Strain identifier

BacDive ID: 140505

Type strain: Yes

Species: Flavisolibacter tropicus

Strain Designation: LCS9

Strain history: <- Kim, Myung Kyum (Seoul Women's Univ.)

NCBI tax ID(s): 1492898 (species)

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General

@ref: 43126

BacDive-ID: 140505

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Flavisolibacter tropicus LCS9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample from tropic zone of Ecorium of the National Institute of Ecology.

NCBI tax id

  • NCBI tax id: 1492898
  • Matching level: species

strain history

@refhistory
67770M. K. Kim LCS9.
67771<- Kim, Myung Kyum (Seoul Women's Univ.)

doi: 10.13145/bacdive140505.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Flavisolibacter
  • species: Flavisolibacter tropicus
  • full scientific name: Flavisolibacter tropicus Lee et al. 2016

@ref: 43126

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Chitinophagales

family: Chitinophagaceae

genus: Flavisolibacter

species: Flavisolibacter tropicus

strain designation: LCS9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43126negative2.2-3.5 µm0.3-0.5 µmrod-shapedno
69480negative99.993

colony morphology

  • @ref: 43126
  • colony color: deep yellow
  • incubation period: 3 days
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowth
43126Reasoner's 2A agar (R2A)yes
43126nutritient agar (NA)yes
43126tryptic soy agar (TSA)no
43126LB (Luria-Bertani) MEDIUMno

culture temp

@refgrowthtypetemperaturerange
43126positiveoptimum25mesophilic
43126positivegrowth10-37
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43126positivegrowth6-10alkaliphile
43126positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.851

halophily

@refsaltgrowthtested relationconcentration
43126NaClpositivegrowth0-0.5 %(w/v)
43126NaClpositiveoptimum0 %(w/v)

observation

@refobservation
43126weakly resistant to gamma radiation (100 kCi)
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4312617632nitrate-reduction
431264853esculin+hydrolysis
431265291gelatin+hydrolysis
43126506227N-acetylglucosamine+carbon source
4312617634D-glucose+carbon source
4312628087glycogen+carbon source
4312617306maltose+carbon source
4312616024D-mannose+carbon source
4312617203L-proline+carbon source
4312617128adipate+assimilation
4312630849L-arabinose+assimilation
4312615589L-malate+assimilation
4312617992sucrose+assimilation
4312630089acetate-assimilation
4312616977L-alanine-assimilation
4312627689decanoate-assimilation
4312616947citrate-assimilation
4312618287L-fucose-assimilation
4312624265gluconate-assimilation
4312615971L-histidine-assimilation
43126161933-hydroxybenzoate-assimilation
43126178794-hydroxybenzoate-assimilation
4312617240itaconate-assimilation
43126168082-dehydro-D-gluconate-assimilation
43126581435-dehydro-D-gluconate-assimilation
4312624996lactate-assimilation
4312615792malonate-assimilation
4312616899D-mannitol-assimilation
4312628053melibiose-assimilation
4312617268myo-inositol-assimilation
4312618401phenylacetate-assimilation
4312617272propionate-assimilation
4312662345L-rhamnose-assimilation
4312616988D-ribose-assimilation
4312617814salicin-assimilation
4312617115L-serine-assimilation
4312617924D-sorbitol-assimilation
431269300suberic acid-assimilation
4312631011valerate-assimilation
43126506227N-acetylglucosamine+builds acid from
431264853esculin+builds acid from
4312628066gentiobiose+builds acid from
4312617234glucose+builds acid from
4312628087glycogen+builds acid from
4312617306maltose+builds acid from
4312616024D-mannose+builds acid from
4312628017starch+builds acid from
4312617992sucrose+builds acid from
4312627082trehalose+builds acid from
4312617057cellobiose+builds acid from
4312612936D-galactose+builds acid from
4312617716lactose+builds acid from
4312628053melibiose+builds acid from
43126320061methyl alpha-D-glucopyranoside+builds acid from
43126581435-dehydro-D-gluconate+builds acid from
4312615963ribitol-builds acid from
4312627613amygdalin-builds acid from
4312617108D-arabinose-builds acid from
4312630849L-arabinose-builds acid from
4312618333D-arabitol-builds acid from
4312618403L-arabitol-builds acid from
4312618305arbutin-builds acid from
4312616813galactitol-builds acid from
4312617113erythritol-builds acid from
4312628847D-fucose-builds acid from
4312618287L-fucose-builds acid from
4312615824D-fructose-builds acid from
4312624265gluconate-builds acid from
4312617754glycerol-builds acid from
4312617268myo-inositol-builds acid from
4312615443inulin-builds acid from
43126168082-dehydro-D-gluconate-builds acid from
4312662318D-lyxose-builds acid from
4312629864mannitol-builds acid from
431266731melezitose-builds acid from
4312643943methyl alpha-D-mannoside-builds acid from
4312674863methyl beta-D-xylopyranoside-builds acid from
4312616634raffinose-builds acid from
4312662345L-rhamnose-builds acid from
4312633942ribose-builds acid from
4312617814salicin-builds acid from
4312630911sorbitol-builds acid from
4312617266L-sorbose-builds acid from
4312616443D-tagatose-builds acid from
4312632528turanose-builds acid from
4312617151xylitol-builds acid from
4312665327D-xylose-builds acid from
4312665328L-xylose-builds acid from

