Strain identifier

BacDive ID: 8496

Type strain: Yes

Species: Mycobacterium palustre

Strain Designation: E170-1, E846

Strain history: CIP <- 2002, DSMZ <- P. Torkko, National Public Health Inst., Helsinki, Finland: strain E846 <- E. Livanainen

NCBI tax ID(s): 153971 (species)

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General

@ref: 11768

BacDive-ID: 8496

DSM-Number: 44572

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

description: Mycobacterium palustre E170-1 is a mesophilic human pathogen that was isolated from a stream water.

NCBI tax id

  • NCBI tax id: 153971
  • Matching level: species

strain history

@refhistory
11768<- P. Torkko, Natl. Pub. Health Inst., Finland; E846 <- E. Iivanainen
121517CIP <- 2002, DSMZ <- P. Torkko, National Public Health Inst., Helsinki, Finland: strain E846 <- E. Livanainen

doi: 10.13145/bacdive8496.20230509.8.1

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 palustre
  • full scientific name: Mycobacterium palustre Torkko et al. 2002

@ref: 11768

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium palustre

full scientific name: Mycobacterium palustre Torkko et al. 2002 emend. Nouioui et al. 2018

strain designation: E170-1, E846

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.381
69480100positive
121517norod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11768MIDDLEBROOK 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
36372MEDIUM 93 - for Mycobacterium avium subsp. sylvaticumyesDistilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)
121517CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperaturerange
11768positivegrowth37mesophilic
36372positivegrowth37mesophilic
121517positivegrowth22-45
121517nogrowth10psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no90
69480no99.827

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121517606565hippurate-hydrolysis
12151717632nitrate-reduction
12151716301nitrite-reduction

metabolite production

  • @ref: 121517
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121517oxidase-
121517beta-galactosidase-3.2.1.23
121517catalase+1.11.1.6
121517gamma-glutamyltransferase+2.3.2.2
121517urease+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
121517--++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11768a stream waterKarstulaFinlandFINEurope
121517Environment, Stream waterFinlandFINEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11768yesyes2Risk group (German classification)
1215171Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium palustre strain DSM 44572 16S ribosomal RNA gene, partial sequenceAY943210515ena153971
11768Mycobacterium palustre 16S rRNA gene and internal transcribed spacer 1 (ITS1), strain E846AJ3086031823ena153971

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium palustre DSM 44572GCA_002101785contigncbi153971
66792Mycobacterium palustre strain DSM 44572153971.3wgspatric153971
66792Mycobacterium palustre DSM 445722865389921draftimg153971
66792Mycobacterium palustre DSM 44572GCA_025821485scaffoldncbi153971

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno94.756no
gram-positiveyes87.773no
anaerobicno98.951no
aerobicyes86.623no
halophileno94.611no
spore-formingno84.214no
thermophileno97.67no
glucose-utilyes66.11no
flagellatedno98.908no
glucose-fermentno91.004no

External links

@ref: 11768

culture collection no.: DSM 44572, ATCC BAA 377, CIP 107748

straininfo link

  • @ref: 77890
  • straininfo: 100789

literature

  • topic: Phylogeny
  • Pubmed-ID: 12361253
  • title: Mycobacterium palustre sp. nov., a potentially pathogenic, slowly growing mycobacterium isolated from clinical and veterinary specimens and from Finnish stream waters.
  • authors: Torkko P, Suomalainen S, Iivanainen E, Tortoli E, Suutari M, Seppanen J, Paulin L, Katila ML
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-5-1519
  • year: 2002
  • mesh: Animals, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Finland, Fresh Water/microbiology, Humans, Lipids/analysis, Lymphadenitis/microbiology, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification/pathogenicity, Mycobacterium Infections/microbiology, Phylogeny, Sequence Homology, Amino Acid, Sus scrofa
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11768Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44572)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44572
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
36372Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5218
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)
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
77890Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100789.1StrainInfo: A central database for resolving microbial strain identifiers
121517Curators of the CIPCollection of Institut Pasteur (CIP 107748)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107748