Strain identifier
BacDive ID: 5642
Type strain: 
Species: Salegentibacter mishustinae
Strain history: <- Y. Nakagawa, NBRC <- S. B. Kim, KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok
NCBI tax ID(s): 270918 (species)
version 8.1 (current version)
General
@ref: 16846
BacDive-ID: 5642
DSM-Number: 23404
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Salegentibacter mishustinae DSM 23404 is a mesophilic bacterium that was isolated from sea urchin, Strongylocentrotus intermedius.
NCBI tax id
- NCBI tax id: 270918
- Matching level: species
strain history
- @ref: 16846
- history: <- Y. Nakagawa, NBRC <- S. B. Kim, KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok
doi: 10.13145/bacdive5642.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Salegentibacter
- species: Salegentibacter mishustinae
- full scientific name: Salegentibacter mishustinae Nedashkovskaya et al. 2005
@ref: 16846
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Salegentibacter
species: Salegentibacter mishustinae
full scientific name: Salegentibacter mishustinae Nedashkovskaya et al. 2005
type strain: yes
Culture and growth conditions
culture medium
- @ref: 16846
- 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: 16846
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 16846
- sample type: sea urchin, Strongylocentrotus intermedius
- host species: Strongylocentrotus intermedius
- geographic location: Sea of Japan, Gulf of Peter the Great, Troitsa Bay
- country: Russia
- origin.country: RUS
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Echinodermata
taxonmaps
- @ref: 69479
- File name: preview.99_5093.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_114;97_121;98_3802;99_5093&stattab=map
- Last taxonomy: Salegentibacter mishustinae
- 16S sequence: AY576653
- Sequence Identity:
- Total samples: 92
- soil counts: 1
- aquatic counts: 79
- animal counts: 4
- plant counts: 8
Safety information
risk assessment
- @ref: 16846
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Salegentibacter mishustinae gene for 16S rRNA, partial sequence, strain: NBRC 100592 | AB681203 | 1455 | ena | 270918 |
| 16846 | Salegentibacter mishustinae strain KMM 6049 16S ribosomal RNA gene, partial sequence | AY576653 | 1438 | ena | 270918 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Salegentibacter mishustinae DSM 23404 | GCA_002900095 | contig | ncbi | 270918 |
| 66792 | Salegentibacter mishustinae KCTC 12263 | GCA_014651335 | contig | ncbi | 270918 |
| 66792 | Salegentibacter mishustinae DSM 23404 | GCA_003254095 | scaffold | ncbi | 270918 |
| 66792 | Salegentibacter mishustinae KCTC 12263 | GCA_001431365 | contig | ncbi | 270918 |
| 66792 | Salegentibacter mishustinae strain DSM 23404 | 270918.14 | wgs | patric | 270918 |
| 66792 | Salegentibacter mishustinae strain DSM 23404 | 270918.15 | wgs | patric | 270918 |
| 66792 | Salegentibacter mishustinae strain KCTC 12263 | 270918.16 | wgs | patric | 270918 |
| 66792 | Salegentibacter mishustinae strain KCTC 12263 | 270918.21 | wgs | patric | 270918 |
| 66792 | Salegentibacter mishustinae DSM 23404 | 2593339291 | draft | img | 270918 |
| 66792 | Salegentibacter mishustinae DSM 23404 | 2839527574 | draft | img | 270918 |
GC content
- @ref: 16846
- GC-content: 37.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 93.685 | no |
| gram-positive | no | 97.973 | no |
| anaerobic | no | 98.643 | no |
| halophile | yes | 67.204 | no |
| spore-forming | no | 92.569 | no |
| aerobic | yes | 87.152 | no |
| glucose-util | yes | 88.811 | no |
| thermophile | no | 99.562 | no |
| motile | no | 88.864 | no |
| glucose-ferment | no | 89.433 | no |
External links
@ref: 16846
culture collection no.: DSM 23404, KCTC 12263, KMM 6049, LMG 22584, NBRC 100592
straininfo link
- @ref: 75125
- straininfo: 131131
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653880 | Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. | Nedashkovskaya OI, Kim SB, Lysenko AM, Mikhailov VV, Bae KS, Kim IS | Int J Syst Evol Microbiol | 10.1099/ijs.0.63297-0 | 2005 | Animals, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA | Genetics |
| Phylogeny | 24478205 | Salegentibacter chungangensis sp. nov., isolated from a sea sand and emended description of the genus Salegentibacter. | Siamphan C, Kim W | Int J Syst Evol Microbiol | 10.1099/ijs.0.059170-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Genetics | 27081136 | Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete Subtype I-B CRISPR-Cas System. | Zhang F, Lin W, Zhang R, Zheng Q, Jiao N | Genome Announc | 10.1128/genomeA.00267-16 | 2016 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16846 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23404) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23404 | |||
| 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 | |||
| 75125 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131131.1 | StrainInfo: A central database for resolving microbial strain identifiers |