Strain identifier
BacDive ID: 13086
Type strain:
Species: Pseudomonas plecoglossicida
Strain history: CIP <- 2000, H. Wakabayashi, Tokyo Univ., Tokyo, Japan: strain FPC 951 <- K. Sawada, "Pseudomonas ayucida"
NCBI tax ID(s): 1215115 (strain), 70775 (species)
General
@ref: 5701
BacDive-ID: 13086
DSM-Number: 15088
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, animal pathogen
description: Pseudomonas plecoglossicida CCUG 49623 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from diseased ayu, Plecoglossus altevelis.
NCBI tax id
NCBI tax id | Matching level |
---|---|
70775 | species |
1215115 | strain |
strain history
@ref | history |
---|---|
5701 | <- ATCC <- H. Wakabayashi and K. Sawada |
67770 | H. Wakabayashi; Grad. Sch. of Agric. & Life Sci., Univ. of Tokyo, Japan; FPC 951. |
121868 | CIP <- 2000, H. Wakabayashi, Tokyo Univ., Tokyo, Japan: strain FPC 951 <- K. Sawada, "Pseudomonas ayucida" |
doi: 10.13145/bacdive13086.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas plecoglossicida
- full scientific name: Pseudomonas plecoglossicida Nishimori et al. 2000
@ref: 5701
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas plecoglossicida
full scientific name: Pseudomonas plecoglossicida Nishimori et al. 2000
type strain: yes
Morphology
cell morphology
- @ref: 121868
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 121868
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5701 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
41751 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121868 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5701 | positive | growth | 28 | mesophilic |
41751 | positive | growth | 30 | mesophilic |
58634 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
121868 | positive | growth | 10-37 | |
121868 | no | growth | 5 | psychrophilic |
121868 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
58634 | aerobe |
121868 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121868 | NaCl | positive | growth | 0-6 % |
121868 | NaCl | no | growth | 8 % |
121868 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | + | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
121868 | 16947 | citrate | + | carbon source |
121868 | 4853 | esculin | - | hydrolysis |
121868 | 17632 | nitrate | + | reduction |
121868 | 16301 | nitrite | - | reduction |
121868 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 121868
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121868 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | + | 3.5.3.6 |
121868 | oxidase | + | |
121868 | beta-galactosidase | - | 3.2.1.23 |
121868 | alcohol dehydrogenase | + | 1.1.1.1 |
121868 | gelatinase | - | |
121868 | amylase | - | |
121868 | DNase | - | |
121868 | caseinase | - | 3.4.21.50 |
121868 | catalase | + | 1.11.1.6 |
121868 | tween esterase | - | |
121868 | lecithinase | - | |
121868 | lipase | - | |
121868 | lysine decarboxylase | - | 4.1.1.18 |
121868 | ornithine decarboxylase | - | 4.1.1.17 |
121868 | protease | - | |
121868 | tryptophan deaminase | - | |
121868 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121868 | - | - | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5701 | + | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | - | + | + | + | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121868 | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | + | + | + | + | + | - | - | + | - | - | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | - | - | + | + | + | + | + | + | + | + | - | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|---|
5701 | diseased ayu, Plecoglossus altevelis | Plecoglossus altevelis | Tokushima | Japan | JPN | Asia | ||
58634 | Ayu,Plecoglossus altivelis | Tokushima | Japan | JPN | Asia | 1994 | ||
67770 | Ayu (Plecoglossus altivelis) with bacterial haemorrhagic ascites | Plecoglossus altivelis | Tokushima Pref. | Japan | JPN | Asia | ||
121868 | Animal, Ayu, Plecoglossus altivelis | Tokushima | Japan | JPN | Asia | 1994 |
isolation source categories
- Cat1: #Host
- Cat2: #Fishes
taxonmaps
- @ref: 69479
- File name: preview.99_239.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_239&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: AB009457
- Sequence Identity:
- Total samples: 2133
- soil counts: 368
- aquatic counts: 543
- animal counts: 799
- plant counts: 423
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
5701 | yes | 1 | Risk group (German classification) |
