Strain identifier

BacDive ID: 141120

Type strain: Yes

Species: Ideonella paludis

Strain Designation: KBP-31

NCBI tax ID(s): 1233411 (species)

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General

@ref: 44032

BacDive-ID: 141120

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

description: Ideonella paludis KBP-31 is an obligate aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from water sample.

NCBI tax id

  • NCBI tax id: 1233411
  • Matching level: species

doi: 10.13145/bacdive141120.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ideonella
  • species: Ideonella paludis
  • full scientific name: Ideonella paludis Sheu et al. 2016

@ref: 44032

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiales, not assigned to family

genus: Ideonella

species: Ideonella paludis

strain designation: KBP-31

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44032negative0.8-1.4 µm0.4-0.8 µmrod-shapedyes
69480yes95.493
69480negative99.997

colony morphology

  • @ref: 44032
  • colony size: 0.8-1.2 mm
  • colony color: light-yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
44032nutrient brothno
44032Reasoner's 2A agar (R2A)yes
44032tryptic soy brothyes

culture temp

@refgrowthtypetemperaturerange
44032positivegrowth10-37
44032positiveoptimum25mesophilic
44032mesophilic

culture pH

@refabilitytypepH
44032positivegrowth6.0-8.0
44032positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 44032
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 44032
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentrationhalophily level
44032NaClpositivegrowth0-1 %(w/v)
44032NaClpositiveoptimum0 %(w/v)
44032non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4403217128adipate-assimilation
4403222599arabinose-assimilation
440328295beta-hydroxybutyrate-assimilation
4403227689decanoate-assimilation
4403216947citrate-assimilation
4403224265gluconate-assimilation
4403217234glucose-assimilation
4403225115malate-assimilation
4403217306maltose-assimilation
4403229864mannitol-assimilation
4403237684mannose-assimilation
44032506227N-acetylglucosamine-assimilation
4403218401phenylacetate-assimilation
4403217634D-glucose-builds acid from
4403285146carboxymethylcellulose-hydrolysis
4403217029chitin-hydrolysis
44032corn oil-hydrolysis
4403216991dna-hydrolysis
440324853esculin-hydrolysis
4403261995lecithin-hydrolysis
4403228017starch-hydrolysis
4403253423tween 40-hydrolysis
4403253425tween 60-hydrolysis
4403253426tween 80-hydrolysis
4403217632nitrate-reduction
4403258187alginate+hydrolysis
44032casein+hydrolysis
440325291gelatin+hydrolysis
4403253424tween 20+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4403228971ampicillinyesyes10 µg (disc)
4403217698chloramphenicolyesyes30 µg (disc)
440326104kanamycinyesyes30 µg (disc)
44032100147nalidixic acidyesyes30 µg (disc)
4403228368novobiocinyesyes30 µg (disc)
4403218208penicillin gyesyes10 Unit (disc)
4403228077rifampicinyesyes5 µg (disc)
4403217076streptomycinyesyes10 µg (disc)
4403227902tetracyclineyesyes30 µg (disc)
440329332sulfamethoxazoleyesyes23.75 µg (disc)
4403245924trimethoprimyesyes1.25 µg (disc)
4403217833gentamicinyesyes10 µg (disc)

metabolite production

  • @ref: 44032
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44032cytochrome oxidase+1.9.3.1
44032catalase-1.11.1.6
44032lipase-
44032arginine dihydrolase-3.5.3.6
44032urease-3.5.1.5
44032alkaline phosphatase+3.1.3.1
44032esterase (C 4)+
44032esterase Lipase (C 8)+
44032leucine arylamidase+3.4.11.1
44032valine arylamidase+
44032trypsin+3.4.21.4
44032alpha-chymotrypsin+3.4.21.1
44032acid phosphatase+3.1.3.2
44032naphthol-AS-BI-phosphohydrolase+
44032lipase (C 14)-
44032cystine arylamidase-3.4.11.3
44032alpha-galactosidase-3.2.1.22
44032beta-galactosidase-3.2.1.23
44032beta-glucuronidase-3.2.1.31
44032alpha-glucosidase-3.2.1.20
44032beta-glucosidase-3.2.1.21
44032N-acetyl-beta-glucosaminidase-3.2.1.52
44032alpha-mannosidase-3.2.1.24
44032alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44032C10:01.8
    44032C10:0 3OH5.2
    44032C12:04.1
    44032C14:02.6
    44032C15:1ω6c1.3
    44032C16:028.6
    44032C16:1ω7c / C16:1ω6c46.4
    44032C17:01.4
    44032C18:01.9
    44032C18:1ω7c3.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

  • @ref: 44032
  • sample type: water sample
  • geographic location: Banping Lake Wetland Park, Kaohsiung City
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia
  • latitude: 22.6917
  • longitude: 120.309
  • enrichment culture: R2A agar (BD Difco)
  • enrichment culture duration: 3 days
  • enrichment culture temperature: 25

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Sequence information

16S sequences

  • @ref: 44032
  • description: 16S rRNA gene sequence
  • accession: HE993549
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ideonella paludis KCTC 32238GCA_018069865contigncbi1233411
66792Ideonella paludis strain KCTC 322381233411.3wgspatric1233411

GC content

  • @ref: 44032
  • GC-content: 67.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.95no
gram-positiveno99.003yes
anaerobicno98.409no
aerobicyes87.23yes
halophileno94.044yes
spore-formingno95.918no
thermophileno97.226yes
glucose-utilyes59.046yes
flagellatedyes80.511no
glucose-fermentno86.959no

External links

@ref: 44032

culture collection no.: BCRC 80524, KCTC 32238

literature

  • topic: Phylogeny
  • Pubmed-ID: 26651339
  • title: Ideonella paludis sp. nov., isolated from a marsh.
  • authors: Sheu SY, Chen ZH, Young CC, Chen WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000832
  • year: 2015

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
44032Shih-Yi Sheu, Zih-Han Chen, Chiu-Chung Young and Wen-Ming ChenIdeonella paludis sp. nov., isolated from a marsh10.1099/ijsem.0.000832IJSEM 66: 1052-1057 201626651339
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
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