Strain identifier
BacDive ID: 5715
Type strain:
Species: Bizionia echini
Strain history: <- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia
NCBI tax ID(s): 649333 (species)
General
@ref: 17308
BacDive-ID: 5715
DSM-Number: 23925
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Bizionia echini DSM 23925 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin Strongylocentrotus intermedius.
NCBI tax id
- NCBI tax id: 649333
- Matching level: species
strain history
@ref | history |
---|---|
17308 | <- KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia |
67771 | <- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia |
doi: 10.13145/bacdive5715.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Bizionia
- species: Bizionia echini
- full scientific name: Bizionia echini Nedashkovskaya et al. 2010
synonyms
- @ref: 20215
- synonym: Algorimicrobium echini
@ref: 17308
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Bizionia
species: Bizionia echini
full scientific name: Bizionia echini Nedashkovskaya et al. 2010
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
29440 | negative | 1.4-3.5 µm | 0.4-0.5 µm | rod-shaped | yes | gliding | |
67771 | rod-shaped | no | |||||
67771 | negative | ||||||
69480 | negative | 99.985 |
pigmentation
- @ref: 29440
- production: yes
Culture and growth conditions
culture medium
- @ref: 17308
- 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 |
---|---|---|---|---|
17308 | positive | growth | 28 | mesophilic |
29440 | positive | growth | 04-39 | |
29440 | positive | optimum | 30-37 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29440 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29440 | NaCl | positive | growth | 01-08 % |
29440 | NaCl | positive | optimum | 02-03 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29440 | 16947 | citrate | + | carbon source |
29440 | 17234 | glucose | + | carbon source |
29440 | 37684 | mannose | + | carbon source |
metabolite production
- @ref: 29440
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
29440 | alkaline phosphatase | + | 3.1.3.1 |
29440 | catalase | + | 1.11.1.6 |
29440 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
17308 | sea urchin Strongylocentrotus intermedius | Strongylocentrotus intermedius | Sea of Japan, Gulf of Peter the Great, Troitsa Bay | Russia | RUS | Asia |
67771 | From sea urchin `Strongylocentrotus intermedius` | Troitsa Bay, Gulf of Peter the Great, East Sea | Russia | RUS | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Invertebrates (Other) | #Echinodermata |
#Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_7030.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_2813;97_3454;98_5165;99_7030&stattab=map
- Last taxonomy: Bizionia
- 16S sequence: FJ716799
- Sequence Identity:
- Total samples: 760
- soil counts: 12
- aquatic counts: 616
- animal counts: 125
- plant counts: 7
Safety information
risk assessment
- @ref: 17308
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17308
- description: Bizionia echini 16S ribosomal RNA gene, partial sequence
- accession: FJ716799
- length: 1478
- database: ena
- NCBI tax ID: 649333
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bizionia echini DSM 23925 | GCA_900115185 | scaffold | ncbi | 649333 |
66792 | Bizionia echini strain DSM 23925 | 649333.4 | wgs | patric | 649333 |
66792 | Bizionia echini DSM 23925 | 2622736504 | draft | img | 649333 |
GC content
@ref | GC-content | method |
---|---|---|
17308 | 34.4 | thermal denaturation, midpoint method (Tm) |
29440 | 34.4 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 88.535 | yes |
flagellated | no | 95.096 | yes |
gram-positive | no | 98.195 | yes |
anaerobic | no | 99.364 | yes |
aerobic | yes | 91.569 | no |
halophile | no | 69.093 | no |
spore-forming | no | 95.475 | no |
glucose-ferment | no | 91.694 | no |
thermophile | no | 98.284 | no |
glucose-util | yes | 83.818 | no |
External links
@ref: 17308
culture collection no.: DSM 23925, KCTC 22015, KMM 6177, LMG 25220
straininfo link
- @ref: 75197
- straininfo: 264738
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19661492 | Bizionia echini sp. nov., isolated from a sea urchin. | Nedashkovskaya OI, Vancanneyt M, Kim SB | Int J Syst Evol Microbiol | 10.1099/ijs.0.013193-0 | 2009 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 25103949 | Bizionia psychrotolerans sp. nov., a psychrophilic bacterium isolated from the intestine of a sea cucumber (Apostichopus japonicus). | Song EJ, Lee MH, Seo MJ, Yim KJ, Hyun DW, Bae JW, Park SL, Roh SW, Nam YD | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0253-x | 2014 | Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Intestines/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sea Cucumbers/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysis | Genetics |
Phylogeny | 30303476 | Hanstruepera crassostreae sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from an oyster. | He RH, Liang QY, Zhao JX, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003053 | 2018 | Animals, Bacterial Typing Techniques, Base Composition, China, Crassostrea/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17308 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23925) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23925 | |||
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 | |||
29440 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25846 | 28776041 | |
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) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
75197 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID264738.1 | StrainInfo: A central database for resolving microbial strain identifiers |