Strain identifier

BacDive ID: 140767

Type strain: Yes

Species: Larkinella ripae

Strain Designation: 15J11-11

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

NCBI tax ID(s): 1892557 (species)

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General

@ref: 43545

BacDive-ID: 140767

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

description: Larkinella ripae 15J11-11 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from a soil sample collected from the seashore.

NCBI tax id

  • NCBI tax id: 1892557
  • Matching level: species

strain history

@refhistory
67770H.-Y. Jung; Kyungpook Natl. Univ., South Korea; 15J11-11.
67771<- Myung Kyum, Kim, Seoul Womens Univ.

doi: 10.13145/bacdive140767.20240510.9

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 ripae
  • full scientific name: Larkinella ripae Lee et al. 2017

@ref: 43545

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Larkinella

species: Larkinella ripae

strain designation: 15J11-11

type strain: yes

Morphology

cell morphology

  • @ref: 43545
  • gram stain: negative
  • cell length: 1.3-2.4 µm
  • cell width: 0.8-1.1 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: gliding

colony morphology

  • @ref: 43545
  • colony size: 0.5-1.5 mm
  • colony color: pale pink, translucent
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A plates

pigmentation

  • @ref: 43545
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

  • @ref: 43545
  • name: R2A plates
  • growth: yes

culture temp

@refgrowthtypetemperature
43545positivegrowth15-30
43545positiveoptimum25
67770positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepH
43545positivegrowth6-7
43545positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43545NaClpositivegrowth0-2 %(w/v)
43545NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43545161933-hydroxybenzoate-assimilation
43545178794-hydroxybenzoate-assimilation
4354530089acetate-assimilation
4354517128adipate-assimilation
4354527689decanoate-assimilation
4354516947citrate-assimilation
4354516899D-mannitol-assimilation
4354517924D-sorbitol-assimilation
43545370543-hydroxybutyrate-assimilation
4354524996lactate-assimilation
4354528087glycogen-assimilation
4354517240itaconate-assimilation
4354516977L-alanine-assimilation
4354530849L-arabinose-assimilation
4354518287L-fucose-assimilation
4354515971L-histidine-assimilation
4354515589L-malate-assimilation
4354562345L-rhamnose-assimilation
4354517115L-serine-assimilation
4354517268myo-inositol-assimilation
4354518401phenylacetate-assimilation
4354517272propionate-assimilation
4354562983sodium malonate-assimilation
435459300suberic acid-assimilation
4354531011valerate-assimilation
43545168082-dehydro-D-gluconate-builds acid from
4354515963ribitol-builds acid from
4354518333D-arabitol-builds acid from
4354516899D-mannitol-builds acid from
4354517924D-sorbitol-builds acid from
4354516813galactitol-builds acid from
4354517113erythritol-builds acid from
4354524265gluconate-builds acid from
4354517754glycerol-builds acid from
4354528087glycogen-builds acid from
4354517268myo-inositol-builds acid from
4354515443inulin-builds acid from
4354518403L-arabitol-builds acid from
4354517266L-sorbose-builds acid from
4354574863methyl beta-D-xylopyranoside-builds acid from
4354528017starch-builds acid from
4354517151xylitol-builds acid from
4354585146carboxymethylcellulose-hydrolysis
43545casein-hydrolysis
4354517029chitin-hydrolysis
435455291gelatin-hydrolysis
4354517309pectin-hydrolysis
4354553424tween 20-hydrolysis
4354553426tween 80-hydrolysis
4354516199urea-hydrolysis
4354517632nitrate-reduction
4354517634D-glucose+assimilation
4354516024D-mannose+assimilation
4354524265gluconate+assimilation
43545maltose hydrate+assimilation
4354528053melibiose+assimilation
43545506227N-acetylglucosamine+assimilation
4354517814salicin+assimilation
4354517992sucrose+assimilation
4354518305arbutin+builds acid from
4354517057cellobiose+builds acid from
4354517108D-arabinose+builds acid from
4354515824D-fructose+builds acid from
4354512936D-galactose+builds acid from
4354517634D-glucose+builds acid from
4354562318D-lyxose+builds acid from
4354516024D-mannose+builds acid from
4354516443D-tagatose+builds acid from
4354565327D-xylose+builds acid from
435454853esculin+builds acid from
4354528066gentiobiose+builds acid from
4354517716lactose+builds acid from
4354517306maltose+builds acid from
4354528053melibiose+builds acid from
43545320061methyl alpha-D-glucopyranoside+builds acid from
4354543943methyl alpha-D-mannoside+builds acid from
43545506227N-acetylglucosamine+builds acid from
4354516634raffinose+builds acid from
4354517814salicin+builds acid from
4354517992sucrose+builds acid from
4354527082trehalose+builds acid from
4354532528turanose+builds acid from
435454853esculin+hydrolysis
4354528017starch+hydrolysis
43545168082-dehydro-D-gluconate+/-assimilation
43545581435-dehydro-D-gluconate+/-assimilation
4354516988D-ribose+/-assimilation
4354517203L-proline+/-assimilation
43545581435-dehydro-D-gluconate+/-builds acid from
4354527613amygdalin+/-builds acid from
4354528847D-fucose+/-builds acid from
4354516988D-ribose+/-builds acid from
4354530849L-arabinose+/-builds acid from
4354518287L-fucose+/-builds acid from
4354562345L-rhamnose+/-builds acid from
435456731melezitose+/-builds acid from
4354518222xylose+/-builds acid from

