Strain identifier
BacDive ID: 11937
Type strain: 
Species: Pirellula staleyi
Strain history: <- ATCC <- J.T. Staley, Michigan (Pasteuria ramosa)
NCBI tax ID(s): 530564 (strain), 125 (species)
version 8.1 (current version)
General
@ref: 2429
BacDive-ID: 11937
DSM-Number: 6068
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pirellula staleyi DSM 6068 is a mesophilic, Gram-negative bacterium of the family Pirellulaceae.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 530564 | strain |
| 125 | species |
strain history
- @ref: 2429
- history: <- ATCC <- J.T. Staley, Michigan (Pasteuria ramosa)
doi: 10.13145/bacdive11937.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Planctomycetia
- order: Pirellulales
- family: Pirellulaceae
- genus: Pirellula
- species: Pirellula staleyi
- full scientific name: Pirellula staleyi (Schlesner and Hirsch 1984) Schlesner and Hirsch 1987
synonyms
@ref synonym 20215 Planctomyces staleyi 20215 Pirella staleyi
@ref: 2429
domain: Bacteria
phylum: Planctomycetes
class: Planctomycetia
order: Planctomycetales
family: Pirellulaceae
genus: Pirellula
species: Pirellula staleyi
full scientific name: Pirellula staleyi (Schlesner and Hirsch 1984) Schlesner and Hirsch 1987 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.984
multimedia
- @ref: 66793
- multimedia content: EM_DSM_6068_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 2429
- name: M14 (PIRELLULA MARINA) MEDIUM (DSMZ Medium 600)
- growth: yes
- link: https://mediadive.dsmz.de/medium/600
- composition: Name: M14 (PIRELLULA MARINA) MEDIUM (DSMZ Medium 600) Composition: NaCl 5.8675 g/l MgCl2 x 6 H2O 2.66 g/l Glucose 1.0 g/l Yeast extract 1.0 g/l Na2SO4 0.98 g/l MgSO4 x 7 H2O 0.594 g/l CaCl2 0.275 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 KBr 0.024 g/l H3BO3 0.0065 g/l SrCl2 0.006 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 Nicotinamide 9e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Calcium pantothenate 5e-05 g/l Riboflavin 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: 2429
- growth: positive
- type: growth
- temperature: 26
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 2429
- geographic location: Michigan, Lake Lansing
- country: USA
- origin.country: USA
- continent: North America
Safety information
risk assessment
- @ref: 2429
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Pirellula staleyi (strain DSM 6068T) 16S rRNA gene, partial | AJ231183 | 1477 | ena | 530564 |
| 20218 | P.staleyi 16S ribosomal RNA | M34126 | 1525 | ena | 125 |
| 20218 | P.staleyi partial 16S rRNA gene (DSM 6068) | X81946 | 1475 | ena | 530564 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pirellula staleyi DSM 6068 | GCA_000025185 | complete | ncbi | 530564 |
| 66792 | Pirellula staleyi DSM 6068 | 530564.3 | complete | patric | 530564 |
| 66792 | Pirellula staleyi DSM 6068 | 646311948 | complete | img | 530564 |
| 66792 | Pirellula staleyi DSM 6068 AE-03may19-312 | GCA_945861035 | contig | ncbi | 530564 |
| 66792 | Pirellula staleyi DSM 6068 AE-24oct19-290 | GCA_945870455 | contig | ncbi | 530564 |
| 66792 | Pirellula staleyi DSM 6068 MiH-22jul19-314 | GCA_945875845 | contig | ncbi | 530564 |
| 66792 | Pirellula staleyi DSM 6068 ZH-13nov19-202 | GCA_945900945 | contig | ncbi | 530564 |
| 66792 | Pirellula staleyi DSM 6068 strain ZH-13nov19-202 | 530564.21 | wgs | patric | 530564 |
| 66792 | Pirellula staleyi DSM 6068 strain MiH-22jul19-314 | 530564.20 | wgs | patric | 530564 |
| 66792 | Pirellula staleyi DSM 6068 strain AE-24oct19-290 | 530564.19 | wgs | patric | 530564 |
| 66792 | Pirellula staleyi DSM 6068 strain AE-03may19-312 | 530564.22 | wgs | patric | 530564 |
GC content
- @ref: 2429
- GC-content: 57.5
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | yes | 77.276 | no |
| flagellated | no | 82.079 | no |
| gram-positive | no | 97.433 | no |
| anaerobic | no | 97.804 | no |
| aerobic | yes | 89.435 | no |
| halophile | no | 87.854 | no |
| spore-forming | no | 90.147 | no |
| thermophile | no | 86.289 | no |
| glucose-util | yes | 84.763 | no |
| glucose-ferment | no | 89.783 | no |
External links
@ref: 2429
culture collection no.: DSM 6068, ATCC 27377, DSM 940, ICPB 4128
straininfo link
- @ref: 81151
- straininfo: 38971
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 12361271 | Molecular and ultrastructural confirmation of classification of ATCC 35122 as a strain of Pirellula staleyi. | Butler MK, Wang J, Webb RI, Fuerst JA | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1663 | 2002 | Bacteria/*classification/genetics/isolation & purification/ultrastructure, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Genetics |
| Genetics | 21304671 | Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). | Clum A, Tindall BJ, Sikorski J, Ivanova N, Mavrommatis K, Lucas S, Glavina T, Del Rio, Nolan M, Chen F, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Kuske C, Bruce D, Goodwin L, Ovchinikova G, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A | Stand Genomic Sci | 10.4056/sigs.51657 | 2009 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6068) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6068 | |||
| 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 | |
| 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 | |||
| 81151 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38971.1 | StrainInfo: A central database for resolving microbial strain identifiers |