Strain identifier

BacDive ID: 159714

Type strain: Yes

Species: Caballeronia insecticola

Strain Designation: RPE64

Strain history: Y. Kikuchi; Bioprod. Res. Inst., AIST, Japan; RPE64.

NCBI tax ID(s): 758793 (species)

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

@ref: 66600

BacDive-ID: 159714

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

description: Caballeronia insecticola RPE64 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from midgut crypts of the bean bug, Riptortus pedestris, from a pea field.

NCBI tax id

  • NCBI tax id: 758793
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. Kikuchi; Bioprod. Res. Inst., AIST, Japan; RPE64.

doi: 10.13145/bacdive159714.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Caballeronia
  • species: Caballeronia insecticola
  • full scientific name: Caballeronia insecticola (Takeshita et al. 2018) Dobritsa and Samadpour 2019
  • synonyms

    • @ref: 20215
    • synonym: Burkholderia insecticola

@ref: 66600

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Caballeronia

species: Caballeronia insecticola

strain designation: RPE64

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
66600negative2.4-3.2 µm0.9 µmrod-shapedyespolar
69480yes92.821
69480negative99.988

colony morphology

  • @ref: 66600
  • colony color: white-creamy
  • colony shape: circular
  • medium used: yeast glucose agar

Culture and growth conditions

culture medium

@refnamegrowth
66600MacConkey agaryes
66600yeast glucose agaryes

culture temp

@refgrowthtypetemperaturerange
66600positiveoptimum30mesophilic
66600positivegrowth15-35
67770positivegrowth30mesophilic

culture pH

  • @ref: 66600
  • ability: positive
  • type: growth
  • pH: 6-8

Physiology and metabolism

oxygen tolerance

  • @ref: 66600
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
66600no
69480no99.983
69481no100

halophily

@refsaltgrowthtested relationconcentration
66600NaClpositivegrowth0-2.5 %(w/v)
66600NaClpositiveoptimum1.5 %(w/v)

observation

  • @ref: 66600
  • observation: motile by two or three polar flagella

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6660017128adipate-assimilation
6660017306maltose-assimilation
6660053258citric acid-assimilation
6660017234glucose+assimilation
6660018401phenylacetate+assimilation
6660022599arabinose+assimilation
6660024265gluconate+assimilation
6660025115malate+assimilation
6660027689decanoate+assimilation
6660029864mannitol+assimilation
6660037684mannose+assimilation
6660059640N-acetylglucosamine+assimilation
6660017234glucose-fermentation
6660053424tween 20-growth
6660053426tween 80-growth
6660053423tween 40+growth
6660053425tween 60+growth
666004853esculin-hydrolysis
666005291gelatin-hydrolysis
6660028017starch-hydrolysis
6660053423tween 40-hydrolysis
6660053424tween 20-hydrolysis
6660053426tween 80-hydrolysis
66600casein-hydrolysis
6660053425tween 60+hydrolysis
6660017632nitrate-reduction

enzymes

@refvalueactivityec
66600alkaline phosphatase-3.1.3.1
66600alpha-fucosidase-3.2.1.51
66600alpha-galactosidase-3.2.1.22
66600alpha-glucosidase-3.2.1.20
66600alpha-mannosidase-3.2.1.24
66600arginine dihydrolase-3.5.3.6
66600beta-galactosidase-3.2.1.23
66600beta-glucosidase-3.2.1.21
66600beta-glucuronidase-3.2.1.31
66600chymotrypsin-3.4.4.5
66600cystine arylamidase-3.4.11.3
66600cytochrome oxidase-1.9.3.1
66600DNase-
66600esterase Lipase (C 8)-
66600leucine arylamidase-3.4.11.1
66600N-acetyl-beta-glucosaminidase-3.2.1.52
66600phosphoamidase-3.9.1.1
66600trypsin-3.4.21.4
66600tryptophanase-4.1.99.1
66600urease-3.5.1.5
66600valine arylamidase-
66600acid phosphatase+3.1.3.2
66600catalase+1.11.1.6
66600esterase (C 4)+
66600lipase (C 14)+

Isolation, sampling and environmental information

isolation

@refsample typehost speciessampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
66600midgut crypts of the bean bug, Riptortus pedestris, from a pea fieldRiptortus pedestris2007TsukubaJapanJPNAsiayeast glucose agar(0.5 % yeast extract, 0.4 % glucose, 0.1 % NaCl and 1.5 % agar, pH 7.0)3 days26
67770Midgut crypts of the bean bug, Riptortus pedestris, Japan in 2007Riptortus pedestrisTsukubaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

Sequence information

16S sequences

  • @ref: 66600
  • description: Burkholderia insecticola gene for 16S rRNA, partial sequence
  • accession: AB558208
  • length: 1456
  • database: ena
  • NCBI tax ID: 758793

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caballeronia insecticola RPE64GCA_000402035completencbi758793
66792Caballeronia insecticola RPE642773857905completeimg758793
66792Caballeronia insecticola RPE642597489944completeimg758793

GC content

  • @ref: 66600
  • GC-content: 63.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.729yes
flagellatedno81.142no
gram-positiveno97.931yes
anaerobicno98.69yes
aerobicyes90.986yes
halophileno93.483yes
spore-formingno94.286yes
thermophileno99.476no
glucose-utilyes89.05yes
glucose-fermentno90.224yes

External links

@ref: 66600

culture collection no.: NCIMB 15023, JCM 31142

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29863457Burkholderia insecticola sp. nov., a gut symbiotic bacterium of the bean bug Riptortus pedestris.Takeshita K, Tamaki H, Ohbayashi T, Meng XY, Sone T, Mitani Y, Peeters C, Kikuchi Y, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0028482018Animals, Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Digestive System/*microbiology, Fatty Acids/chemistry, Heteroptera/*microbiology, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Symbiosis, Ubiquinone/chemistryTranscriptome
Phylogeny31091185Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies.Dobritsa AP, Samadpour MInt J Syst Evol Microbiol10.1099/ijsem.0.0034312019Bacterial Typing Techniques, Burkholderia/*classification, Burkholderiaceae/*classification, DNA, Bacterial/genetics, INDEL Mutation, *Phylogeny, RNA, Ribosomal, 16S/genetics, Reproducibility of Results, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
66600Kazutaka Takeshita, Hideyuki Tamaki, Tsubasa Ohbayashi, Xian-Ying Meng, Teruo Sone, Yasuo Mitani, Charlotte Peeters, Yoshitomo Kikuchi, Peter VandammeBurkholderia insecticola sp. nov., a gut symbiotic bacterium of the bean bug Riptortus pedestris10.1099/ijsem.0.002848IJSEM 68: 2370-2374 201829863457
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1