Strain identifier
BacDive ID: 164042
Type strain: 
Species: Halocatena pleomorpha
Strain history: S. Krishnamurthi; MTCC, India; SPP-AMP-1.
NCBI tax ID(s): 1785090 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 164042
keywords: genome sequence, 16S sequence, Archaea, mesophilic
description: Halocatena pleomorpha JCM 31368 is a mesophilic archaeon that was isolated from Salt pan soil in Panaji.
NCBI tax id
- NCBI tax id: 1785090
- Matching level: species
strain history
- @ref: 67770
- history: S. Krishnamurthi; MTCC, India; SPP-AMP-1.
doi: 10.13145/bacdive164042.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Halobacteriaceae
- genus: Halocatena
- species: Halocatena pleomorpha
- full scientific name: Halocatena pleomorpha Verma et al. 2020
@ref: 67770
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halobacteriaceae
genus: Halocatena
species: Halocatena pleomorpha
full scientific name: Halocatena pleomorpha Verma et al. 2020
type strain: yes
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.1
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Salt pan soil in Panaji
- geographic location: Goa
- country: India
- origin.country: IND
- continent: Asia
Sequence information
16S sequences
- @ref: 67770
- description: Halomarina sp. SPP-AMP-1 partial 16S rRNA gene, isolate SPP-AMP-1
- accession: LT009694
- length: 1465
- database: nuccore
- NCBI tax ID: 1785090
Genome sequences
- @ref: 67770
- description: Halocatena pleomorpha SPP-AMP-1
- accession: GCA_003862495
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1785090
GC content
- @ref: 67770
- GC-content: 57.7
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 76.21 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 81.725 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.129 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 79.57 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 74.483 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 86 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 80.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 58.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 88.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.1 |
External links
@ref: 67770
culture collection no.: JCM 31368, KCTC 4276, MTCC 12579
literature
- topic: Phylogeny
- Pubmed-ID: 32421488
- title: Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil.
- authors: Verma A, Pal Y, Kumar P, Krishnamurthi S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.004222
- year: 2020
- mesh: Base Composition, DNA, Archaeal/genetics, Halobacteriaceae/*classification/isolation & purification, India, Lipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Sodium Chloride, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |