Strain identifier

BacDive ID: 133331

Type strain: Yes

Species: Lacibacter nakdongensis

Strain Designation: SS2-56

Strain history: <- Ji-Hye Han, NNIBR

NCBI tax ID(s): 1843099 (species)

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General

@ref: 25190

BacDive-ID: 133331

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

description: Lacibacter nakdongensis SS2-56 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface sediment.

NCBI tax id

  • NCBI tax id: 1843099
  • Matching level: species

strain history

@refhistory
67770J.-H. Han; Nakdonggang Natl. Inst. of Biol. Resour., South Korea; SS2-56.
67771<- Ji-Hye Han, NNIBR

doi: 10.13145/bacdive133331.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Lacibacter
  • species: Lacibacter nakdongensis
  • full scientific name: Lacibacter nakdongensis Han et al. 2017

@ref: 25190

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Chitinophagales

family: Chitinophagaceae

genus: Lacibacter

species: Lacibacter nakdongensis

strain designation: SS2-56

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
25190negative1.6-3.8 µm0.4-0.5 µmrod-shapedyes
67771rod-shapedyesgliding
67771negative

colony morphology

  • @ref: 25190
  • colony color: orange
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
25190nutrient agar (NA)yes
25190tryptic soy agar (TSA)no
25190Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
25190positivegrowth15.0-37.0
25190positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
25190positivegrowth5.0-8.0
25190positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25190aerobe
67771aerobe

spore formation

@refspore formation
25190no
67771no

halophily

  • @ref: 25190
  • salt: NaCl
  • tested relation: maximum
  • concentration: 0 %

observation

@refobservation
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25190167632-oxobutanoate-carbon source
25190309162-oxoglutarate-carbon source
2519017128adipate-carbon source
2519017968butyrate-carbon source
2519085146carboxymethylcellulose-degradation
25190casein-degradation
2519016947citrate-carbon source
2519015570D-alanine-carbon source
2519017108D-arabinose-builds acid from
2519018333D-arabitol-builds acid from
2519018333D-arabitol-carbon source
2519015824D-fructose-carbon source
2519028847D-fucose-builds acid from
2519014314D-glucose 6-phosphate-carbon source
2519062318D-lyxose-builds acid from
2519016899D-mannitol-builds acid from
2519016988D-ribose-builds acid from
2519017924D-sorbitol-builds acid from
2519017924D-sorbitol-carbon source
2519065327D-xylose-builds acid from
2519016991dna-degradation
2519017113erythritol-builds acid from
251904853esculin-builds acid from
2519017234glucose-fermentation
2519017754glycerol-builds acid from
2519017754glycerol-carbon source
2519028087glycogen-carbon source
2519073804glycyl L-aspartic acid-carbon source
2519017368hypoxanthine-degradation
2519017268myo-inositol-carbon source
2519016977L-alanine-carbon source
2519030849L-arabinose-carbon source
2519017196L-asparagine-carbon source
2519018287L-fucose-builds acid from
2519018287L-fucose-carbon source
2519015603L-leucine-carbon source
2519062345L-rhamnose-carbon source
2519065328L-xylose-builds acid from
2519024996lactate-carbon source
2519025115malate-carbon source
2519015792malonate-carbon source
2519017306maltose-builds acid from
2519028037N-acetylgalactosamine-carbon source
2519017632nitrate-reduction
2519016301nitrite-reduction
2519018401phenylacetate-carbon source
2519016634raffinose-carbon source
2519028017starch-degradation
2519030031succinate-carbon source
2519027897tryptophan-energy source
2519053423tween 40-carbon source
2519053426tween 80-carbon source
2519015318xanthine-degradation
2519017151xylitol-builds acid from
2519017151xylitol-carbon source
2519017925alpha-D-glucose+carbon source
2519036219alpha-lactose+carbon source
2519027613amygdalin+builds acid from
2519018305arbutin+builds acid from
2519017057cellobiose+builds acid from
2519017057cellobiose+carbon source
2519012936D-galactose+carbon source
2519017634D-glucose+builds acid from
2519017716lactose+builds acid from
2519016899D-mannitol+carbon source
2519016024D-mannose+builds acid from
2519016024D-mannose+carbon source
2519032528turanose+builds acid from
2519065327D-xylose+builds acid from
251904853esculin+hydrolysis
251905291gelatin+hydrolysis
2519028066gentiobiose+builds acid from
2519028066gentiobiose+carbon source
2519024265gluconate+carbon source
2519017234glucose+carbon source
2519028087glycogen+builds acid from
2519015443inulin+builds acid from
2519029985L-glutamate+carbon source
2519017203L-proline+carbon source
2519062345L-rhamnose+builds acid from
2519016857L-threonine+carbon source
251906359lactulose+carbon source
2519017306maltose+builds acid from
2519017306maltose+carbon source
251906731melezitose+builds acid from
2519028053melibiose+builds acid from
2519028053melibiose+carbon source
25190320061methyl alpha-D-glucopyranoside+builds acid from
2519043943methyl alpha-D-mannoside+builds acid from
25190320055methyl beta-D-glucopyranoside+carbon source
2519051850methyl pyruvate+carbon source
2519075146monomethyl succinate+carbon source
25190506227N-acetylglucosamine+builds acid from
25190506227N-acetylglucosamine+carbon source
2519016634raffinose+builds acid from
2519017814salicin+builds acid from
2519028017starch+builds acid from
2519017992sucrose+builds acid from
2519017992sucrose+carbon source
2519027082trehalose+builds acid from
2519027082trehalose+carbon source
2519032528turanose+carbon source
2519018186tyrosine+degradation

