Strain identifier
BacDive ID: 10421
Type strain:
Species: Plesiocystis pacifica
Strain Designation: SHI-1
Strain history: T. Iizuka SHI-1.
NCBI tax ID(s): 191768 (species)
version 8.1 (current version)
General
@ref: 5592
BacDive-ID: 10421
DSM-Number: 14876
keywords: 16S sequence, Bacteria, mesophilic
description: Plesiocystis pacifica SHI-1 is a mesophilic bacterium that was isolated from coastal sands.
NCBI tax id
- NCBI tax id: 191768
- Matching level: species
strain history
@ref | history |
---|---|
5592 | <- T. Iizuka; SHI-1 |
67770 | T. Iizuka SHI-1. |
doi: 10.13145/bacdive10421.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Myxococcales
- family: Nannocystaceae
- genus: Plesiocystis
- species: Plesiocystis pacifica
- full scientific name: Plesiocystis pacifica Iizuka et al. 2003
@ref: 5592
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Myxococcales
family: Nannocystaceae
genus: Plesiocystis
species: Plesiocystis pacifica
full scientific name: Plesiocystis pacifica Iizuka et al. 2003
strain designation: SHI-1
type strain: no
Culture and growth conditions
culture medium
- @ref: 5592
- name: VY/4-SWS AGAR (DSMZ Medium 958)
- growth: yes
- link: https://mediadive.dsmz.de/medium/958
- composition: Name: VY/4-SWS AGAR (DSMZ Medium 958) Composition: NaCl 20.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 8.0 g/l Yeast cell paste 2.5 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.5 g/l NaHCO3 0.16 g/l KBr 0.08 g/l SrCl2 x 6 H2O 0.03 g/l Sodium beta-glycerophosphate 0.01 g/l Ferric citrate 0.01 g/l Cyanocobalamine 0.0005 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l Na2MoO4 x 2 H2O 3e-06 g/l MnCl2 x 4 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5592 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5592 | coastal sands | Hachijyo Island, Tokyo | Japan | JPN | Asia |
67770 | Sand | Hachijo-jima Island | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Sandy
taxonmaps
- @ref: 69479
- File name: preview.99_3266.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_385;96_1701;97_2036;98_2502;99_3266&stattab=map
- Last taxonomy: Plesiocystis pacifica subclade
- 16S sequence: AB016469
- Sequence Identity:
- Total samples: 3138
- soil counts: 471
- aquatic counts: 1671
- animal counts: 937
- plant counts: 59
Safety information
risk assessment
- @ref: 5592
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5592
- description: Myxobacterium SHI-1 16S rRNA gene, partial sequence
- accession: AB016469
- length: 1483
- database: ena
- NCBI tax ID: 80815
GC content
@ref | GC-content | method |
---|---|---|
5592 | 69.3-70.0 | high performance liquid chromatography (HPLC) |
67770 | 70 | high performance liquid chromatography (HPLC) |
External links
@ref: 5592
culture collection no.: DSM 14876, AJ 13393, JCM 11592
straininfo link
- @ref: 79703
- straininfo: 111749
literature
- topic: Phylogeny
- Pubmed-ID: 12656172
- title: Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan.
- authors: Iizuka T, Jojima Y, Fudou R, Hiraishi A, Ahn JW, Yamanaka S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02418-0
- year: 2003
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Vitamin K 2/*analogs & derivatives/*metabolism
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5592 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14876) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14876 | |
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
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 | |
79703 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID111749.1 | StrainInfo: A central database for resolving microbial strain identifiers |