Strain identifier
BacDive ID: 11940
Type strain: 
Species: Planctopirus limnophila
Strain Designation: Müller 290
Strain history: <- IFAM <- Müller, 290
NCBI tax ID(s): 521674 (strain), 120 (species)
version 8.1 (current version)
General
@ref: 1470
BacDive-ID: 11940
DSM-Number: 3776
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Planctopirus limnophila Müller 290 is a mesophilic, Gram-negative bacterium that was isolated from surface water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 120 | species |
| 521674 | strain |
strain history
- @ref: 1470
- history: <- IFAM <- Müller, 290
doi: 10.13145/bacdive11940.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/planctomycetota
- domain: Bacteria
- phylum: Planctomycetota
- class: Planctomycetia
- order: Planctomycetales
- family: Planctomycetaceae
- genus: Planctopirus
- species: Planctopirus limnophila
- full scientific name: Planctopirus limnophila corrig. (Hirsch and Müller 1986) Scheuner et al. 2015
synonyms
@ref synonym 20215 Planctopirus limnophilus 20215 Planctomyces limnophilus
@ref: 1470
domain: Bacteria
phylum: Planctomycetes
class: Planctomycetia
order: Planctomycetales
family: Planctomycetaceae
genus: Planctopirus
species: Planctopirus limnophila
full scientific name: Planctopirus limnophila (Hirsch and Müller 1986) Scheuner et al. 2015
strain designation: Müller 290
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.991
multimedia
- @ref: 66793
- multimedia content: EM_DSM_3776_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1470
- name: PYGV AGAR (DSMZ Medium 621)
- growth: yes
- link: https://mediadive.dsmz.de/medium/621
- composition: Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
culture temp
- @ref: 1470
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.991 |
Isolation, sampling and environmental information
isolation
- @ref: 1470
- sample type: surface water
- geographic location: Holstein
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Surface water
Safety information
risk assessment
- @ref: 1470
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: P.limnophilus 16S rDNA
- accession: X62911
- length: 1528
- database: ena
- NCBI tax ID: 521674
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Planctopirus limnophila DSM 3776 | GCA_000092105 | complete | ncbi | 521674 |
| 66792 | Planctomyces limnophilus DSM 3776 | 521674.6 | complete | patric | 521674 |
| 66792 | Planctopirus limnophila DSM 3776 | 521674.22 | plasmid | patric | 521674 |
| 66792 | Planctopirus limnophila DSM 3776 | 646564559 | complete | img | 521674 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 81.172 | no |
| flagellated | no | 85.611 | no |
| gram-positive | no | 98.43 | no |
| anaerobic | no | 95.505 | no |
| aerobic | yes | 80.169 | no |
| halophile | no | 87.891 | no |
| spore-forming | no | 90.363 | no |
| thermophile | no | 74.525 | yes |
| glucose-util | yes | 88.158 | no |
| glucose-ferment | no | 89.241 | no |
External links
@ref: 1470
culture collection no.: DSM 3776, ATCC 43296, IFAM 1008
straininfo link
- @ref: 81153
- straininfo: 41761
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 8606164 | Physical map of the genome of Planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage. | Ward-Rainey N, Rainey FA, Wellington EM, Stackebrandt E | J Bacteriol | 10.1128/jb.178.7.1908-1913.1996 | 1996 | Base Sequence, DNA Primers, Genetic Markers/genetics, *Genome, Bacterial, Gram-Negative Bacteria/classification/*genetics, Molecular Sequence Data, Phylogeny, Restriction Mapping | Genetics |
| Phylogeny | 17978240 | Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands. | Kulichevskaya IS, Ivanova AO, Belova SE, Baulina OI, Bodelier PLE, Rijpstra WIC, Sinninghe Damste JS, Zavarzin GA, Dedysh SN | Int J Syst Evol Microbiol | 10.1099/ijs.0.65157-0 | 2007 | Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Species Specificity, *Sphagnopsida, *Wetlands | 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 | |||
| 27594849 | Developing Techniques for the Utilization of Planctomycetes As Producers of Bioactive Molecules. | Jeske O, Surup F, Ketteniss M, Rast P, Forster B, Jogler M, Wink J, Jogler C | Front Microbiol | 10.3389/fmicb.2016.01242 | 2016 | |||
| Phylogeny | 29467380 | Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis. | Yadav S, Vaddavalli R, Siripuram S, Eedara RVV, Yadav S, Rabishankar O, Lodha T, Chintalapati S, Chintalapati V | J Antibiot (Tokyo) | 10.1038/s41429-018-0035-1 | 2018 | Anti-Bacterial Agents/*biosynthesis, Bacteria/*genetics/metabolism, Classification, Computer Simulation, DNA, Fungal/analysis, Genome, Fungal, Hydrocharitaceae/*microbiology, Nucleic Acid Hybridization, RNA, Fungal/analysis, RNA, Ribosomal, 16S/analysis | Genetics |
| Phylogeny | 31785948 | Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge. | Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Jetten MSM, Schuler M, Becker S, Rohde C, Muller RW, Brummer F, Rohde M, Engelhardt H, Jogler M, Jogler C | Syst Appl Microbiol | 10.1016/j.syapm.2019.126022 | 2019 | Animals, Fresh Water, Microbiota, *Phylogeny, Planctomycetales/*classification/isolation & purification, Porifera/*microbiology | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1470 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3776) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3776 | |||
| 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 | |||
| 81153 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41761.1 | StrainInfo: A central database for resolving microbial strain identifiers |