Strain identifier
BacDive ID: 134138
Type strain:
Species: Roseivirga echinicomitans
Strain history: <- KCTC 12370
NCBI tax ID(s): 296218 (species)
General
@ref: 66352
BacDive-ID: 134138
DSM-Number: 102948
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Roseivirga echinicomitans KCTC 12370 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from sea urchin.
NCBI tax id
- NCBI tax id: 296218
- Matching level: species
strain history
- @ref: 66352
- history: <- KCTC 12370
doi: 10.13145/bacdive134138.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Roseivirgaceae
- genus: Roseivirga
- species: Roseivirga echinicomitans
- full scientific name: Roseivirga echinicomitans Nedashkovskaya et al. 2005
@ref: 66352
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Roseivirgaceae
genus: Roseivirga
species: Roseivirga echinicomitans
full scientific name: Roseivirga echinicomitans Nedashkovskaya et al. 2005 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31464 | negative | 2.65 µm | 0.4 µm | rod-shaped | no | |
69480 | negative | 99.987 |
pigmentation
- @ref: 31464
- production: yes
Culture and growth conditions
culture medium
- @ref: 66352
- 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 | growth | type | temperature | range |
---|---|---|---|---|
31464 | positive | growth | 04-31 | |
31464 | positive | optimum | 22 | psychrophilic |
66352 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 31464
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31464 | no | |
69481 | no | 100 |
69480 | no | 99.979 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31464 | NaCl | positive | growth | 01-08 % |
31464 | NaCl | positive | optimum | 4 % |
observation
- @ref: 31464
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31464 | 62064 | 2,3-butanediol | + | carbon source |
31464 | 16947 | citrate | + | carbon source |
31464 | 28260 | galactose | + | carbon source |
31464 | 24175 | galacturonate | + | carbon source |
31464 | 17754 | glycerol | + | carbon source |
31464 | 17596 | inosine | + | carbon source |
31464 | 25017 | leucine | + | carbon source |
31464 | 17306 | maltose | + | carbon source |
31464 | 506227 | N-acetylglucosamine | + | carbon source |
31464 | 18257 | ornithine | + | carbon source |
31464 | 28044 | phenylalanine | + | carbon source |
31464 | 26271 | proline | + | carbon source |
31464 | 30911 | sorbitol | + | carbon source |
31464 | 17748 | thymidine | + | carbon source |
31464 | 4853 | esculin | + | hydrolysis |
31464 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 31464
- value: gelatinase
- activity: +
Isolation, sampling and environmental information
isolation
- @ref: 31464
- sample type: sea urchin
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Echinodermata
taxonmaps
- @ref: 69479
- File name: preview.99_4834.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_492;96_2388;97_2904;98_3620;99_4834&stattab=map
- Last taxonomy: Roseivirga
- 16S sequence: AY753206
- Sequence Identity:
- Total samples: 1110
- soil counts: 42
- aquatic counts: 992
- animal counts: 68
- plant counts: 8
Safety information
risk assessment
- @ref: 66352
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 31464
- description: Roseivirga echinicomitans strain KMM 6058 16S ribosomal RNA gene, partial sequence
- accession: AY753206
- length: 1415
- database: nuccore
- NCBI tax ID: 296218
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Roseivirga echinicomitans KMM 6058 | GCA_001592935 | contig | ncbi | 296218 |
66792 | Roseivirga echinicomitans strain KMM 6058 | 296218.3 | wgs | patric | 296218 |
66792 | Roseivirga echinicomitans KMM 6058 | 2651870325 | draft | img | 296218 |
GC content
@ref | GC-content | method |
---|---|---|
31464 | 41.3 | |
66352 | 40.0 | sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.447 | no |
anaerobic | no | 99.389 | no |
halophile | no | 82.588 | no |
spore-forming | no | 96.306 | no |
glucose-util | yes | 84.372 | no |
flagellated | no | 98.181 | yes |
thermophile | no | 97.672 | yes |
aerobic | yes | 93.413 | yes |
motile | no | 93.398 | yes |
glucose-ferment | no | 91.589 | no |
External links
@ref: 66352
culture collection no.: KCTC 12370, LMG 22587, KMM 6058, DSM 102948
straininfo link
- @ref: 91737
- straininfo: 133050
literature
- topic: Phylogeny
- Pubmed-ID: 16166668
- title: Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga.
- authors: Nedashkovskaya OI, Kim SB, Lysenko AM, Park MS, Mikhailov VV, Bae KS, Park HY
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63621-0
- year: 2005
- mesh: Animals, Base Composition, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Strongylocentrotus/*microbiology
- topic2: Genetics
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | |||
31464 | 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 | 27765 | 28776041 | |
66352 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102948 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102948) | |||
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 | |||
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/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91737 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID133050.1 |