Strain identifier

BacDive ID: 158687

Type strain: Yes

Species: Larkinella knui

Strain Designation: 15J6-3T6

Strain history: <- Myung Kyum, Kim, Seoul Womens Univ.

NCBI tax ID(s): 2025310 (species)

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General

@ref: 65423

BacDive-ID: 158687

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

description: Larkinella knui 15J6-3T6 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a soil sample.

NCBI tax id

  • NCBI tax id: 2025310
  • Matching level: species

strain history

@refhistory
67770H.-Y. Jung; Kyungpook Natl. Univ., South Korea; 15J6-3T6.
67771<- Myung Kyum, Kim, Seoul Womens Univ.

doi: 10.13145/bacdive158687.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Larkinella
  • species: Larkinella knui
  • full scientific name: Larkinella knui Jeon et al. 2018

@ref: 65423

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Larkinella

species: Larkinella knui

strain designation: 15J6-3T6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65423negative1.9-4.2 µm0.7-0.9 µmrod-shapedyesgliding
69480no91.599
69480negative99.999

colony morphology

  • @ref: 65423
  • colony size: 0.5-1.5 mm
  • colony color: pink
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A plates

Culture and growth conditions

culture medium

  • @ref: 65423
  • name: R2A plates
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65423positivegrowth4-30
65423positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
65423positivegrowth6-8
65423positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.997
69481no100

halophily

@refsaltgrowthtested relationconcentration
65423NaClpositivegrowth0-1 %(w/v)
65423NaClpositiveoptimum0 %(w/v)

observation

@refobservation
65423grows on NA and R2A, but not on LB or TSA agar
65423the predominant isoprenoid quinone is MK-7
65423the major polar lipids are phosphatidylethanolamine and an unidentified polar lipid

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6542317108D-arabinose+builds acid from
6542330849L-arabinose-assimilation
65423168082-dehydro-D-gluconate-assimilation
65423168082-dehydro-D-gluconate-builds acid from
65423161933-hydroxybenzoate-assimilation
65423581435-dehydro-D-gluconate-assimilation
65423581435-dehydro-D-gluconate+builds acid from
6542317128adipate-assimilation
6542327613amygdalin-builds acid from
6542318305arbutin+builds acid from
6542327689decanoate-assimilation
6542315963ribitol-builds acid from
6542318333D-arabitol-builds acid from
6542317057cellobiose+builds acid from
6542315824D-fructose+builds acid from
6542328847D-fucose-builds acid from
6542312936D-galactose-builds acid from
6542317634D-glucose-assimilation
6542317634D-glucose+builds acid from
6542362318D-lyxose-builds acid from
6542316899D-mannitol-assimilation
6542316899D-mannitol-builds acid from
6542316024D-mannose+assimilation
6542316024D-mannose+builds acid from
6542316988D-ribose-assimilation
6542316988D-ribose+builds acid from
6542317924D-sorbitol-assimilation
6542317924D-sorbitol-builds acid from
6542316443D-tagatose-builds acid from
6542365327D-xylose+builds acid from
65423370543-hydroxybutyrate-assimilation
6542316813galactitol-builds acid from
6542317113erythritol-builds acid from
654234853esculin+hydrolysis
65423esculin ferric citrate+builds acid from
654235291gelatin+hydrolysis
6542328066gentiobiose+builds acid from
6542324265gluconate-assimilation
6542324265gluconate-builds acid from
6542317234glucose+fermentation
6542317754glycerol-builds acid from
6542328087glycogen-assimilation
6542328087glycogen-builds acid from
6542315443inulin+builds acid from
6542316087isocitrate-assimilation
6542348942isovalerate-assimilation
6542317240itaconate-assimilation
65423L-alanine 4-nitroanilide-assimilation
6542330849L-arabinose+builds acid from
6542318403L-arabitol-builds acid from
6542318287L-fucose-assimilation
6542318287L-fucose-builds acid from
6542315971L-histidine-assimilation
6542315589L-malate-assimilation
6542317203L-proline-assimilation
6542362345L-rhamnose-assimilation
6542362345L-rhamnose+builds acid from
6542317115L-serine-assimilation
6542317266L-sorbose-builds acid from
6542365328L-xylose+builds acid from
6542324996lactate-assimilation
6542317716lactose+builds acid from
6542317306maltose+assimilation
6542317306maltose+builds acid from
654236731melezitose-builds acid from
6542328053melibiose+assimilation
6542328053melibiose+builds acid from
65423320061methyl alpha-D-glucopyranoside-builds acid from
6542343943methyl alpha-D-mannoside+builds acid from
6542374863methyl beta-D-xylopyranoside-builds acid from
6542317268myo-inositol-assimilation
65423506227N-acetylglucosamine-assimilation
65423506227N-acetylglucosamine-builds acid from
6542317632nitrate+reduction
6542318401phenylacetate-assimilation
6542316634raffinose+builds acid from
6542317814salicin+assimilation
6542317814salicin+builds acid from
6542332954sodium acetate-assimilation
6542362983sodium malonate-assimilation
65423132106sodium propionate-assimilation
6542328017starch-builds acid from
654239300suberic acid-assimilation
6542317992sucrose-assimilation
6542317992sucrose+builds acid from
6542327082trehalose+builds acid from
6542332528turanose+builds acid from
6542316199urea-hydrolysis
6542317151xylitol-builds acid from