metabolite production

  • @ref: 25190
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25190
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25190acid phosphatase-3.1.3.2
25190alkaline phosphatase+3.1.3.1
25190alpha-chymotrypsin+3.4.21.1
25190alpha-fucosidase+3.2.1.51
25190alpha-galactosidase+3.2.1.22
25190alpha-glucosidase+3.2.1.20
25190arginine dihydrolase-3.5.3.6
25190beta-galactosidase+3.2.1.23
25190catalase+1.11.1.6
25190cystine arylamidase+3.4.11.3
25190cytochrome oxidase+1.9.3.1
25190esterase (C 4)+
25190esterase Lipase (C 8)+
25190leucine arylamidase+3.4.11.1
25190N-acetyl-beta-glucosaminidase+3.2.1.52
25190naphthol-AS-BI-phosphohydrolase+
25190trypsin+3.4.21.4
25190tryptophan deaminase-4.1.99.1
25190valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25190C15:0 anteiso4.2
    25190C12:00.3
    25190C14:01
    25190C16:05.5
    25190C16:0 3OH1
    25190C16:1ω6c / C16:1ω7c7
    25190C13:0 iso2.2
    25190C15:0 iso47.6
    25190C15:0 iso 3OH2.4
    25190C15:1 iso G7.2
    25190C16:0 iso2.1
    25190C16:0 iso 3OH1.1
    25190C17:0 iso1.2
    25190C17:0 iso 3OH13.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6.2
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedurelatitudelongitude
25190surface sedimentNakdong RiverRepublic of KoreaKORAsiaR2A agar (BD)14 days25serially diluted with 1/4 strength Ringer solution (per litre: NaCl 2.25 g, KCl 0.105 g, CaCl2 0.12 g, NaHCO3 0.05 g) and suitable ten-fold dilutions
67770Sediment of the Nakdong River in Sangju-siRepublic of KoreaKORAsia
67771From surface sediment, Nakdong RiverSanju-siRepublic of KoreaKORAsia36.44128.257

isolation source categories

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

Sequence information

16S sequences

  • @ref: 25190
  • description: Lacibacter sp. SS2-56 16S ribosomal RNA gene, partial sequence
  • accession: KU341406
  • length: 1450
  • database: nuccore
  • NCBI tax ID: 1843099

GC content

@refGC-contentmethod
2519043.8Thermal denaturation, fluorometry
6777143.8
6777043.8thermal denaturation, midpoint method (Tm)

External links

@ref: 25190

culture collection no.: KCTC 52160, JCM 31372, BCRC 81229

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902234Lacibacter nakdongensis sp. nov., isolated from river sediment.Han JH, Baek K, Lee MHInt J Syst Evol Microbiol10.1099/ijsem.0.0016312017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31851601Lacibacter luteus sp. nov., isolated from a freshwater river.Sheu SY, Chen TY, Kwon SW, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0039262020Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
25190J. H. B. Han, K.,Lee, M. H.Lacibacter nakdongensis sp. nov., isolated from river sediment10.1099/ijsem.0.001631IJSEM 67: 352-356 201727902234
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc