Strain identifier
BacDive ID: 13782
Type strain:
Species: Ruegeria lacuscaerulensis
Strain Designation: ITI-1157
Strain history: <- S. K. Pétursdóttir, ITI-1157
NCBI tax ID(s): 644107 (strain), 55218 (species)
General
@ref: 4293
BacDive-ID: 13782
DSM-Number: 11314
keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative
description: Ruegeria lacuscaerulensis ITI-1157 is a thermophilic, Gram-negative bacterium of the family Roseobacteraceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
55218 | species |
644107 | strain |
strain history
- @ref: 4293
- history: <- S. K. Pétursdóttir, ITI-1157
doi: 10.13145/bacdive13782.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Ruegeria
- species: Ruegeria lacuscaerulensis
- full scientific name: Ruegeria lacuscaerulensis (Petursdottir and Kristjansson 1999) Yi et al. 2007
synonyms
- @ref: 20215
- synonym: Silicibacter lacuscaerulensis
@ref: 4293
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Ruegeria
species: Ruegeria lacuscaerulensis
full scientific name: Ruegeria lacuscaerulensis (Petursdottir and Kristjansson 1999) Yi et al. 2007 emend. Vandecandelaere et al. 2008
strain designation: ITI-1157
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
colony morphology
- @ref: 4293
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 4293
- 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
- @ref: 4293
- growth: positive
- type: growth
- temperature: 45
- range: thermophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 4293
- geographic location: Blue Lagoon, geothermal lake in Reykjanes peninsula
- country: Iceland
- origin.country: ISL
- continent: Europe
taxonmaps
- @ref: 69479
- File name: preview.99_1966.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_588;97_688;98_803;99_1966&stattab=map
- Last taxonomy: Ruegeria lacuscaerulensis
- 16S sequence: U77644
- Sequence Identity:
- Total samples: 1005
- soil counts: 15
- aquatic counts: 900
- animal counts: 88
- plant counts: 2
Safety information
risk assessment
- @ref: 4293
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Silicibacter lacuscaerulensis strain DSM11314 16S ribosomal RNA gene, partial sequence | DQ915630 | 1307 | ena | 644107 |
4293 | Ruegeria lacuscaerulensis strain ITI-1157 16S ribosomal RNA gene, partial sequence | U77644 | 1339 | ena | 644107 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ruegeria lacuscaerulensis ITI-1157 | GCA_900141625 | contig | ncbi | 644107 |
66792 | Ruegeria lacuscaerulensis ITI-1157 | GCA_000161775 | scaffold | ncbi | 644107 |
66792 | Silicibacter lacuscaerulensis ITI-1157 | 644107.12 | wgs | patric | 644107 |
66792 | Ruegeria lacuscaerulensis ITI-1157 | 647533208 | draft | img | 644107 |
66792 | Ruegeria lacuscaerulensis DSM 11314 | 2698536695 | draft | img | 644107 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 64.204 | no |
flagellated | no | 83.424 | no |
gram-positive | no | 98.244 | no |
anaerobic | no | 98.529 | no |
aerobic | yes | 89.658 | no |
halophile | yes | 84.843 | no |
spore-forming | no | 97.108 | no |
thermophile | no | 82.52 | yes |
glucose-util | yes | 62.635 | no |
glucose-ferment | no | 90.665 | no |
External links
@ref: 4293
culture collection no.: DSM 11314
straininfo link
- @ref: 82961
- straininfo: 49076
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9680308 | Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland. | Petursdottir SK, Kristjansson JK | Extremophiles | 10.1007/s007920050020 | 1997 | Bacteria, Aerobic/genetics/*isolation & purification, DNA, Bacterial, Fresh Water, Iceland, Phenotype, RNA, Ribosomal, 16S/genetics, *Water Microbiology | Phenotype |
Phylogeny | 17684242 | Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea. | Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.64825-0 | 2007 | China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Petroleum/metabolism, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/genetics/metabolism, Seawater/*microbiology | Genetics |
Phylogeny | 17684263 | Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. | Lee K, Choo YJ, Giovannoni SJ, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijs.0.65032-0 | 2007 | Atlantic Ocean, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sodium Chloride/metabolism | Genetics |
Phylogeny | 22228657 | Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii. | Lee J, Whon TW, Shin NR, Roh SW, Kim J, Park SK, Kim MS, Shin KS, Lee JS, Lee KC, Kim YO, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.037283-0 | 2012 | Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Scapharca/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
Phylogeny | 22712501 | Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus. | Christie-Oleza JA, Pina-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud J | Environ Microbiol | 10.1111/j.1462-2920.2012.02812.x | 2012 | Bacterial Proteins/analysis, Bacterial Typing Techniques, Biomarkers/*analysis, *Chromatography, Liquid, Environmental Microbiology, Environmental Monitoring/*methods, Phylogeny, *Proteomics, *Rhodobacteraceae/classification/genetics/metabolism, Seawater/microbiology, *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, *Tandem Mass Spectrometry | Proteome |
Phylogeny | 23243093 | Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. | Kampfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.047910-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spermidine/analysis, Taiwan, Ubiquinone/analogs & derivatives/analysis | Genetics |
Metabolism | 24443527 | Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. | Bullock HA, Reisch CR, Burns AS, Moran MA, Whitman WB | J Bacteriol | 10.1128/JB.00026-14 | 2014 | Alphaproteobacteria/*genetics/*metabolism, Cluster Analysis, Coenzyme A Ligases/genetics/*metabolism, Enzyme Inhibitors/metabolism, *Gene Expression Regulation, Bacterial, *Metabolic Networks and Pathways, Phylogeny, Sequence Homology, Amino Acid, Sodium Chloride/metabolism, Substrate Specificity, Sulfonium Compounds/*metabolism | Phylogeny |
Phylogeny | 35333154 | Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. | Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005286 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Pacific Ocean, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4293 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11314) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11314 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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) | |||
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 | |
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
82961 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49076.1 | StrainInfo: A central database for resolving microbial strain identifiers |