Strain identifier

BacDive ID: 13086

Type strain: Yes

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)

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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 idMatching level
70775species
1215115strain

strain history

@refhistory
5701<- ATCC <- H. Wakabayashi and K. Sawada
67770H. Wakabayashi; Grad. Sch. of Agric. & Life Sci., Univ. of Tokyo, Japan; FPC 951.
121868CIP <- 2000, H. Wakabayashi, Tokyo Univ., Tokyo, Japan: strain FPC 951 <- K. Sawada, "Pseudomonas ayucida"

doi: 10.13145/bacdive13086.20250331.9.3

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

@refgram staincell shapemotilityconfidence
121868negativerod-shapedyes
125438yes92.006
125438negative99
125439yes92.8
125439negative99.1

pigmentation

  • @ref: 121868
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5701CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
41751MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121868CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
5701positivegrowth28
41751positivegrowth30
58634positivegrowth30
67770positivegrowth30
121868positivegrowth10-37
121868nogrowth5
121868nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
58634aerobe
121868obligate aerobe
125438aerobe92.259
125439obligate aerobe95.9

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.9

halophily

@refsaltgrowthtested relationconcentration
121868NaClpositivegrowth0-6 %
121868NaClnogrowth8 %
121868NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12186816947citrate+carbon source
1218684853esculin-hydrolysis
12186817632nitrate+reduction
12186816301nitrite-reduction
12186817632nitrate-respiration
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

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

@refChebi-IDmetaboliteproduction
6836935581indoleno
12186835581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
121868oxidase+
121868beta-galactosidase-3.2.1.23
121868alcohol dehydrogenase+1.1.1.1
121868gelatinase-
121868amylase-
121868DNase-
121868caseinase-3.4.21.50
121868catalase+1.11.1.6
121868tween esterase-
121868lecithinase-
121868lipase-
121868lysine decarboxylase-4.1.1.18
121868ornithine decarboxylase-4.1.1.17
121868protease-
121868tryptophan deaminase-
121868urease-3.5.1.5
68369gelatinase-
68369urease-3.5.1.5
68382alpha-galactosidase-3.2.1.22
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase+3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121868--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5701+--+----+-----++-++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121868++-----------------------------+------------+----++--+------+++++--+--++++++++++++-++--++++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateisolation date
5701diseased ayu, Plecoglossus altevelisPlecoglossus altevelisTokushimaJapanJPNAsia
58634Ayu,Plecoglossus altivelisTokushimaJapanJPNAsia1994
67770Ayu (Plecoglossus altivelis) with bacterial haemorrhagic ascitesPlecoglossus altivelisTokushima Pref.JapanJPNAsia
121868Animal, Ayu, Plecoglossus altivelisTokushimaJapanJPNAsia1994

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

@refpathogenicity animalbiosafety levelbiosafety level comment
5701yes1Risk group (German classification)
1218681Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas plecoglossicida gene for 16S rRNA, partial sequence, strain: NBRC 103162AB6819701462nuccore70775
5701Pseudomonas plecoglossicida gene for 16S rRNAAB0094571498nuccore70775
124043Pseudomonas plecoglossicida NBRC 103162 gene for 16S rRNA, partial sequence.LC752399587nuccore70775

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas plecoglossicida NBRC 103162 = DSM 150881215115.4wgspatric1215115
66792Pseudomonas plecoglossicida NBRC 103162 = DSM 150881215115.3wgspatric1215115
66792Pseudomonas plecoglossicida NBRC 1031622585427685draftimg1215115
66792Pseudomonas plecoglossicida DSM 150882556921648draftimg1215115
67770Pseudomonas plecoglossicida NBRC 103162 = DSM 15088GCA_000730665contigncbi1215115
67770Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 DSM 15088GCA_000688275scaffoldncbi1215115

GC content

  • @ref: 67770
  • GC-content: 62.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.1
125439BacteriaNetmotilityAbility to perform movementyes92.8
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.9
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.445yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.84no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.259yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.986no
125438motile2+flagellatedAbility to perform flagellated movementyes92.006no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826790Pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossus altivelis.Nishimori E, Kita-Tsukamoto K, Wakabayashi HInt J Syst Evol Microbiol10.1099/00207713-50-1-832000Animals, 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, DNAGenetics
Phylogeny24562759Pseudomonas hunanensis sp. nov., isolated from soil subjected to long-term manganese pollution.Gao J, Li BY, Wang HH, Liu ZQCurr Microbiol10.1007/s00284-014-0545-42014Bacterial 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 MicrobiologyGenetics
Phylogeny30566068Pseudomonas sichuanensis sp. nov., isolated from hospital sewage.Qin J, Hu Y, Feng Y, Xaioju L, Zong ZInt J Syst Evol Microbiol10.1099/ijsem.0.0031882018Bacterial 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/*microbiologyTranscriptome
Phylogeny32553047Pseudomonas defluvii sp. nov., isolated from hospital sewage.Qin J, Hu Y, Wu W, Feng Y, Zong ZInt J Syst Evol Microbiol10.1099/ijsem.0.0042722020Bacterial 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 WaterTranscriptome
Genetics32974501High-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 JAccess Microbiol10.1099/acmi.0.0000672019

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5701Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15088)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15088
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41751Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18629
58634Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49623)https://www.ccug.se/strain?id=49623
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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
82296Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43905.1StrainInfo: A central database for resolving microbial strain identifiers
121868Curators of the CIPCollection of Institut Pasteur (CIP 106493)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106493
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1