Strain identifier

BacDive ID: 134340

Type strain: Yes

Species: Natrinema gari

Strain Designation: HIS40-3

Strain history: W. Visessanguan HIS40-3.

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General

@ref: 32533

BacDive-ID: 134340

keywords: genome sequence, 16S sequence, Archaea, aerobe, Gram-positive, motile, rod-shaped

description: Natrinema gari HIS40-3 is an aerobe, Gram-positive, motile archaeon that was isolated from anchovy fish sauce.

NCBI tax id

NCBI tax idMatching level
419186species
1230459strain

strain history

  • @ref: 67770
  • history: W. Visessanguan HIS40-3.

doi: 10.13145/bacdive134340.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Natrialbales
  • family: Natrialbaceae
  • genus: Natrinema
  • species: Natrinema gari
  • full scientific name: Natrinema gari Tapingkae et al. 2008

@ref: 32533

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Natrialbales

family: Natrialbaceae

genus: Natrinema

species: Natrinema gari

strain designation: HIS40-3

type strain: yes

Morphology

cell morphology

  • @ref: 32533
  • gram stain: positive
  • cell length: 02-03 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 32533
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32533positivegrowth20-60
32533positiveoptimum37-40
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32533positivegrowth5.5-8.5alkaliphile
32533positiveoptimum6-6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32533
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32533
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32533NaClpositivegrowth9.86-19.72 %
32533NaClpositiveoptimum15.08-19.72 %

observation

@refobservation
32533aggregates in chains
67770quinones: MK-8, MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3253322599arabinose+carbon source
3253317234glucose+carbon source
3253317754glycerol+carbon source

enzymes

@refvalueactivityec
32533catalase+1.11.1.6
32533cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
32533anchovy fish sauce
67770Anchovy fish sauce (nam-pla) produced in Thailand

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_187636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17652;96_69120;97_89802;98_122117;99_187636&stattab=map
  • Last taxonomy: Natrinema
  • 16S sequence: AB289741
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Sequence information

16S sequences

  • @ref: 32533
  • description: Natrinema gari gene for 16S ribosomal RNA, partial sequence, strain: HIS40-3
  • accession: AB289741
  • length: 1405
  • database: nuccore
  • NCBI tax ID: 1230459

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Natrinema gari JCM 146632554235484draftimg1230459
67770Natrinema gari JCM 14663GCA_000337175contigncbi1230459
66792Natrinema gari JCM 146631230459.4wgspatric1230459

GC content

@refGC-contentmethod
3253364-65.4
6777065.4high performance liquid chromatography (HPLC)

External links

@ref: 32533

culture collection no.: BCC 24370, JCM 14663, PCU 303

literature

  • topic: Phylogeny
  • Pubmed-ID: 18842859
  • title: Natrinema gari sp. nov., a halophilic archaeon isolated from fish sauce in Thailand.
  • authors: Tapingkae W, Tanasupawat S, Itoh T, Parkin KL, Benjakul S, Visessanguan W, Valyasevi R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65644-0
  • year: 2008
  • mesh: Base Composition, DNA, Archaeal/genetics, Fish Products/*microbiology, Food Microbiology, Genes, Archaeal, Genes, rRNA, Glycolipids/chemistry, Halobacteriaceae/chemistry/*classification/*genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Thailand
  • topic2: Biotechnology

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
32533Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172875128776041
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/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/