Strain identifier

BacDive ID: 6806

Type strain: Yes

Species: Leptospira broomii

Strain Designation: 5399

Strain history: <- R. Galloway, CDC; strain 5399 {2008} <- P. N. Levett

NCBI tax ID(s): 301541 (species)

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General

@ref: 15766

BacDive-ID: 6806

DSM-Number: 21534

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

description: Leptospira broomii 5399 is a mesophilic bacterium that was isolated from human patient with leptospirosis.

NCBI tax id

  • NCBI tax id: 301541
  • Matching level: species

strain history

  • @ref: 15766
  • history: <- R. Galloway, CDC; strain 5399 {2008} <- P. N. Levett

doi: 10.13145/bacdive6806.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Leptospirales
  • family: Leptospiraceae
  • genus: Leptospira
  • species: Leptospira broomii
  • full scientific name: Leptospira broomii Levett et al. 2006

@ref: 15766

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Leptospiraceae

genus: Leptospira

species: Leptospira broomii

full scientific name: Leptospira broomii Levett et al. 2006

strain designation: 5399

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 15766
  • name: LEPTOSPIRA-MEDIUM (DSMZ Medium 1113)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1113
  • composition: Name: LEPTOSPIRA-MEDIUM (DSMZ Medium 1113) Composition: Leptospira Medium Base EMJH 2.3 g/l Agarose 1.5 g/l Leptospira Enrichment EMJH Distilled water

culture temp

  • @ref: 15766
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Isolation, sampling and environmental information

isolation

  • @ref: 15766
  • sample type: human patient with leptospirosis
  • country: Denmark
  • origin.country: DNK
  • continent: Europe

isolation source categories

Cat1Cat2
#Infection#Disease
#Infection#Patient
#Host#Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_2020.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_26;96_1119;97_1314;98_1583;99_2020&stattab=map
  • Last taxonomy: Leptospira
  • 16S sequence: AY796065
  • Sequence Identity:
  • Total samples: 3007
  • soil counts: 169
  • aquatic counts: 1106
  • animal counts: 1640
  • plant counts: 92

Safety information

risk assessment

  • @ref: 15766
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15766
  • description: Leptospira broomii strain 5399 16S ribosomal RNA gene, partial sequence
  • accession: AY796065
  • length: 1431
  • database: ena
  • NCBI tax ID: 301541

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leptospira broomii serovar Hurstbridge str. 5399GCA_000243715contigncbi1049789
66792Leptospira broomii serovar Hurstbridge str. 53991049789.4wgspatric1049789
66792Leptospira broomii 53992541047153draftimg1049789

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.808no
flagellatedno69.123no
gram-positiveno97.717no
anaerobicno97.175no
aerobicyes81.238no
halophileno93.725no
spore-formingno91.392no
thermophileno95.195no
glucose-utilyes60.036no
glucose-fermentno88.622no

External links

@ref: 15766

culture collection no.: DSM 21534, ATCC BAA 1107, KIT 5399

straininfo link

  • @ref: 76274
  • straininfo: 290984

literature

  • topic: Phylogeny
  • Pubmed-ID: 16514048
  • title: Leptospira broomii sp. nov., isolated from humans with leptospirosis.
  • authors: Levett PN, Morey RE, Galloway RL, Steigerwalt AG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63783-0
  • year: 2006
  • mesh: Base Composition, DNA, Ribosomal/chemistry, Electrophoresis, Gel, Pulsed-Field, Humans, Leptospira/*classification/*isolation & purification, Leptospirosis/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitle
15766Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21534)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21534
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
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)
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76274Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290984.1StrainInfo: A central database for resolving microbial strain identifiers