100
69480no99.77

halophily

  • @ref: 30098
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 7 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3009815963ribitol+carbon source
3009828757fructose+carbon source
3009824265gluconate+carbon source
3009817234glucose+carbon source
3009817754glycerol+carbon source
3009825115malate+carbon source
3009829864mannitol+carbon source
3009837684mannose+carbon source
30098506227N-acetylglucosamine+carbon source
3009830911sorbitol+carbon source
3009817992sucrose+carbon source
3009827082trehalose+carbon source
3009818222xylose+carbon source
3009817632nitrate+reduction
122036606565hippurate-hydrolysis
12203617632nitrate+reduction
12203616301nitrite-reduction
12203617632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 122036
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122036
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30098acid phosphatase+3.1.3.2
30098catalase+1.11.1.6
30098urease+3.5.1.5
68379gelatinase-
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
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
122036oxidase-
122036beta-galactosidase-3.2.1.23
122036gelatinase-
122036amylase+
122036DNase-
122036caseinase-3.4.21.50
122036catalase+1.11.1.6
122036tween esterase+
122036gamma-glutamyltransferase+2.3.2.2
122036lecithinase-
122036lipase+
122036protease+
122036urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20096-+++/---+--+/--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20096++++++++-++---++---
122036+++-+-++-++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122036-+-------------------+-----+----+----+--+--------+----------+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11888water pond near an uranium mineSalamancaSpainESPEurope
67770Pond water near a uranium mineSalamancaSpainESPEurope
122036Environment, Water collected in a pondSalamancaSpainESPEurope2002

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Aquatic#Pond (small)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118881Risk group (German classification)
200961German classification
1220361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium psychrotolerans strain DSM 44697 16S ribosomal RNA gene, partial sequenceAY943215484ena216929
11888Mycobacterium psychrotolerans 16S rRNA gene, type strain WA101TAJ5348861517ena216929

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium psychrotolerans JCM 13323GCA_010729305completencbi216929
66792Mycolicibacterium psychrotolerans strain JCM 13323216929.8completepatric216929
66792Mycolicibacterium psychrotolerans DSM 44697GCA_025821805scaffoldncbi216929

GC content

@refGC-contentmethod
1188864
6777064thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.403yes
flagellatedno98.487yes
gram-positiveyes90.163yes
anaerobicno99.53no
aerobicyes92.48no
halophileno92.012yes
spore-formingno88.447yes
thermophileno99.15yes
glucose-utilyes89.244yes
glucose-fermentno90.074yes

External links

@ref: 11888

culture collection no.: DSM 44697, CIP 108547, LMG 21953, WA 101, JCM 13323

straininfo link

  • @ref: 77911
  • straininfo: 99940

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388695
  • title: Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine.
  • authors: Trujillo ME, Velazquez E, Kroppenstedt RM, Schumann P, Rivas R, Mateos PF, Martinez-Molina E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02938-0
  • year: 2004
  • mesh: Anti-Bacterial Agents/pharmacology, Carbohydrate Metabolism, Citric Acid/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Drug Resistance, Multiple, Bacterial, Enzymes/analysis, Fatty Acids/analysis, Genes, rRNA, Mining, Molecular Sequence Data, Mycobacterium/*classification/genetics/*isolation & purification/physiology, Mycolic Acids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature, Uranium, *Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11888Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44697)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44697
20096Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44697.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
30098Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126454
36342Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6181
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/
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
77911Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99940.1StrainInfo: A central database for resolving microbial strain identifiers
122036Curators of the CIPCollection of Institut Pasteur (CIP 108547)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108547