Strain identifier

BacDive ID: 140611

Type strain: Yes

Species: Pseudoxanthomonas putridarboris

Strain Designation: WD12

NCBI tax ID(s): 752605 (species)

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General

@ref: 43260

BacDive-ID: 140611

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

description: Pseudoxanthomonas putridarboris WD12 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from rotten tree samples.

NCBI tax id

  • NCBI tax id: 752605
  • Matching level: species

doi: 10.13145/bacdive140611.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Pseudoxanthomonas
  • species: Pseudoxanthomonas putridarboris
  • full scientific name: Pseudoxanthomonas putridarboris Lee et al. 2017

@ref: 43260

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Lysobacteraceae

genus: Pseudoxanthomonas

species: Pseudoxanthomonas putridarboris

strain designation: WD12

type strain: yes

Morphology

cell morphology

  • @ref: 43260
  • gram stain: negative
  • cell length: 1.2-2.0 µm
  • cell width: 0.4-0.7 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous

colony morphology

  • @ref: 43260
  • colony size: 2.0-4.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43260Reasoner's 2A agar (R2A)yes
43260Trypticase Soy Agar (TSA)yes
43260Nutrient agar (NA)yes
43260MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
43260positiveoptimum30-37mesophilic
43260positivegrowth10-40

culture pH

@refabilitytypepHPH range
43260positivegrowth6.0-8.5alkaliphile
43260positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43260
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43260NaClpositivegrowth0-3.0 %(w/v)
43260NaClpositiveoptimum0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4326017632nitrate-reduction
4326017234glucose-fermentation
432605291gelatin+hydrolysis
432604853esculin+hydrolysis
4326016991dna+hydrolysis
43260casein+hydrolysis
4326053426tween 80+hydrolysis
4326037166xylan-hydrolysis
4326017029chitin-hydrolysis
4326085146carboxymethylcellulose-hydrolysis
4326028017starch-hydrolysis
4326017634D-glucose+builds acid from
4326065327D-xylose+builds acid from
4326030849L-arabinose+builds acid from
4326012936D-galactose+builds acid from
4326017057cellobiose+builds acid from
4326017306maltose+builds acid from
4326016551D-trehalose+builds acid from
4326017754glycerol-builds acid from
4326017108D-arabinose-builds acid from
4326017992sucrose-builds acid from
4326065327D-xylose+assimilation
4326012936D-galactose+assimilation
4326017634D-glucose+assimilation
43260506227N-acetylglucosamine+assimilation
4326018305arbutin+assimilation
4326017057cellobiose+assimilation
4326017306maltose+assimilation
4326016551D-trehalose+assimilation
4326028066gentiobiose+assimilation
4326025115malate+assimilation
43260potassium 5-dehydro-D-gluconate+assimilation
4326027689decanoate-assimilation
4326017128adipate-assimilation
4326016947citrate-assimilation
4326018401phenylacetate-assimilation
4326017113erythritol-assimilation
4326017754glycerol-assimilation
4326017108D-arabinose-assimilation
4326030849L-arabinose-assimilation
4326016988D-ribose-assimilation
4326065328L-xylose-assimilation
4326015963ribitol-assimilation
4326074863methyl beta-D-xylopyranoside-assimilation
4326015824D-fructose-assimilation
4326016024D-mannose-assimilation
4326017266L-sorbose-assimilation
4326062345L-rhamnose-assimilation
4326016813galactitol-assimilation
4326017268myo-inositol-assimilation
4326016899D-mannitol-assimilation
4326017924D-sorbitol-assimilation
4326043943methyl alpha-D-mannoside-assimilation
43260320061methyl alpha-D-glucopyranoside-assimilation
4326027613amygdalin-assimilation
4326017814salicin-assimilation
4326017716lactose-assimilation
4326028053melibiose-assimilation
4326017992sucrose-assimilation
4326015443inulin-assimilation
432606731melezitose-assimilation
4326016634raffinose-assimilation
4326028017starch-assimilation
4326028087glycogen-assimilation
4326017151xylitol-assimilation
4326032528turanose-assimilation
4326062318D-lyxose-assimilation
4326016443D-tagatose-assimilation
4326028847D-fucose-assimilation
4326018287L-fucose-assimilation
4326018333D-arabitol-assimilation
4326018403L-arabitol-assimilation
4326032032potassium gluconate-assimilation
43260potassium 2-dehydro-D-gluconate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4326035581indoleno
4326016136hydrogen sulfideno
4326015688acetoinno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4326017234glucose-
4326015688acetoin-

enzymes

@refvalueactivityec
43260catalase+1.11.1.6
43260cytochrome oxidase+1.9.3.1
43260L-arginine dihydrolase-
43260urease-3.5.1.5
43260beta-galactosidase-3.2.1.23
43260alkaline phosphatase+3.1.3.1
43260esterase (C 4)+
43260esterase Lipase (C 8)+
43260leucine arylamidase+3.4.11.1
43260acid phosphatase+3.1.3.2
43260naphthol-AS-BI-phosphohydrolase+
43260beta-glucosidase+3.2.1.21
43260lipase (C 14)+/-
43260valine arylamidase+/-
43260alpha-chymotrypsin+/-3.4.21.1
43260beta-galactosidase+/-3.2.1.23
43260cystine arylamidase-3.4.11.3
43260trypsin-3.4.21.4
43260alpha-glucosidase-3.2.1.20
43260alpha-galactosidase-3.2.1.22
43260beta-glucuronidase-3.2.1.31
43260N-acetyl-beta-glucosaminidase-3.2.1.52
43260alpha-mannosidase-3.2.1.24
43260alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43260C10:01.3
    43260C12:02.7
    43260C13:02.4
    43260C14:03
    43260C15:01.3
    43260C16:010
    43260C18:02
    43260C11:0 iso3.2
    43260C12:0 iso1.9
    43260C14:0 iso3.9
    43260C15:0 iso7.3
    43260C15:0 anteiso5.8
    43260C16:0 iso19.8
    43260C16:1 iso H1.6
    43260C17:0 anteiso1.7
    43260C18:1ω9c1
    43260C10:0 3OH1.7
    43260C11:0 iso 3OH2.7
    43260C12:0 iso 3OH1.9
    43260cyclo-C17:08
    43260C16:1ω7c / C15:0 iso 2OH6.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 4.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43260
  • sample type: rotten tree samples
  • geographic location: Chungbuk, Korea
  • country: Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 36
  • longitude: 127

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Tree

Sequence information

16S sequences

  • @ref: 43260
  • description: 16S rRNA gene sequences
  • accession: GU908487
  • length: 1487
  • database: ena
  • NCBI tax ID: 752605

GC content

  • @ref: 43260
  • GC-content: 69.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43260

culture collection no.: KACC 15045, LMG 25968

literature

  • topic: Phylogeny
  • Pubmed-ID: 28598308
  • title: Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree.
  • authors: Lee JK, Oh JS, Cho WD, Roh DH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001867
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, Wood/*microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification
  • topic2: Transcriptome

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
43260Je-Kwan Lee, Ji-Sung Oh, Woon-Dong Cho and Dong-Hyun RohPseudoxanthomonas putridarboris sp. nov. isolated from rotten tree10.1099/ijsem.0.001867IJSEM 67: 1807-1812 201728598308