Strain identifier
BacDive ID: 13864
Type strain: 
Species: Pararhodobacter aggregans
Strain Designation: D1-19
Strain history: <- B. Fösel, Dept. Ecological Microbiology, Univ. Bayreuth, Germany; D1-19
NCBI tax ID(s): 404875 (species)
version 8.1 (current version)
General
@ref: 7796
BacDive-ID: 13864
DSM-Number: 18938
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pararhodobacter aggregans D1-19 is a mesophilic, Gram-negative bacterium that was isolated from digestion basin of a marine aquaculture system.
NCBI tax id
- NCBI tax id: 404875
- Matching level: species
strain history
- @ref: 7796
- history: <- B. Fösel, Dept. Ecological Microbiology, Univ. Bayreuth, Germany; D1-19
doi: 10.13145/bacdive13864.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Pararhodobacter
- species: Pararhodobacter aggregans
- full scientific name: Pararhodobacter aggregans Foesel et al. 2013
@ref: 7796
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pararhodobacter
species: Pararhodobacter aggregans
full scientific name: Pararhodobacter aggregans Foesel et al. 2013
strain designation: D1-19
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.98
Culture and growth conditions
culture medium
- @ref: 7796
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 7796
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 97 |
| 69480 | no | 99.989 |
Isolation, sampling and environmental information
isolation
- @ref: 7796
- sample type: digestion basin of a marine aquaculture system
- geographic location: Rehovot
- country: Israel
- origin.country: ISR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Aquaculture |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_60710.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2882;97_3541;98_43096;99_60710&stattab=map
- Last taxonomy: Pararhodobacter aggregans subclade
- 16S sequence: AM403160
- Sequence Identity:
- Total samples: 317
- soil counts: 15
- aquatic counts: 231
- animal counts: 69
- plant counts: 2
Safety information
risk assessment
- @ref: 7796
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7796
- description: Pararhodobacter aggregans partial 16S rRNA gene, type strain D1-19T
- accession: AM403160
- length: 1195
- database: ena
- NCBI tax ID: 404875
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pararhodobacter aggregans DSM 18938 | GCA_003054005 | contig | ncbi | 404875 |
| 66792 | Pararhodobacter aggregans D1-19 | GCA_003075525 | contig | ncbi | 404875 |
| 66792 | Pararhodobacter aggregans strain D1-19 | 404875.3 | wgs | patric | 404875 |
| 66792 | Pararhodobacter aggregans strain DSM 18938 | 404875.4 | wgs | patric | 404875 |
| 66792 | Pararhodobacter aggregans DSM 18938 | 2734482252 | draft | img | 404875 |
| 66792 | Pararhodobacter aggregans D1-19 | 2832804499 | draft | img | 404875 |
GC content
- @ref: 7796
- GC-content: 68.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 97 | no |
| gram-positive | no | 98.47 | no |
| anaerobic | no | 97.837 | no |
| halophile | no | 65.038 | no |
| spore-forming | no | 97.184 | no |
| glucose-util | yes | 79.893 | no |
| aerobic | yes | 90.034 | no |
| motile | no | 50 | no |
| flagellated | no | 75.86 | no |
| thermophile | no | 99.004 | yes |
| glucose-ferment | no | 87.239 | no |
External links
@ref: 7796
culture collection no.: DSM 18938, ATCC BAA 1446
straininfo link
- @ref: 83040
- straininfo: 407252
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21959289 | Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. | Foesel BU, Drake HL, Schramm A | Syst Appl Microbiol | 10.1016/j.syapm.2011.08.006 | 2011 | *Aquaculture, Base Composition, Carbohydrate Metabolism, Denitrification, Fatty Acids/physiology, Genes, Bacterial, Genes, rRNA, Microscopy, Electron, Transmission, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology/ultrastructure, Ribotyping, Species Specificity, *Water Microbiology | Genetics |
| Phylogeny | 25572494 | Plastorhodobacter daqingensis gen. nov., sp. nov.: a non-phototrophic bacterium isolated from Daqing Oilfield. | Xie BS, Lv XL, Cai M, Tang YQ, Wang YN, Cui HL, Liu XY, Tan Y, Wu XL | Curr Microbiol | 10.1007/s00284-014-0769-3 | 2015 | Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 30608229 | Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. | Lai Q, Liu X, Yuan J, Xie S, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003219 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30694171 | Pararhodobacter oceanensis sp. nov., isolated from marine intertidal sediment and emended description of the genus Pararhodobacter. | Wang XL, Zhao YN, Wang K, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003255 | 2019 | Bacterial Typing Techniques, Base Composition, Bays, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7796 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18938) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18938 | |||
| 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 | |||
| 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) | |||
| 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 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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 | |||
| 83040 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407252.1 | StrainInfo: A central database for resolving microbial strain identifiers |