Strain identifier

BacDive ID: 11938

Type strain: Yes

Species: Rubinisphaera brasiliensis

Strain history: IAM 15109 <-- DSM 5305 <-- H. Schlesner IFAM 1448.

NCBI tax ID(s): 756272 (strain), 119 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
119species
756272strain

strain history

@refhistory
1983<- H. Schlesner, IFAM
67770IAM 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

@refgrowthtypetemperaturerange
1983positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.996

compound production

@refcompound
1983catalase
1983cytochrome oxidase
1983H2S

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1983water from salt pitLagoa Vermelha, near Rio de JanerioBrazilBRAMiddle and South America
67770Water from salt pit

isolation source categories

Cat1Cat2
#Environmental#Aquatic
#Condition#Saline

Safety information

risk assessment

  • @ref: 1983
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218P.brasiliensis partial 16S rRNA gene (DSM 5305)X819491200ena756272
20218P.brasiliensis 16S rRNA geneX852471092ena756272
1983Planctomyces brasiliensis (strain DSM 5305T) 16S rRNA gene, partialAJ2311901447ena756272

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rubinisphaera brasiliensis DSM 5305GCA_000165715completencbi756272
66792Planctomyces brasiliensis DSM 5305756272.5completepatric756272
66792Rubinisphaera brasiliensis DSM 5305649633083completeimg756272

GC content

  • @ref: 1983
  • GC-content: 55.1-57.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes86.242no
flagellatedno69.908no
gram-positiveno98.187no
anaerobicno97.523no
aerobicyes88.567no
halophileno61.691no
spore-formingno89.39no
thermophileno96.227yes
glucose-utilyes87.938no
glucose-fermentno90.637no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19700920Phycisphaera 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 SJ Gen Appl Microbiol10.2323/jgam.55.2672009Base 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 MicrobiologyGenetics
23766281Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm.Cayrou C, Raoult D, Drancourt MEnviron Microbiol Rep10.1111/j.1758-2229.2010.00176.x2010
Genetics25780503Complete 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 HPStand Genomic Sci10.1186/1944-3277-9-102014Phylogeny
Phylogeny35687662Rubinisphaera 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 OMInt J Syst Evol Microbiol10.1099/ijsem.0.0054252022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Geologic Sediments/microbiology, Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1983Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5305)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5305
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81152Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42463.1StrainInfo: A central database for resolving microbial strain identifiers