Strain identifier
BacDive ID: 8209
Type strain:
Species: Perlucidibaca piscinae
Strain history: <- J.-C. Cho, Inha University, Incheon
NCBI tax ID(s): 1122951 (strain), 392589 (species)
General
@ref: 15825
BacDive-ID: 8209
DSM-Number: 21586
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Perlucidibaca piscinae DSM 21586 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from eutrophic pond.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1122951 | strain |
392589 | species |
strain history
- @ref: 15825
- history: <- J.-C. Cho, Inha University, Incheon
doi: 10.13145/bacdive8209.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Moraxellaceae
- genus: Perlucidibaca
- species: Perlucidibaca piscinae
- full scientific name: Perlucidibaca piscinae Song et al. 2008
@ref: 15825
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Perlucidibaca
species: Perlucidibaca piscinae
full scientific name: Perlucidibaca piscinae Song et al. 2008 emend. França et al. 2015
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32149 | negative | 0.95 µm | 0.6 µm | rod-shaped | yes | |
69480 | negative | 99.996 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_21586_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21586_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21586_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21586_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_21586_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 15825
- 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 |
---|---|---|---|---|
15825 | positive | growth | 28 | mesophilic |
32149 | positive | growth | 08-37 | |
32149 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32149 | positive | growth | 06-10 | alkaliphile |
32149 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32149
- oxygen tolerance: facultative aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 100 |
halophily
- @ref: 32149
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32149 | 22599 | arabinose | + | carbon source |
32149 | 18403 | L-arabitol | + | carbon source |
32149 | 29016 | arginine | + | carbon source |
32149 | 16947 | citrate | + | carbon source |
32149 | 28260 | galactose | + | carbon source |
32149 | 24265 | gluconate | + | carbon source |
32149 | 5417 | glucosamine | + | carbon source |
32149 | 17234 | glucose | + | carbon source |
32149 | 17754 | glycerol | + | carbon source |
32149 | 15428 | glycine | + | carbon source |
32149 | 27570 | histidine | + | carbon source |
32149 | 17240 | itaconate | + | carbon source |
32149 | 15792 | malonate | + | carbon source |
32149 | 17306 | maltose | + | carbon source |
32149 | 29864 | mannitol | + | carbon source |
32149 | 37684 | mannose | + | carbon source |
32149 | 17268 | myo-inositol | + | carbon source |
32149 | 506227 | N-acetylglucosamine | + | carbon source |
32149 | 18257 | ornithine | + | carbon source |
32149 | 15361 | pyruvate | + | carbon source |
32149 | 16634 | raffinose | + | carbon source |
32149 | 26546 | rhamnose | + | carbon source |
32149 | 33942 | ribose | + | carbon source |
32149 | 17822 | serine | + | carbon source |
32149 | 30911 | sorbitol | + | carbon source |
32149 | 17992 | sucrose | + | carbon source |
32149 | 27082 | trehalose | + | carbon source |
32149 | 17151 | xylitol | + | carbon source |
32149 | 18222 | xylose | + | carbon source |
32149 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 32149
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 32149
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
32149 | alkaline phosphatase | + | 3.1.3.1 |
32149 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 15825
- sample type: eutrophic pond
- geographic location: Incheon
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Pond (small)
taxonmaps
- @ref: 69479
- File name: preview.99_33705.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_669;96_3622;97_4450;98_24952;99_33705&stattab=map
- Last taxonomy: Perlucidibaca piscinae
- 16S sequence: AB681750
- Sequence Identity:
- Total samples: 920
- soil counts: 74
- aquatic counts: 511
- animal counts: 327
- plant counts: 8
Safety information
risk assessment
- @ref: 15825
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Perlucidibaca piscinae gene for 16S rRNA, partial sequence, strain: NBRC 102354 | AB681750 | 1450 | ena | 392589 |
15825 | Perlucidibaca piscinae strain IMCC1704 16S ribosomal RNA gene, partial sequence | DQ664237 | 1467 | ena | 392589 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Perlucidibaca piscinae DSM 21586 | GCA_000420045 | contig | ncbi | 1122951 |
66792 | Perlucidibaca piscinae DSM 21586 | 1122951.3 | wgs | patric | 1122951 |
66792 | Perlucidibaca piscinae DSM 21586 | 2524614877 | draft | img | 1122951 |
GC content
- @ref: 32149
- GC-content: 63.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.466 | yes |
flagellated | yes | 57.315 | no |
gram-positive | no | 98.877 | yes |
anaerobic | no | 99.129 | yes |
aerobic | yes | 85.639 | yes |
halophile | no | 94.316 | yes |
spore-forming | no | 96.151 | no |
glucose-util | no | 85.458 | no |
thermophile | no | 98.545 | yes |
glucose-ferment | no | 93.046 | no |
External links
@ref: 15825
culture collection no.: DSM 21586, KCCM 42363, NBRC 102354, IMCC 1704
straininfo link
- @ref: 77612
- straininfo: 399154
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18175691 | Perlucidibaca piscinae gen. nov., sp. nov., a freshwater bacterium belonging to the family Moraxellaceae. | Song J, Choo YJ, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijs.0.65039-0 | 2008 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Moraxellaceae/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 20601489 | Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater. | Oh KH, Lee SY, Lee MH, Oh TK, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.023994-0 | 2010 | Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Moraxellaceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis | Genetics |
Phylogeny | 23749278 | Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus Paraperlucidibaca Oh et al. 2011. | Yoon JH, Park S, Jung YT, Lee JS, Lee KC | Int J Syst Evol Microbiol | 10.1099/ijs.0.048645-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Moraxellaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Water Microbiology | Genetics |
Phylogeny | 28741994 | Perlucidibaca aquatica sp. nov., isolated from fresh water. | Baek K, Han JH, Lee MH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001940 | 2017 | Bacterial Typing Techniques, Base Composition, Caves, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Moraxellaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 30783797 | Amnimonas aquatica gen. nov., sp. nov., Isolated from a Freshwater River. | Lee Y, Park HY, Jeon CO | Curr Microbiol | 10.1007/s00284-019-01652-5 | 2019 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial/genetics, Moraxellaceae/chemistry/*classification/genetics/*physiology, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Species Specificity, Ubiquinone/chemistry, *Water Microbiology | Phenotype |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
15825 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21586) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21586 | ||||
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 | ||
32149 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 28392 | ||
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 | ||
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 | ||||
77612 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399154.1 | StrainInfo: A central database for resolving microbial strain identifiers |