metabolite production

  • @ref: 43126
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43126cytochrome oxidase+1.9.3.1
43126catalase+1.11.1.6
43126N-acetyl-beta-glucosaminidase+3.2.1.52
43126acid phosphatase+3.1.3.2
43126alkaline phosphatase+3.1.3.1
43126alpha-chymotrypsin+3.4.21.1
43126cystine arylamidase+3.4.11.3
43126alpha-glucosidase+3.2.1.20
43126leucine arylamidase+3.4.11.1
43126naphthol-AS-BI-phosphohydrolase+
43126gelatinase+
43126trypsin+3.4.21.4
43126valine arylamidase+
43126esterase (C 4)+
43126esterase Lipase (C 8)+
43126arginine dihydrolase-3.5.3.6
43126alpha-fucosidase-3.2.1.51
43126alpha-galactosidase-3.2.1.22
43126beta-galactosidase+/-3.2.1.23
43126beta-glucosidase-3.2.1.21
43126beta-glucuronidase-3.2.1.31
43126lipase (C 14)-
43126alpha-mannosidase-3.2.1.24
43126urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43126C15:0 iso27.4
    43126C15:0 anteiso6.4
    43126C15:0 2OH2.5
    43126C15:0 iso 3OH2.7
    43126C16:02.1
    43126C16:0 iso3.3
    43126C17:0 iso1.1
    43126C17:0 2OH2.1
    43126C17:0 iso 3OH18.1
    43126C15:1 iso G8.3
    43126C15:1 anteiso A5.7
    43126C17:1ω6c1.8
    43126C13:0 3-OH / iso-C15:1H1.7
    43126C16:1ω7c / C16:1ω6c9
    43126C17:1 iso ω9c / C16:0 10-methyl2.5
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
43126soil sample from tropic zone of Ecorium of the National Institute of EcologySeocheonRepublic of KoreaKORAsia36126R2A agar1 week25serial dilution plating method
67770Soil at the tropical zone within the Ecorium of the National Institute of EcologySeocheonRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7687.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_3572;97_4388;98_5619;99_7687&stattab=map
  • Last taxonomy: Flavisolibacter tropicus subclade
  • 16S sequence: KJ461518
  • Sequence Identity:
  • Total samples: 5224
  • soil counts: 3590
  • aquatic counts: 1076
  • animal counts: 216
  • plant counts: 342

Sequence information

16S sequences

  • @ref: 43126
  • description: Flavisolibacter sp. LCS9 16S ribosomal RNA gene, partial sequence
  • accession: KJ461518
  • length: 1439
  • database: nuccore
  • NCBI tax ID: 1492898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavisolibacter tropicus LCS9GCA_001644645completencbi1492898
66792Flavisolibacter tropicus LCS92758568004completeimg1492898
66792Flavisolibacter tropicus LCS92602042012draftimg1492898

GC content

  • @ref: 67770
  • GC-content: 39.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedno98.003no
gram-positiveno97.496yes
anaerobicno98.743yes
aerobicyes86.875yes
halophileno96.327yes
spore-formingno92.848no
glucose-utilyes93.032yes
motileno93.666no
thermophileno98.02no
glucose-fermentno81.843no

External links

@ref: 43126

culture collection no.: KCTC 42070, JCM 19972

literature

  • topic: Phylogeny
  • Pubmed-ID: 27259556
  • title: Flavisolibacter tropicus sp. nov., isolated from tropical soil.
  • authors: Lee JJ, Kang MS, Kim GS, Lee CS, Lim S, Lee J, Roh SH, Kang H, Ha JM, Bae S, Jung HY, Kim MK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001207
  • year: 2016
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Tropical Climate, Vitamin K 2/analogs & derivatives/chemistry
  • 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
43126Jae-Jin Lee, Myung-Suk Kang, Gyung Soon Kim, Chang Soek Lee, Sangyong Lim, Jidam Lee, Si Hyeon Roh, Hyerin Kang, Jung Min Ha, Sojung Bae, Hee-Young Jung, Myung Kyum KimFlavisolibacter tropicus sp. nov., isolated from tropical soil10.1099/ijsem.0.001207IJSEM 66: 3413-3419 201627259556
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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