Strain identifier

BacDive ID: 13126

Type strain: Yes

Species: Pseudomonas fulva

Strain history: CIP <- 2000, IAM <- Iizuka and Komagata, strain: AJ2219

NCBI tax ID(s): 1215102 (strain), 47880 (species)

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General

@ref: 7159

BacDive-ID: 13126

DSM-Number: 17717

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, antibiotic resistance

description: Pseudomonas fulva DSM 17717 is an aerobe, mesophilic, Gram-negative bacterium that has multiple antibiotic resistances and was isolated from rice paddy.

NCBI tax id

NCBI tax idMatching level
47880species
1215102strain

strain history

@refhistory
7159<- IAM
67770IAM 1529 <-- H. Iizuka and K. Komagata Y-8.
119484CIP <- 2000, IAM <- Iizuka and Komagata, strain: AJ2219

doi: 10.13145/bacdive13126.20230509.8.1

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 fulva
  • full scientific name: Pseudomonas fulva Iizuka and Komagata 1963 (Approved Lists 1980)

@ref: 7159

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas fulva

full scientific name: Pseudomonas fulva Iizuka and Komagata 1963

type strain: yes

Morphology

cell morphology

  • @ref: 119484
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 119484
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7159TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
39573MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119484CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7159positivegrowth28mesophilic
39573positivegrowth25mesophilic
58993positivegrowth30mesophilic
67770positivegrowth25mesophilic
119484positivegrowth5-37
119484nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58993aerobe
119484obligate aerobe

antibiogram

  • @ref: 7159
  • medium: Mueller-Hinton Agar
  • incubation temperature: 30
  • incubation time: 1
  • oxygen condition: aerob
  • Penicillin G: 0
  • oxacillin: 0
  • ampicillin: 0
  • ticarcillin: 16-18
  • mezlocillin: 16
  • cefalotin: 0
  • cefazolin: 0
  • cefotaxime: 20
  • aztreonam: 20
  • imipenem: 38-40
  • tetracycline: 24
  • chloramphenicol: 16-18
  • gentamycin: 20-22
  • amikacin: 24-26
  • vancomycin: 0
  • erythromycin: 0
  • lincomycin: 0
  • ofloxacin: 22-24
  • norfloxacin: 30
  • colistin: 16
  • pipemidic acid: 20-22
  • nitrofurantoin: 0
  • bacitracin: 0
  • polymyxin b: 18
  • kanamycin: 26-28
  • neomycin: 20
  • doxycycline: 22
  • ceftriaxone: 20-22
  • clindamycin: 0
  • fosfomycin: 0
  • moxifloxacin: 20
  • linezolid: 0
  • nystatin: 0
  • quinupristin/dalfopristin: 0
  • teicoplanin: 0
  • piperacillin/tazobactam: 22

halophily

  • @ref: 119484
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
6836927897tryptophan-energy source
6836917632nitrate-reduction
11948416947citrate+carbon source
1194844853esculin-hydrolysis
11948417632nitrate-reduction
11948416301nitrite-reduction
11948417632nitrate-respiration

antibiotic resistance

  • @ref: 119484
  • 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
11948435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
119484oxidase+
119484beta-galactosidase-3.2.1.23
119484alcohol dehydrogenase+1.1.1.1
119484gelatinase-
119484amylase-
119484DNase-
119484caseinase-3.4.21.50
119484catalase+1.11.1.6
119484tween esterase+
119484lecithinase-
119484lipase-
119484lysine decarboxylase-4.1.1.18
119484ornithine decarboxylase-4.1.1.17
119484protease-
119484tryptophan deaminase-
119484urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119484-++++++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7159--++----+-----++-++--
7159---+----+-----++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119484++--+--------------+-----------+------------+----+++-+--+---+-+-+-----++++-+++-++++++--++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7159rice paddyJapanJPNAsia
119484Food, Japanese unhulled riceJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_278.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_278&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB060136
  • Sequence Identity:
  • Total samples: 250
  • soil counts: 47
  • aquatic counts: 36
  • animal counts: 93
  • plant counts: 74

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71591Risk group (German classification)
1194841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas fulva gene for 16S rRNA, partial sequence, strain:NRIC 0180(T)AB0469981484ena47880
20218Pseudomonas fulva 16S rRNA gene, complete sequenceD840151526ena47880
7159Pseudomonas fulva gene for 16S rRNA, partial sequence, strain: NRIC 0180AB0601361484ena47880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas fulva NBRC 16637 = DSM 177171215102.3wgspatric1215102
66792Pseudomonas fulva NBRC 16637 = DSM 177171215102.4wgspatric1215102
66792Pseudomonas fulva NBRC 166372585427679draftimg1215102
66792Pseudomonas fulva DSM 177172556921649draftimg1215102
67770Pseudomonas fulva NBRC 16637 = DSM 17717GCA_000730565contigncbi1215102
67770Pseudomonas fulva NBRC 16637 = DSM 17717GCA_000621265scaffoldncbi1215102

GC content

  • @ref: 67770
  • GC-content: 60
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.748no
gram-positiveno98.595no
anaerobicno97.407yes
aerobicyes91.053yes
halophileno83.547no
spore-formingno94.392no
thermophileno99.805yes
glucose-utilyes89.118yes
flagellatedyes85.4no
glucose-fermentno87.335no

External links

@ref: 7159

culture collection no.: DSM 17717, IAM 1529, IFO 16637, JCM 11242, NRIC 0180, CCUG 50780, CIP 106765, CIP 106819, ATCC 31418, LMG 11722, NBRC 16637, JCM 20202, BCRC 11058, BCRC 17506, CCUG 106765, KACC 10774, KACC 10795, AJ 2219

straininfo link

  • @ref: 82334
  • straininfo: 8243

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12483612Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov.Uchino M, Shida O, Uchimura T, Komagata KJ Gen Appl Microbiol10.2323/jgam.47.2472001
Phylogeny15774686Pseudomonas pachastrellae sp. nov., isolated from a marine sponge.Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.63176-02005Animals, Bacterial Typing Techniques, DNA, Bacterial, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Metabolism20066562Control of pyrimidine nucleotide formation in Pseudomonas fulva.West TPAntonie Van Leeuwenhoek10.1007/s10482-009-9410-z2010Aspartate Carbamoyltransferase/metabolism, Cytidine Triphosphate/pharmacology, Dihydroorotase/metabolism, Dihydroorotate Dehydrogenase, Diphosphates/pharmacology, Enzyme Inhibitors, *Gene Expression Regulation, Bacterial, *Gene Expression Regulation, Enzymologic, Glucose, Guanosine Diphosphate/pharmacology, Guanosine Triphosphate/pharmacology, Orotate Phosphoribosyltransferase/metabolism, Oxidoreductases Acting on CH-CH Group Donors/metabolism, Pseudomonas/metabolism/*physiology, Pyrimidine Nucleotides/*biosynthesis, Uracil/metabolismEnzymology
Genetics27594974High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains.Pena A, Busquets A, Gomila M, Mulet M, Gomila RM, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Garcia-Valdes E, Goker M, Woyke T, Klenk HP, Kyrpides N, Lalucat JStand Genomic Sci10.1186/s40793-016-0178-22016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7159Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17717)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17717
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
39573Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18931
58993Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50780)https://www.ccug.se/strain?id=50780
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
82334Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8243.1StrainInfo: A central database for resolving microbial strain identifiers
119484Curators of the CIPCollection of Institut Pasteur (CIP 106765)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106765