Strain identifier
BacDive ID: 5873
Type strain:
Species: Halogeometricum borinquense
Strain Designation: PR3
Strain history: ATCC 700274 <-- R. Montalvo-Rodríguez PR3.
NCBI tax ID(s): 469382 (strain), 60847 (species)
General
@ref: 4413
BacDive-ID: 5873
DSM-Number: 11551
keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative
description: Halogeometricum borinquense PR3 is a mesophilic, Gram-negative archaeon that was isolated from solar salterns.
NCBI tax id
NCBI tax id | Matching level |
---|---|
60847 | species |
469382 | strain |
strain history
@ref | history |
---|---|
4413 | <- R. Montalvo-Rodríguez; PR3 |
67770 | ATCC 700274 <-- R. Montalvo-Rodríguez PR3. |
doi: 10.13145/bacdive5873.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Haloferacaceae
- genus: Halogeometricum
- species: Halogeometricum borinquense
- full scientific name: Halogeometricum borinquense Montalvo-Rodríguez et al. 1998
@ref: 4413
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Haloferacaceae
genus: Halogeometricum
species: Halogeometricum borinquense
full scientific name: Halogeometricum borinquense Montalvo-Rodríguez et al. 1998
strain designation: PR3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.991
multimedia
- @ref: 66793
- multimedia content: EM_DSM_11551_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 4413
- name: HALOBACTERIA MEDIUM (DSMZ Medium 372)
- growth: yes
- link: https://mediadive.dsmz.de/medium/372
- composition: Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4413 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.942 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4413 | solar salterns | Cabor Rojo | Puerto Rico | PRI | Middle and South America |
67770 | Solar saltern | Cabo Rojo | Puerto Rico | PRI | North America |
isolation source categories
- Cat1: #Condition
- Cat2: #Saline
Safety information
risk assessment
- @ref: 4413
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Halogeometricum borinquense 16S ribosomal RNA gene, complete sequence
- accession: AF002984
- length: 1451
- database: ena
- NCBI tax ID: 469382
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halogeometricum borinquense DSM 11551 | GCA_000172995 | complete | ncbi | 469382 |
66792 | Halogeometricum borinquense PR3, DSM 11551 | 649633053 | complete | img | 469382 |
66792 | Halogeometricum borinquense PR3, DSM 11551 | 2537561588 | draft | img | 469382 |
67770 | Halogeometricum borinquense DSM 11551 | GCA_000337855 | contig | ncbi | 469382 |
66792 | Halogeometricum borinquense DSM 11551 strain PR 3 | 469382.37 | plasmid | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 strain PR 3 | 469382.33 | plasmid | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 strain PR 3 | 469382.34 | plasmid | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 strain PR 3 | 469382.36 | plasmid | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 strain PR 3 | 469382.35 | plasmid | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 | 469382.18 | complete | patric | 469382 |
66792 | Halogeometricum borinquense DSM 11551 | 469382.19 | wgs | patric | 469382 |
GC content
@ref | GC-content | method |
---|---|---|
4413 | 59.0 | |
67770 | 59 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 71.471 | no |
flagellated | no | 95.252 | no |
gram-positive | no | 96.908 | no |
anaerobic | no | 93.676 | no |
aerobic | yes | 77.585 | no |
halophile | yes | 82.984 | no |
spore-forming | no | 92.944 | no |
thermophile | no | 82.313 | yes |
glucose-util | yes | 87.946 | no |
glucose-ferment | no | 86.973 | no |
External links
@ref: 4413
culture collection no.: DSM 11551, ATCC 700274, JCM 10706, CGMCC 1.6168, KCTC 4070
straininfo link
- @ref: 75353
- straininfo: 43858
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9828431 | Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico. | Montalvo-Rodriguez R, Vreeland RH, Oren A, Kessel M, Betancourt C, Lopez-Garriga J | Int J Syst Bacteriol | 10.1099/00207713-48-4-1305 | 1998 | Base Composition, DNA, Archaeal/chemistry, DNA, Ribosomal/chemistry, Halobacteriaceae/*classification/*isolation & purification/physiology/ultrastructure, Lipids/analysis, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Puerto Rico, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Terminology as Topic, Water Microbiology | Genetics |
Cultivation | 12951519 | Organic solvent tolerance of halophilic archaea. | Usami R, Fukushima T, Mizuki T, Inoue A, Yoshida Y, Horikoshi K | Biosci Biotechnol Biochem | 10.1271/bbb.67.1809 | 2003 | Alkanes/chemistry/*pharmacology, Culture Media, Ether/analogs & derivatives/*pharmacology, Halobacteriaceae/drug effects/genetics/*growth & development, Solvents, Species Specificity | Phylogeny |
Phylogeny | 24097833 | Taxonomic study of the genera Halogeometricum and Halosarcina: transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively. | Qiu XX, Zhao ML, Han D, Zhang WJ, Dyall-Smith ML, Cui HL | Int J Syst Evol Microbiol | 10.1099/ijs.0.055038-0 | 2013 | DNA, Archaeal/genetics, Genes, Archaeal, Halobacteriaceae/*classification/genetics, Lipids/analysis, Molecular Sequence Data, Peptide Elongation Factor 2/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4413 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11551) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11551 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75353 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43858.1 | StrainInfo: A central database for resolving microbial strain identifiers |