Strain identifier
BacDive ID: 132890
Type strain: 
Species: Phycisphaera mikurensis
Strain Designation: FYK2301M01
Strain history: <- Y. Fukunaga, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; FYK2301M01
NCBI tax ID(s): 1142394 (strain), 547188 (species)
version 8.1 (current version)
General
@ref: 24678
BacDive-ID: 132890
DSM-Number: 103959
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Phycisphaera mikurensis FYK2301M01 is a mesophilic, Gram-negative bacterium that was isolated from Marine alga, Porphyra sp..
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1142394 | strain |
| 547188 | species |
strain history
- @ref: 24678
- history: <- Y. Fukunaga, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; FYK2301M01
doi: 10.13145/bacdive132890.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Phycisphaerae
- order: Phycisphaerales
- family: Phycisphaeraceae
- genus: Phycisphaera
- species: Phycisphaera mikurensis
- full scientific name: Phycisphaera mikurensis Fukunaga et al. 2010
@ref: 24678
domain: Bacteria
phylum: Planctomycetes
class: Phycisphaerae
order: Phycisphaerales
family: Phycisphaeraceae
genus: Phycisphaera
species: Phycisphaera mikurensis
full scientific name: Phycisphaera mikurensis Fukunaga et al. 2010
strain designation: FYK2301M01
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.93
multimedia
- @ref: 24678
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_103959.jpg
- caption: DSM 103959 grown on medium 514.
- intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Culture and growth conditions
culture medium
- @ref: 24678
- 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: 24678
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 24678
- sample type: Marine alga, Porphyra sp.
- host species: Porphyra sp.
- geographic location: Mikurajima, Tokyo
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Host | #Algae | #Red algae |
taxonmaps
- @ref: 69479
- File name: preview.99_7534.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16570;96_3514;97_4312;98_5521;99_7534&stattab=map
- Last taxonomy: Phycisphaera mikurensis subclade
- 16S sequence: AB447464
- Sequence Identity:
- Total samples: 1451
- soil counts: 198
- aquatic counts: 1213
- animal counts: 35
- plant counts: 5
Safety information
risk assessment
- @ref: 24678
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24678
- description: Phycisphaera mikurensis gene for 16S ribosomal RNA, partial sequence, strain: NBRC 102666
- accession: AB447464
- length: 1461
- database: ena
- NCBI tax ID: 1142394
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Phycisphaera mikurensis NBRC 102666 | GCA_000284115 | complete | ncbi | 1142394 |
| 66792 | Phycisphaera mikurensis DSM 103959 | GCA_014207395 | scaffold | ncbi | 547188 |
| 66792 | Phycisphaera mikurensis NBRC 102666 | 1142394.8 | complete | patric | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 | 1142394.11 | plasmid | patric | 1142394 |
| 66792 | Phycisphaera mikurensis strain DSM 103959 | 547188.13 | wgs | patric | 547188 |
| 66792 | Phycisphaera mikurensis NBRC 102666 | 2561511149 | complete | img | 1142394 |
| 66792 | Phycisphaera mikurensis DSM 103959 | 2861168098 | draft | img | 547188 |
| 66792 | Phycisphaera mikurensis NBRC 102666 AE-24oct19-296 | GCA_945870475 | contig | ncbi | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 LE-05nov19-197 | GCA_945877905 | scaffold | ncbi | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 MsE-30jul19-209 | GCA_945878575 | contig | ncbi | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 ME-08apr19-305 | GCA_945890745 | contig | ncbi | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 strain MsE-30jul19-209 | 1142394.44 | wgs | patric | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 strain ME-08apr19-305 | 1142394.45 | wgs | patric | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 strain LE-05nov19-197 | 1142394.43 | wgs | patric | 1142394 |
| 66792 | Phycisphaera mikurensis NBRC 102666 strain AE-24oct19-296 | 1142394.42 | wgs | patric | 1142394 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 62 | no |
| motile | yes | 55.462 | no |
| flagellated | no | 90.734 | no |
| gram-positive | no | 95.517 | no |
| anaerobic | no | 97.14 | no |
| aerobic | yes | 87.957 | no |
| halophile | no | 63.645 | no |
| spore-forming | no | 96.556 | no |
| thermophile | no | 95.507 | yes |
| glucose-util | yes | 88.574 | no |
| glucose-ferment | no | 84.197 | no |
External links
@ref: 24678
culture collection no.: DSM 103959, NBRC 102666, KCTC 22515
straininfo link
- @ref: 91170
- straininfo: 402438
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19700920 | Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes. | Fukunaga Y, Kurahashi M, Sakiyama Y, Ohuchi M, Yokota A, Harayama S | J Gen Appl Microbiol | 10.2323/jgam.55.267 | 2009 | Base Composition, DNA, Bacterial/analysis/genetics, Gram-Negative Anaerobic Cocci/*classification/genetics/*isolation & purification/ultrastructure, Japan, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Porphyra/*microbiology, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Species Specificity, *Water Microbiology | Genetics |
| Phylogeny | 24264814 | Algisphaera agarilytica gen. nov., sp. nov., a novel representative of the class Phycisphaerae within the phylum Planctomycetes isolated from a marine alga. | Yoon J, Jang JH, Kasai H | Antonie Van Leeuwenhoek | 10.1007/s10482-013-0076-1 | 2013 | Amino Acids/analysis, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Chlorophyta/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/physiology, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 25404483 | Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov. | Kovaleva OL, Merkel AY, Novikov AA, Baslerov RV, Toshchakov SV, Bonch-Osmolovskaya EA | Int J Syst Evol Microbiol | 10.1099/ijs.0.070151-0 | 2014 | Bacteria, Aerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA | Genetics |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 24678 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103959 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103959) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | 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 | |||
| 91170 | 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-ID402438.1 |