Strain identifier

BacDive ID: 13109

Type strain: Yes

Species: Pseudomonas cremoricolorata

Strain Designation: KS 0031

Strain history: CIP <- 2002, JCM <- M. Uchino <- NRIC 0181 <- IAM 1541 <- K. Komagata: strain KS 0031 <- AJ 2127 <- H. Lizuka and K. Komagata CC-8

NCBI tax ID(s): 1215098 (strain), 157783 (species)

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General

@ref: 6728

BacDive-ID: 13109

DSM-Number: 17059

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

description: Pseudomonas cremoricolorata KS 0031 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Oryza sativa.

NCBI tax id

NCBI tax idMatching level
157783species
1215098strain

strain history

@refhistory
6728<- M. Uchino, Tokyo University of Agriculture <- NRIC <- IAM <- S. Ikemoto <- Central Research Labs, Ajinomoto Co., Ltd, Kawasaki <- H. Iizuka and K. Komagata; CC-8
67770IAM 1541 <-- S. Ikemoto KS 0031 <-- H. Iizuka and K. Komagata CC-8.
118782CIP <- 2002, JCM <- M. Uchino <- NRIC 0181 <- IAM 1541 <- K. Komagata: strain KS 0031 <- AJ 2127 <- H. Lizuka and K. Komagata CC-8

doi: 10.13145/bacdive13109.20230509.8.1

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 cremoricolorata
  • full scientific name: Pseudomonas cremoricolorata Uchino et al. 2002

@ref: 6728

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas cremoricolorata

full scientific name: Pseudomonas cremoricolorata Uchino et al. 2002

strain designation: KS 0031

type strain: yes

Morphology

cell morphology

  • @ref: 118782
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 118782
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6728CASO 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
38217MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118782CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6728positivegrowth30mesophilic
38217positivegrowth30mesophilic
60048positivegrowth30mesophilic
67770positivegrowth25mesophilic
118782positivegrowth25-41
118782nogrowth5psychrophilic
118782nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60048aerobe
118782obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118782NaClpositivegrowth0-6 %
118782NaClnogrowth8 %
118782NaClnogrowth10 %

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
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
11878216947citrate+carbon source
1187824853esculin-hydrolysis
11878217632nitrate-reduction
11878216301nitrite-reduction
11878217632nitrate-respiration

antibiotic resistance

  • @ref: 118782
  • 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
11878235581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118782oxidase+
118782beta-galactosidase-3.2.1.23
118782alcohol dehydrogenase-1.1.1.1
118782gelatinase-
118782amylase-
118782DNase-
118782caseinase+3.4.21.50
118782catalase+1.11.1.6
118782tween esterase+
118782lecithinase-
118782lipase-
118782lysine decarboxylase-4.1.1.18
118782ornithine decarboxylase-4.1.1.17
118782protease-
118782tryptophan deaminase-
118782urease-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
118782--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6728+-------+-----++-++-+
6728--------+-----++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118782++-----------------+-----------+------------+--+-+++-+--+---+-+-+-----++++-+++-+++++---++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
6728Oryza sativaOryza sativaJapanJPNAsia
60048Japanese rice paddyJapanJPNAsia
67770Japanese rice paddy
118782Food, Japanese rice paddyJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67281Risk group (German classification)
1187821Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6728Pseudomonas cremoricolorata gene for 16S rRNA, partial sequence, strain: IAM 1541AB0601371484ena1215098
67770Pseudomonas fulva gene for 16S rRNA, partial sequence, strain:IAM 1541AB0469991484ena47880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas cremoricolorata DSM 170591292028.3wgspatric1215098
66792Pseudomonas cremoricolorata NBRC 166341215098.3wgspatric1215098
66792Pseudomonas cremoricolorata DSM 170592523533534draftimg1215098
66792Pseudomonas cremoricolorata NBRC 166342585427684draftimg1215098
67770Pseudomonas cremoricolorata DSM 17059 = NBRC 16634GCA_000425745scaffoldncbi1215098

GC content

@refGC-contentmethod
672862.1
6777060high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.475no
gram-positiveno98.37no
anaerobicno97.649no
aerobicyes89.388no
halophileno80.189no
spore-formingno93.427no
thermophileno99.669yes
glucose-utilyes88.967no
flagellatedyes79.467no
glucose-fermentno89.936yes

External links

@ref: 6728

culture collection no.: DSM 17059, AJ 2127, IFO 16634, JCM 11246, NRIC 0181, CCUG 53878, NBRC 16634, JCM 20204, BCRC 17510, CIP 107616, DSM 10759, IAM 1541, LMG 24039, LMG 27905

straininfo link

  • @ref: 82317
  • straininfo: 370254

literature

topicPubmed-IDtitleauthorsjournalDOIyear
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
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
6728Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17059)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17059
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
38217Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5071
60048Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53878)https://www.ccug.se/strain?id=53878
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
82317Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370254.1StrainInfo: A central database for resolving microbial strain identifiers
118782Curators of the CIPCollection of Institut Pasteur (CIP 107616)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107616