Strain identifier

BacDive ID: 13168

Type strain: Yes

Species: Pseudomonas ficuserectae

Strain Designation: L7

Strain history: M. Goto strain L7.

NCBI tax ID(s): 53410 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2910

BacDive-ID: 13168

DSM-Number: 6929

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, plant pathogen

description: Pseudomonas ficuserectae L7 is a Gram-negative plant pathogen that was isolated from Ficus erectae.

NCBI tax id

  • NCBI tax id: 53410
  • Matching level: species

strain history

@refhistory
2910<- ATCC <- M. Goto; L7
67770M. Goto strain L7.

doi: 10.13145/bacdive13168.20240510.9

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 ficuserectae
  • full scientific name: Pseudomonas ficuserectae Goto 1983

@ref: 2910

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas ficuserectae

full scientific name: Pseudomonas ficuserectae Goto 1983

strain designation: L7

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480negative98.19
6948090.547yes

Culture and growth conditions

culture medium

  • @ref: 2910
  • name: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220a
  • composition: Name: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperature
2910positivegrowth28
51178positivegrowth28
67770positivegrowth28

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 95.262

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2910--------+-+---++-+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
2910Ficus erectaeFicus erectaeJapanJPNAsia
51178Ficus erectaJapanJPNAsia
67770Ficus erecta Thunb.Ficus erecta

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

Safety information

risk assessment

  • @ref: 2910
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas ficuserectae gene for 16S rRNA, strain: JCM 2400AB0213781513nuccore53410
20218P.ficuserectae 16S rRNA geneZ766611493nuccore53410

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas ficuserectae strain ICMP784853410.3wgspatric53410
66792Pseudomonas ficuserectae ICMP 78482671180595draftimg53410
67770Pseudomonas ficuserectae ICMP 7848GCA_001400815scaffoldncbi53410

GC content

  • @ref: 2910
  • GC-content: 59.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.19no
anaerobicno98.349no
halophileno93.985no
spore-formingno95.262no
glucose-utilyes96.247yes
thermophileno99.697no
motileyes90.547no
flagellatedyes70.337no
aerobicyes95.434no
glucose-fermentno90.034yes

External links

@ref: 2910

culture collection no.: ICMP 7848, DSM 6929, ATCC 35104, CCUG 32779, CFBP 3224, JCM 2400, LMG 5694, PDDCC 7848, CGMCC 1.1791, NCPPB 3693

straininfo link

  • @ref: 82376
  • straininfo: 265423

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27283223Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry.Kaluzna M, Willems A, Pothier JF, Ruinelli M, Sobiczewski P, Pulawska JSyst Appl Microbiol10.1016/j.syapm.2016.05.0052016*Bacterial Typing Techniques, Base Composition, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Genes, Essential/genetics, Nucleic Acid Hybridization, Phylogeny, Prunus avium/*microbiology, Pseudomonas/*classification/*genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methodsTranscriptome
Phylogeny33999789Pseudomonas quercus sp. nov, associated with leaf spot disease of Quercus mongolica.Li Y, Wang S, Bian D, Sun S, Ma TInt J Syst Evol Microbiol10.1099/ijsem.0.0048002021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Diseases/*microbiology, Pseudomonas/*classification/isolation & purification, Quercus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2910Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6929)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6929
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
51178Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32779)https://www.ccug.se/strain?id=32779
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
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)
82376Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265423.1StrainInfo: A central database for resolving microbial strain identifiers