Strain identifier
BacDive ID: 130825
Type strain: 
Species: Paludibacterium paludis
Strain Designation: KBP-21
Strain history: <- WM Chen, Nat Kaohsiung Marine Uinv., Taiwan
NCBI tax ID(s): 1225769 (species)
version 8.1 (current version)
General
@ref: 22061
BacDive-ID: 130825
DSM-Number: 29672
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, rod-shaped
description: Paludibacterium paludis KBP-21 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from water.
NCBI tax id
- NCBI tax id: 1225769
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22061 | <- KCTC <- S.-Y. Sheu, National Kaohsiung Marine University, Taiwan, ROC |
| 67771 | <- WM Chen, Nat Kaohsiung Marine Uinv., Taiwan |
doi: 10.13145/bacdive130825.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Neisseriales
- family: Chromobacteriaceae
- genus: Paludibacterium
- species: Paludibacterium paludis
- full scientific name: Paludibacterium paludis Sheu et al. 2014
@ref: 22061
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Chromobacteriaceae, not assigned to order
family: Chromobacteriaceae
genus: Paludibacterium
species: Paludibacterium paludis
full scientific name: Paludibacterium paludis Sheu et al. 2014
strain designation: KBP-21
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | yes | ||
| 67771 | negative | |||
| 69480 | yes | 95.322 | ||
| 69480 | negative | 99.99 |
multimedia
- @ref: 22061
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29672.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 22061
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22061 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 67771 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.945 |
observation
- @ref: 67771
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22061 | water | Banping Lake Wetland Park, Kaohsiung Country | Taiwan | TWN | Asia | 22.6917 | 120.309 |
| 67771 | From water of the Banping Lake Wetland Park | Kaohsiung Country | Taiwan | TWN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_94725.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_4455;97_29633;98_65068;99_94725&stattab=map
- Last taxonomy: Paludibacterium paludis subclade
- 16S sequence: HE981224
- Sequence Identity:
- Total samples: 159
- soil counts: 23
- aquatic counts: 57
- animal counts: 36
- plant counts: 43
Safety information
risk assessment
- @ref: 22061
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22061
- description: Paludibacterium paludis partial 16S rRNA gene, type strain KBP-21T
- accession: HE981224
- length: 1443
- database: ena
- NCBI tax ID: 1225769
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paludibacterium paludis BCRC 80514 | GCA_018802605 | complete | ncbi | 1225769 |
| 66792 | Paludibacterium paludis KCTC 32182 | GCA_014652495 | contig | ncbi | 1225769 |
| 66792 | Paludibacterium paludis strain BCRC 80514 | 1225769.5 | complete | patric | 1225769 |
| 66792 | Paludibacterium paludis strain KCTC 32182 | 1225769.3 | wgs | patric | 1225769 |
GC content
- @ref: 22061
- GC-content: 62.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 84.199 | no |
| gram-positive | no | 98.369 | yes |
| anaerobic | no | 96.876 | no |
| aerobic | yes | 53.55 | yes |
| halophile | no | 92.02 | no |
| spore-forming | no | 93.309 | yes |
| thermophile | no | 99.386 | no |
| motile | yes | 93.491 | yes |
| glucose-util | yes | 85.764 | no |
| glucose-ferment | no | 76.442 | no |
External links
@ref: 22061
culture collection no.: DSM 29672, BCRC 80514, KCTC 32182, LMG 27230
straininfo link
- @ref: 89312
- straininfo: 399454
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24801157 | Paludibacterium paludis sp. nov., isolated from a marsh. | Sheu SY, Chen ZH, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.060954-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry, *Wetlands | Genetics |
| Phylogeny | 27117681 | Paludibacterium purpuratum sp. nov., isolated from wetland soil. | Kang H, Kim H, Joung Y, Kim KJ, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001112 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, *Wetlands | Transcriptome |
| Phylogeny | 33683417 | Crenobacter intestini sp. nov., Isolated from the Intestinal Tract of Konosirus punctatus. | Shi SB, Wu JF, Yang LF, Jiang MG, Gao CM, Jiang CL, Jiang Y | Curr Microbiol | 10.1007/s00284-021-02372-5 | 2021 | Bacterial Typing Techniques, Betaproteobacteria, China, DNA, Bacterial/genetics, *Fatty Acids, Neisseriaceae, *Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 22061 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29672 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29672) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 89312 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID399454.1 |