Strain identifier

BacDive ID: 164448

Type strain: Yes

Species: Lysobacter terrigena

Strain Designation: 17J7-1

Strain history: H.-Y. Jung and M. K. Kim; Kyungpook Natl. Univ., South Korea; 17J7-1.

NCBI tax ID(s): 2488749 (species)

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General

@ref: 67770

BacDive-ID: 164448

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

description: Lysobacter terrigena 17J7-1 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Soil from Jeju Island.

NCBI tax id

  • NCBI tax id: 2488749
  • Matching level: species

strain history

  • @ref: 67770
  • history: H.-Y. Jung and M. K. Kim; Kyungpook Natl. Univ., South Korea; 17J7-1.

doi: 10.13145/bacdive164448.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter terrigena
  • full scientific name: Lysobacter terrigena Li et al. 2020

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter terrigena

full scientific name: Lysobacter terrigena Li et al. 2020

strain designation: 17J7-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
68263negative1.2-1.7 µm0.4-0.6 µmrod-shapedyesgliding
69480negative99.996

colony morphology

  • @ref: 68263
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Reasoner's 2A agar (R2A)

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
68263positivegrowth10-42
68263positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
68263positivegrowth7-9alkaliphile
68263positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 68263
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.976
69481no100

halophily

@refsaltgrowthtested relationconcentration
68263NaClpositivegrowth1 %(w/v)
68263NaClnogrowth2 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
682634853esculin+hydrolysis
682635291gelatin+hydrolysis
6826317234glucose-builds acid from
6826317632nitrate-reduction
68263370543-hydroxybutyrate+assimilation
6826316947citrate+/-assimilation
68263506227N-acetyl-D-glucosamine-assimilation
6826317128adipate-assimilation
6826316977L-alanine-assimilation
6826330849L-arabinose-assimilation
6826317120hexanoate-assimilation
6826318287L-fucose-assimilation
6826324265gluconate-assimilation
6826317634D-glucose-assimilation
6826328087glycogen-assimilation
6826315971L-histidine-assimilation
68263161933-hydroxybenzoate-assimilation
68263178794-hydroxybenzoate-assimilation
6826317268myo-inositol-assimilation
6826317240itaconate-assimilation
68263168082-dehydro-D-gluconate-assimilation
68263581435-dehydro-D-gluconate-assimilation
6826324996lactate-assimilation
6826315589L-malate-assimilation
6826315792malonate-assimilation
6826317306maltose-assimilation
6826316899D-mannitol-assimilation
6826316024D-mannose-assimilation
6826328053melibiose-assimilation
6826318401phenylacetate-assimilation
6826317203L-proline-assimilation
6826317272propionate-assimilation
6826362345L-rhamnose-assimilation
6826316988D-ribose-assimilation
6826317814salicin-assimilation
6826317115L-serine-assimilation
6826317924D-sorbitol-assimilation
6826376282suberate-assimilation
6826317992sucrose-assimilation
6826331011valerate-assimilation

metabolite production

  • @ref: 68263
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68263catalase+1.11.1.6
68263cytochrome oxidase+1.9.3.1
68263arginine dihydrolase+3.5.3.6
68263urease+3.5.1.5
68263acid phosphatase+3.1.3.2
68263alkaline phosphatase+3.1.3.1
68263cystine arylamidase+3.4.11.3
68263esterase Lipase (C 8)+
68263alpha-glucosidase+3.2.1.20
68263leucine arylamidase+3.4.11.1
68263naphthol-AS-BI-phosphohydrolase+
68263trypsin+3.4.21.4
68263valine arylamidase+
68263alpha-chymotrypsin+/-3.4.21.1
68263esterase (C 4)+/-
68263N-acetyl-beta-glucosaminidase-3.2.1.52
68263alpha-fucosidase-3.2.1.51
68263alpha-galactosidase-3.2.1.22
68263beta-galactosidase-3.2.1.23
68263beta-glucosidase-3.2.1.21
68263beta-glucuronidase-3.2.1.31
68263lipase (C 14)-
68263alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68263C11:0 iso4.7
    68263C15:0 iso17.7
    68263C15:0 anteiso1.7
    68263C16:03.2
    68263C16:0 iso29.8
    68263C17:0 iso3
    68263C17:0 anteiso2
    68263C18:01.1
    68263C11:0 iso 3-OH5.6
    68263C16:1 iso H1.4
    68263C 16:1 w7c/C16:1 w6c3.9
    68263C17:1 iso w9c / C16:0 10-methyl20.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 30
  • incubation time: 3
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
67770Soil from Jeju IslandRepublic of KoreaKORAsia
68263soilRepublic of KoreaKORAsiaJeju Island33.3259126.842R2A agar1 week25

Sequence information

16S sequences

  • @ref: 67770
  • description: Lysobacter sp. 17J7-1 gene for 16S ribosomal RNA, partial sequence
  • accession: LC433920
  • length: 1473
  • database: ena
  • NCBI tax ID: 2488749

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter sp. 17J7-12488749.3wgspatric2488749
68263Lysobacter terrigena 17J7-1GCA_004361065contigncbi2488749

GC content

  • @ref: 68263
  • GC-content: 67.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes70.239no
gram-positiveno98.77no
anaerobicno99.35no
aerobicyes89.107no
halophileno95.517yes
spore-formingno96.906no
glucose-utilyes79.576yes
flagellatedno87.258yes
thermophileno94.795yes
glucose-fermentno92.392no

External links

@ref: 67770

culture collection no.: JCM 33057, KCTC 62217

literature

  • topic: Phylogeny
  • Pubmed-ID: 31776587
  • title: Lysobacter terrigena sp. nov., isolated from a Korean soil sample.
  • authors: Li W, Elderiny NS, Ten LN, Lee SY, Kim MK, Jung HY
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-019-01776-z
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis/metabolism, Lysobacter/classification/genetics/*isolation & purification/metabolism, Phospholipids/analysis/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorstitledoi/urljournal
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
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/
68263Weilan Li, Nabil Salah Elderiny, Leonid N. Ten, Seung-Yeol Lee, Myung Kyum Kim & Hee-Young JungLysobacter terrigena sp. nov., isolated from a Korean soil sample10.1007/s00203-019-01776-zArch Microbiol 202: 637-643 2020
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