metabolite production

  • @ref: 65423
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
654236-phospho-beta-galactosidase+3.2.1.85
65423arginine dihydrolase-3.5.3.6
65423N-acetyl-beta-glucosaminidase+3.2.1.52
65423phosphatase+
65423alkaline phosphatase+3.1.3.1
65423alpha-chymotrypsin+3.4.21.1
65423cystine arylamidase+3.4.11.3
65423esterase+
65423esterase Lipase (C 8)+
65423alpha-galactosidase+3.2.1.22
65423beta-galactosidase+3.2.1.23
65423alpha-glucosidase+3.2.1.20
65423beta-glucosidase+3.2.1.21
65423leucine arylamidase+3.4.11.1
65423alpha-mannosidase+3.2.1.24
65423naphthol-AS-BI-phosphohydrolase+
65423trypsin+3.4.21.4
65423valine arylamidase+
65423alpha-fucosidase-3.2.1.51
65423beta-glucuronidase-3.2.1.31
65423lipase (C 14)-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65423C15:0 iso21.4
    65423anteiso-C 15:01.2
    65423C16:03
    65423C17:0 iso1.5
    65423C18:01.1
    65423C20:01.4
    65423C15:0 iso 3OH4.2
    65423C16:0 N alcohol7.5
    65423C17:0 iso 3OH9.5
    65423C16:1ω5c40.4
    65423C16:1ω7c and/or C16:1ω6c3.9
    65423isoC17:1I and/or anteisoC17:1B1.9
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • incubation temperature: 30
  • incubation time: 3
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • instrument: gas chromatography
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
65423a soil sample2015-12Jeju IslandRepublic of KoreaKORAsia33.3069126.29Reasoner's 2A agar plates (Difco)1 week25
67770Soil from Jeju IslandRepublic of KoreaKORAsia
67771From soil(O'sulloc tea fieldsJeju Island)Republic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

  • @ref: 65423
  • description: 16S rRNA gene sequence
  • accession: LC315194
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Larkinella knui KCTC42998GCA_003858645contigncbi2025310
66792Larkinella knui strain KCTC429982025310.3wgspatric2025310
66792Larkinella knui KCTC429982882134870draftimg2025310

GC content

  • @ref: 65423
  • GC-content: 50.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.182no
gram-positiveno96.964yes
anaerobicno99.357yes
aerobicyes88.453yes
halophileno95.232yes
spore-formingno93.831no
glucose-utilyes79.025yes
flagellatedno97.739no
thermophileno98.438yes
glucose-fermentno78.071yes

External links

@ref: 65423

culture collection no.: KCTC 42998, JCM 31989

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29300161Larkinella knui sp. nov., isolated from soil.Jeon J, Ten LN, Lee JJ, Lee SY, Park S, Cho YJ, Kim MK, Jung HYInt J Syst Evol Microbiol10.1099/ijsem.0.0025502018Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32653934Larkinella punicea sp. nov., isolated from manganese mine soil.Zhou Z, Zhu L, Dong Y, Xia X, Wu S, Wang GArch Microbiol10.1007/s00203-020-01863-62020Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, Fatty Acids/analysis, Genome, Bacterial/genetics, Manganese, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil/chemistry, *Soil Microbiology, Species SpecificityGenetics
Phylogeny35179646Larkinella humicola sp. nov., a gamma radiation-resistant bacterium isolated from soil.Park Y, Ten LN, Lee YK, Jung HY, Kim MKArch Microbiol10.1007/s00203-022-02790-42022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Gamma Rays, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil MicrobiologyTranscriptome

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
65423Jongguen Jeon, Leonid N. Ten, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Young-Je Cho, Myung Kyum Kim, Hee-Young JungLarkinella knui sp. nov., isolated from soil10.1099/ijsem.0.002550IJSEM 68: 582-588 201829300161
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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