Strain identifier
BacDive ID: 134340
Type strain:
Species: Natrinema gari
Strain Designation: HIS40-3
Strain history: W. Visessanguan HIS40-3.
NCBI tax ID(s): 1230459 (strain), 419186 (species)
version 8.1 (current version)
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 id | Matching level |
---|---|
419186 | species |
1230459 | strain |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
32533 | positive | growth | 20-60 | |
32533 | positive | optimum | 37-40 | |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32533 | positive | growth | 5.5-8.5 | alkaliphile |
32533 | positive | optimum | 6-6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32533
- oxygen tolerance: aerobe
spore formation
- @ref: 32533
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32533 | NaCl | positive | growth | 9.86-19.72 % |
32533 | NaCl | positive | optimum | 15.08-19.72 % |
observation
@ref | observation |
---|---|
32533 | aggregates in chains |
67770 | quinones: MK-8, MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32533 | 22599 | arabinose | + | carbon source |
32533 | 17234 | glucose | + | carbon source |
32533 | 17754 | glycerol | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32533 | catalase | + | 1.11.1.6 |
32533 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
32533 | anchovy fish sauce |
67770 | Anchovy 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Natrinema gari JCM 14663 | 2554235484 | draft | img | 1230459 |
67770 | Natrinema gari JCM 14663 | GCA_000337175 | contig | ncbi | 1230459 |
66792 | Natrinema gari JCM 14663 | 1230459.4 | wgs | patric | 1230459 |
GC content
@ref | GC-content | method |
---|---|---|
32533 | 64-65.4 | |
67770 | 65.4 | high 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
@id | authors | title | doi/url | ID_cross_reference | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
32533 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 28751 | 28776041 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
69479 | João 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 beta | https://microbeatlas.org/ |