Strain identifier

BacDive ID: 158301

Type strain: Yes

Species: Lebetimonas natsushimae

Strain Designation: HS1857

Strain history: <- S. Nakagawa, Kyoto University, Kyoto, Japan; HS1857

NCBI tax ID(s): 1936991 (species)

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General

@ref: 64962

BacDive-ID: 158301

DSM-Number: 104102

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

description: Lebetimonas natsushimae HS1857 is a thermophilic bacterium that was isolated from deep-sea hydrothermal vent polychaetes nest , 1604 m depth.

NCBI tax id

  • NCBI tax id: 1936991
  • Matching level: species

strain history

  • @ref: 64962
  • history: <- S. Nakagawa, Kyoto University, Kyoto, Japan; HS1857

doi: 10.13145/bacdive158301.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Nautiliales
  • family: Nautiliaceae
  • genus: Lebetimonas
  • species: Lebetimonas natsushimae
  • full scientific name: Lebetimonas natsushimae Nagata et al. 2017

@ref: 64962

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Nautiliales

family: Nautiliaceae

genus: Lebetimonas

species: Lebetimonas natsushimae

full scientific name: Lebetimonas natsushimae Nagata et al. 2017

strain designation: HS1857

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 64962
  • name: PALAEOCOCCUS MEDIUM (DSMZ Medium 377a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/377a
  • composition: Name: PALAEOCOCCUS MEDIUM (DSMZ Medium 377a) Composition: Sulfur 29.2398 g/l Peptone 4.87329 g/l MgCl2 x 6 H2O 2.68031 g/l Yeast extract 0.974659 g/l KH2PO4 0.487329 g/l Na2S x 9 H2O 0.487329 g/l KCl 0.321637 g/l NaBr 0.0487329 g/l MgSO4 x 7 H2O 0.0292398 g/l Nitrilotriacetic acid 0.0146199 g/l (NH4)2SO4 0.00974659 g/l NaCl 0.00974659 g/l SrCl2 x 6 H2O 0.00682261 g/l Citric acid 0.00487329 g/l MnSO4 x H2O 0.00487329 g/l ZnSO4 x 7 H2O 0.00175439 g/l CoSO4 x 7 H2O 0.00175439 g/l FeSO4 x 7 H2O 0.000974659 g/l CaCl2 x 2 H2O 0.000974659 g/l Sodium resazurin 0.000487329 g/l NiCl2 x 6 H2O 0.000292398 g/l AlK(SO4)2 x 12 H2O 0.000194932 g/l H3BO3 9.74659e-05 g/l CuSO4 x 5 H2O 9.74659e-05 g/l Pyridoxine hydrochloride 9.74659e-05 g/l Na2MoO4 x 2 H2O 9.74659e-05 g/l (DL)-alpha-Lipoic acid 4.87329e-05 g/l p-Aminobenzoic acid 4.87329e-05 g/l Calcium D-(+)-pantothenate 4.87329e-05 g/l Nicotinic acid 4.87329e-05 g/l Riboflavin 4.87329e-05 g/l Thiamine HCl 4.87329e-05 g/l KI 4.87329e-05 g/l Folic acid 1.94932e-05 g/l Biotin 1.94932e-05 g/l Na2WO4 x 2 H2O 3.89864e-06 g/l Na2SeO3 x 5 H2O 2.92398e-06 g/l Vitamin B12 9.74659e-07 g/l Distilled water

culture temp

  • @ref: 64962
  • growth: positive
  • type: growth
  • temperature: 55
  • range: thermophilic

Isolation, sampling and environmental information

isolation

  • @ref: 64962
  • sample type: deep-sea hydrothermal vent polychaetes nest (Paralivinella sp.), 1604 m depth
  • geographic location: Pacific, Mid-Okinawa Trough, Sakai field, Noho site
  • country: Japan
  • origin.country: JPN
  • continent: Asia
  • latitude: 27.5167
  • longitude: 126.983

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Annelida
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine

Safety information

risk assessment

  • @ref: 64962
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64962
  • description: Lebetimonas natsushimae gene for 16S ribosomal RNA, partial sequence
  • accession: LC210765
  • length: 1507
  • database: ena
  • NCBI tax ID: 1936991

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lebetimonas natsushimae HS1857GCA_002335445contigncbi1936991
66792Lebetimonas natsushimae HS18572788500348draftimg1936991

GC content

  • @ref: 64962
  • GC-content: 33.2

External links

@ref: 64962

culture collection no.: DSM 104102, NBRC 112478

straininfo link

  • @ref: 111117
  • straininfo: 399916

literature

  • topic: Phylogeny
  • Pubmed-ID: 28690052
  • title: Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough.
  • authors: Nagata R, Takaki Y, Tame A, Nunoura T, Muto H, Mino S, Sawayama S, Takai K, Nakagawa S
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2017.06.002
  • year: 2017
  • mesh: Bacteria, Anaerobic, Base Composition, Epsilonproteobacteria/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Genome, Bacterial, Hydrothermal Vents/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64962Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104102Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104102)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
111117Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399916.1