Strain identifier
BacDive ID: 11938
Type strain:
Species: Rubinisphaera brasiliensis
Strain history: IAM 15109 <-- DSM 5305 <-- H. Schlesner IFAM 1448.
NCBI tax ID(s): 756272 (strain), 119 (species)
General
@ref: 1983
BacDive-ID: 11938
DSM-Number: 5305
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Rubinisphaera brasiliensis DSM 5305 is a mesophilic, Gram-negative bacterium that was isolated from water from salt pit.
NCBI tax id
NCBI tax id | Matching level |
---|---|
119 | species |
756272 | strain |
strain history
@ref | history |
---|---|
1983 | <- H. Schlesner, IFAM |
67770 | IAM 15109 <-- DSM 5305 <-- H. Schlesner IFAM 1448. |
doi: 10.13145/bacdive11938.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Planctomycetia
- order: Planctomycetales
- family: Planctomycetaceae
- genus: Rubinisphaera
- species: Rubinisphaera brasiliensis
- full scientific name: Rubinisphaera brasiliensis (Schlesner 1990) Scheuner et al. 2015
synonyms
- @ref: 20215
- synonym: Planctomyces brasiliensis
@ref: 1983
domain: Bacteria
phylum: Planctomycetes
class: Planctomycetia
order: Planctomycetales
family: Planctomycetaceae
genus: Rubinisphaera
species: Rubinisphaera brasiliensis
full scientific name: Rubinisphaera brasiliensis (Schlesner 1990) Scheuner et al. 2015
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.936
multimedia
- @ref: 66793
- multimedia content: EM_DSM_5305_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1983
- name: M13 VERRUCOMICROBIUM MEDIUM (DSMZ Medium 607)
- growth: yes
- link: https://mediadive.dsmz.de/medium/607
- composition: Name: M13 VERRUCOMICROBIUM MEDIUM (DSMZ Medium 607) Composition: NaCl 5.86925 g/l MgCl2 x 6 H2O 1.24525 g/l Na2SO4 0.97925 g/l MgSO4 x 7 H2O 0.594 g/l CaCl2 0.2755 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.2 g/l KCl 0.166 g/l CaCl2 x 2 H2O 0.0667 g/l NaHCO3 0.048 g/l H3BO3 0.0065 g/l SrCl2 0.006 g/l KBr 0.0015 g/l ZnSO4 x 7 H2O 0.001095 g/l NaF 0.00075 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Nicotinamide 5e-05 g/l Riboflavin 5e-05 g/l Calcium pantothenate 5e-05 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Vitamin B12 1e-06 g/l Tris-HCl buffer Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1983 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.996 |
compound production
@ref | compound |
---|---|
1983 | catalase |
1983 | cytochrome oxidase |
1983 | H2S |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1983 | water from salt pit | Lagoa Vermelha, near Rio de Janerio | Brazil | BRA | Middle and South America |
67770 | Water from salt pit |
isolation source categories
Cat1 | Cat2 |
---|---|
#Environmental | #Aquatic |
#Condition | #Saline |
Safety information
risk assessment
- @ref: 1983
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | P.brasiliensis partial 16S rRNA gene (DSM 5305) | X81949 | 1200 | ena | 756272 |
20218 | P.brasiliensis 16S rRNA gene | X85247 | 1092 | ena | 756272 |
1983 | Planctomyces brasiliensis (strain DSM 5305T) 16S rRNA gene, partial | AJ231190 | 1447 | ena | 756272 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rubinisphaera brasiliensis DSM 5305 | GCA_000165715 | complete | ncbi | 756272 |
66792 | Planctomyces brasiliensis DSM 5305 | 756272.5 | complete | patric | 756272 |
66792 | Rubinisphaera brasiliensis DSM 5305 | 649633083 | complete | img | 756272 |
GC content
- @ref: 1983
- GC-content: 55.1-57.7
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 86.242 | no |
flagellated | no | 69.908 | no |
gram-positive | no | 98.187 | no |
anaerobic | no | 97.523 | no |
aerobic | yes | 88.567 | no |
halophile | no | 61.691 | no |
spore-forming | no | 89.39 | no |
thermophile | no | 96.227 | yes |
glucose-util | yes | 87.938 | no |
glucose-ferment | no | 90.637 | no |
External links
@ref: 1983
culture collection no.: DSM 5305, ATCC 49424, IFAM 1448, JCM 21570, NBRC 103401, IAM 15109
straininfo link
- @ref: 81152
- straininfo: 42463
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 |
23766281 | Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm. | Cayrou C, Raoult D, Drancourt M | Environ Microbiol Rep | 10.1111/j.1758-2229.2010.00176.x | 2010 | |||
Genetics | 25780503 | Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. | Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Goker M, Kyrpides NC, Klenk HP | Stand Genomic Sci | 10.1186/1944-3277-9-10 | 2014 | Phylogeny | |
Phylogeny | 35687662 | Rubinisphaera margarita sp. nov., a novel planctomycete isolated from marine sediments collected in the Portuguese north coast. | Vitorino IR, Lobo-da-Cunha A, Vasconcelos V, Lage OM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005425 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Geologic Sediments/microbiology, Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1983 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5305) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5305 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
81152 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42463.1 | StrainInfo: A central database for resolving microbial strain identifiers |