Strain identifier

BacDive ID: 13128

Type strain: Yes

Species: Pseudomonas straminea

Strain Designation: CB-7

Strain history: CIP <- 2000, IAM <- S. Ikemoto: strain AJ 2124 <- Iizuka and Kamagata: strain CB-7

NCBI tax ID(s): 1215117 (strain), 47882 (species)

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General

@ref: 6923

BacDive-ID: 13128

DSM-Number: 17727

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudomonas straminea CB-7 is an aerobe, mesophilic, motile bacterium that was isolated from rice paddy.

NCBI tax id

NCBI tax idMatching level
47882species
1215117strain

strain history

@refhistory
6923<- IAM
67770K. Komagata KS 0028 <-- AJ 2124 <-- IAM 1598 <-- H. Iizuka and K. Komagata CB-7.
123324CIP <- 2000, IAM <- S. Ikemoto: strain AJ 2124 <- Iizuka and Kamagata: strain CB-7

doi: 10.13145/bacdive13128.20230509.8.1

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 straminea
  • full scientific name: Pseudomonas straminea corrig. Iizuka and Komagata 1963 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas straminae

@ref: 6923

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas straminea

full scientific name: Pseudomonas straminea Iizuka and Komagata 1963 emend. Uchino et al. 2000

strain designation: CB-7

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.952
6948099.987negative
123324yesnegativerod-shaped

colony morphology

  • @ref: 45738
  • incubation period: 1 day

pigmentation

  • @ref: 123324
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6923TRYPTICASE 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
39571MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123324CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6923positivegrowth28mesophilic
39571positivegrowth25mesophilic
45738positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
123324positivegrowth5-37
123324nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45738aerobe
123324obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.935

halophily

@refsaltgrowthtested relationconcentration
123324NaClpositivegrowth0-6 %
123324NaClnogrowth8 %
123324NaClnogrowth10 %

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
6836917632nitrate-reduction
12332416947citrate+carbon source
1233244853esculin-hydrolysis
12332417632nitrate-reduction
12332416301nitrite-reduction
12332417632nitrate-respiration

antibiotic resistance

  • @ref: 123324
  • 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
12332435581indoleno

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
123324oxidase+
123324beta-galactosidase-3.2.1.23
123324alcohol dehydrogenase-1.1.1.1
123324gelatinase+/-
123324amylase-
123324DNase+
123324caseinase-3.4.21.50
123324catalase+1.11.1.6
123324tween esterase-
123324lecithinase-
123324lipase-
123324lysine decarboxylase-4.1.1.18
123324ornithine decarboxylase-4.1.1.17
123324protease-
123324tryptophan deaminase-
123324urease-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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    45738C10:00.210
    45738C11:00.211
    45738C12:010.812
    45738C13:00.213
    45738C14:00.714
    45738C15:01.715
    45738C16:016.216
    45738C17:00.417
    45738C18:00.318
    45738C10:0 3OH4.211.423
    45738C11:0 3OH0.212.441
    45738C12:0 3OH3.113.455
    45738C15:1 ω6c0.514.856
    45738C16:0 iso0.415.626
    45738C16:1 ω7c24.515.819
    45738C17:1 ω6c0.316.862
    45738C17:1 ω8c1.216.792
    45738C18:1 ω7c /12t/9t34.217.824
    45738C18:2 ω6,9c/C18:0 ANTE0.217.724
    45738Unidentified0.218.798
    45738unknown 11.7980.211.798
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123324-+++-++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6923--------++++--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123324+++-+---------------+-----+----+-+---------++----+++-+++--+-+-+++--+--++++-+++-+++-++--++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6923rice paddyJapanJPNAsia
45738Japanese unhulled riceJapanJPNAsiaTokyo
123324Food, Japanese unhulled rice

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3608.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_2761;99_3608&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: LC420056
  • Sequence Identity:
  • Total samples: 2786
  • soil counts: 552
  • aquatic counts: 752
  • animal counts: 734
  • plant counts: 748

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69231Risk group (German classification)
1233241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas straminea 16S rRNA gene, complete sequenceD840231527ena47882
20218Pseudomonas straminea gene for 16S rRNA, partial sequence, strain: NBRC 16665AB6811011461ena47882
67770Pseudomonas straminea JCM 2783 gene for 16S ribosomal RNA, partial sequenceLC4200561474ena47882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas straminea strain JCM 278347882.3wgspatric47882
66792Pseudomonas straminea JCM 27832663762767draftimg47882
67770Pseudomonas straminea JCM 2783GCA_900112645scaffoldncbi47882

GC content

  • @ref: 67770
  • GC-content: 62.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.663no
anaerobicno96.567yes
halophileno89.7no
spore-formingno94.13no
glucose-utilyes94.51yes
aerobicyes93.82yes
motileyes88.461no
flagellatedyes75.424no
thermophileno99.493yes
glucose-fermentno91.073yes

External links

@ref: 6923

culture collection no.: DSM 17727, IAM 1598, JCM 2783, NRIC 0164, CCUG 12539, ATCC 33636, CIP 106745, CCM 7503, AJ 2124, CGMCC 1.1797, IFO 16665, LMG 21615, NBRC 16665

straininfo link

  • @ref: 82336
  • straininfo: 40592

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
Phylogeny15879241Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina.Peix A, Berge O, Rivas R, Abril A, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63445-02005Aerobiosis, Argentina, Bacterial Typing Techniques, Base Composition, Caseins/metabolism, Catalase/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella, Gelatin/metabolism, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/*biosynthesis, Pseudomonas/*classification/cytology/*isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6923Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17727)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17727
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
39571Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18909
45738Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12539)https://www.ccug.se/strain?id=12539
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82336Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40592.1StrainInfo: A central database for resolving microbial strain identifiers
123324Curators of the CIPCollection of Institut Pasteur (CIP 106745)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106745