Strain identifier

BacDive ID: 132248

Type strain: Yes

Species: Shimia sagamensis

Strain history: Y. Nogi; JAMSTEC, Japan; JAMH 011.

NCBI tax ID(s): 1566352 (species)

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General

@ref: 24037

BacDive-ID: 132248

DSM-Number: 29734

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

description: Shimia sagamensis DSM 29734 is a mesophilic bacterium that was isolated from sediment of deep-sea cold-seep.

NCBI tax id

  • NCBI tax id: 1566352
  • Matching level: species

strain history

@refhistory
24037<- Y. Nogi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Research and Development Center for Marine Biosciences, Yokosuka; JAMH 011
67770Y. Nogi; JAMSTEC, Japan; JAMH 011.

doi: 10.13145/bacdive132248.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Shimia
  • species: Shimia sagamensis
  • full scientific name: Shimia sagamensis Nogi et al. 2015

@ref: 24037

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Shimia

species: Shimia sagamensis

full scientific name: Shimia sagamensis Nogi et al. 2015

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 24037
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24037positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
24037-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24037sediment of deep-sea cold-seepSagami-Bay off Hatsushima (35° 009' N 139° 136' E [sic]) from a depth of 1097 mJapanJPNAsia
67770Sediment from the deep-sea cold-seep area off HatsushimaSagami BayJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 24037
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24037
  • description: Shimia sagamensis gene for 16S ribosomal RNA, partial sequence
  • accession: LC008540
  • length: 1395
  • database: ena
  • NCBI tax ID: 1566352

Genome sequences

  • @ref: 66792
  • description: Shimia sagamensis DSM 29734
  • accession: 2724679805
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1566352

GC content

  • @ref: 24037
  • GC-content: 57.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24037

culture collection no.: DSM 29734, JCM 30583, JAMH 011

straininfo link

  • @ref: 90598
  • straininfo: 397465

literature

  • topic: Phylogeny
  • Pubmed-ID: 25977284
  • title: Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment.
  • authors: Nogi Y, Mori K, Uchida H, Hatada Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000333
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, Cold Temperature, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Genetics

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
24037Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29734Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29734)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
90598Reimer, 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-ID397465.1