121868 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudomonas plecoglossicida gene for 16S rRNA, partial sequence, strain: NBRC 103162 | AB681970 | 1462 | ena | 70775 |
5701 | Pseudomonas plecoglossicida gene for 16S rRNA | AB009457 | 1498 | ena | 70775 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 | 1215115.4 | wgs | patric | 1215115 |
66792 | Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 | 1215115.3 | wgs | patric | 1215115 |
66792 | Pseudomonas plecoglossicida NBRC 103162 | 2585427685 | draft | img | 1215115 |
66792 | Pseudomonas plecoglossicida DSM 15088 | 2556921648 | draft | img | 1215115 |
67770 | Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 | GCA_000730665 | contig | ncbi | 1215115 |
67770 | Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 DSM 15088 | GCA_000688275 | scaffold | ncbi | 1215115 |
GC content
- @ref: 67770
- GC-content: 62.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 90.657 | no |
gram-positive | no | 98.476 | no |
anaerobic | no | 97.912 | yes |
aerobic | yes | 94.179 | no |
halophile | no | 84.389 | no |
spore-forming | no | 94.868 | no |
thermophile | no | 99.705 | yes |
glucose-util | yes | 89.618 | no |
flagellated | yes | 83.766 | no |
glucose-ferment | no | 88.59 | yes |
External links
@ref: 5701
culture collection no.: CCUG 49623, CIP 106493, DSM 15088, ATCC 700383, FPC 951, JCM 13297, BCRC 17517, IAM 15126, JCM 21584, LMG 21750, LMG 23766, NBRC 103162, NCIMB 13649, VTT E-072699
straininfo link
- @ref: 82296
- straininfo: 43905
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10826790 | Pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossus altivelis. | Nishimori E, Kita-Tsukamoto K, Wakabayashi H | Int J Syst Evol Microbiol | 10.1099/00207713-50-1-83 | 2000 | Animals, Ascites/microbiology/veterinary, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fish Diseases/*microbiology, Fishes, Genes, rRNA, Hemorrhage/microbiology/veterinary, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/physiology, Pseudomonas Infections/microbiology/*veterinary, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 24562759 | Pseudomonas hunanensis sp. nov., isolated from soil subjected to long-term manganese pollution. | Gao J, Li BY, Wang HH, Liu ZQ | Curr Microbiol | 10.1007/s00284-014-0545-4 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Environmental Pollution, Fatty Acids/analysis, Genotype, Manganese/pharmacology, Molecular Sequence Data, Phenotype, Phylogeny, Pseudomonas/classification/drug effects/genetics/*isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, Soil Microbiology | Genetics |
Phylogeny | 30566068 | Pseudomonas sichuanensis sp. nov., isolated from hospital sewage. | Qin J, Hu Y, Feng Y, Xaioju L, Zong Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003188 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hospitals, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology | Transcriptome |
Phylogeny | 32553047 | Pseudomonas defluvii sp. nov., isolated from hospital sewage. | Qin J, Hu Y, Wu W, Feng Y, Zong Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004272 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hospitals, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Waste Water | Transcriptome |
Genetics | 32974501 | High-quality draft genome sequences of Pseudomonas monteilii DSM 14164(T), Pseudomonas mosselii DSM 17497(T), Pseudomonas plecoglossicida DSM 15088(T), Pseudomonas taiwanensis DSM 21245(T) and Pseudomonas vranovensis DSM 16006(T): taxonomic considerations. | Pena A, Busquets A, Gomila M, Mulet M, Gomila RM, Garcia-Valdes E, Reddy TBK, Huntemann M, Varghese N, Ivanova N, Chen IM, Goker M, Woyke T, Klenk HP, Kyrpides N, Lalucat J | Access Microbiol | 10.1099/acmi.0.000067 | 2019 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5701 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15088) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15088 | |||
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 | |
41751 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18629 | ||||
58634 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 49623) | https://www.ccug.se/strain?id=49623 | |||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
82296 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43905.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121868 | Curators of the CIP | Collection of Institut Pasteur (CIP 106493) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106493 |