metabolite production

  • @ref: 43545
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43545N-acetyl-beta-glucosaminidase+3.2.1.52
43545acid phosphatase+3.1.3.2
43545alkaline phosphatase+3.1.3.1
43545cystine arylamidase+3.4.11.3
43545alpha-glucosidase+3.2.1.20
43545leucine arylamidase+3.4.11.1
43545naphthol-AS-BI-phosphohydrolase+
43545valine arylamidase+
43545esterase (C 4)+/-
43545esterase Lipase (C 8)+/-
43545lipase (C 14)+/-
43545beta-glucosidase+/-3.2.1.21
43545alpha-chymotrypsin-3.4.21.1
43545alpha-fucosidase-3.2.1.51
43545alpha-galactosidase-3.2.1.22
43545beta-galactosidase-3.2.1.23
43545beta-glucuronidase-3.2.1.31
43545alpha-mannosidase-3.2.1.24
43545trypsin-3.4.21.4
43545arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43545C15:0 anteiso62
    43545C17:0 anteiso7.9
    43545C15:01
    43545C16:01.7
    43545C14:0 iso9.2
    43545C15:0 iso9.2
    43545C16:0 iso7
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation pH: 7
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43545a soil sample collected from the seashoreJeju IslandRepublic of KoreaKORAsia33.498126.452
67770Soil from the seashore in JejuRepublic of KoreaKORAsia
67771From soil(Yongdam coastal road under a stone wallJeju Island)Republic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43545
  • description: Larkinella ripae gene for 16S ribosomal RNA, partial sequence
  • accession: LC177338
  • database: nuccore

GC content

  • @ref: 43545
  • GC-content: 53.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43545

culture collection no.: KCTC 42996, JCM 31657

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28879840Larkinella ripae sp. nov., isolated from seashore soil.Lee YH, Lee JJ, Lee SY, Lee DS, Kim MK, Ten LN, Jung HYInt J Syst Evol Microbiol10.1099/ijsem.0.0021882017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29299846Larkinella roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil.Lee JB, Hong S, Lee SY, Park SJ, Park KI, Choi SG, Kim MK, Ten LN, Jung HYJ Microbiol10.1007/s12275-018-7476-x2018Base Composition, Cytophagaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phosphatidylethanolamines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

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
43545Yeon-Hee Lee, Jae-Jin Lee, Seung-Yeo Lee, Dae Sung Lee, Myung Kyum Kim, Leonid N. Ten, Hee-Young JungLarkinella ripae sp. nov., isolated from seashore soil10.1099/ijsem.0.002188IJSEM 67: 3759-3764 201728879840
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc