Strain identifier

BacDive ID: 164350

Type strain: Yes

Species: Flavobacterium nackdongense

Strain Designation: GS13

Strain history: H. Kim; NNIBR, South Korea; GS13.

NCBI tax ID(s): 2547394 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 67770

BacDive-ID: 164350

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

description: Flavobacterium nackdongense GS13 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Sediment of a branch of the Nackdong River in Sangju.

NCBI tax id

  • NCBI tax id: 2547394
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Kim; NNIBR, South Korea; GS13.

doi: 10.13145/bacdive164350.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium nackdongense
  • full scientific name: Flavobacterium nackdongense Kim and Yu 2020

@ref: 67770

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium nackdongense

full scientific name: Flavobacterium nackdongense Kim and Yu 2020

strain designation: GS13

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
68261negativerod-shapedno
69480negative99.996
69480no90.948

colony morphology

  • @ref: 68261
  • colony color: yellow
  • colony shape: circular
  • medium used: Reasoner's 2A agar (R2A)

pigmentation

  • @ref: 68261
  • production: no
  • name: Flexirubin type pigments

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth25mesophilic
68261positivegrowth10-30
68261positiveoptimum20psychrophilic

culture pH

@refabilitytypepH
68261positivegrowth6.5-8
68261positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68261
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.994
69481no100

halophily

@refsaltgrowthtested relationconcentration
68261NaClpositivegrowth0 %(w/v)
68261NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6826117632nitrate+reduction
6826128017starch+hydrolysis
6826162968cellulose+hydrolysis
68261casein-hydrolysis
6826116991dna-hydrolysis
6826153424tween 20-hydrolysis
6826153423tween 40-hydrolysis
6826153425tween 60-hydrolysis
6826153426tween 80-hydrolysis

enzymes

@refvalueactivityec
68261cytochrome oxidase+1.9.3.1
68261catalase+1.11.1.6
68261alkaline phosphatase+3.1.3.1
68261leucine arylamidase+3.4.11.1
68261valine arylamidase+
68261trypsin+3.4.21.4
68261acid phosphatase+3.1.3.2
68261naphthol-AS-BI-phosphohydrolase+
68261esterase (C 4)-
68261esterase Lipase (C 8)-
68261lipase (C 14)-
68261cystine arylamidase-3.4.11.3
68261alpha-chymotrypsin-3.4.21.1
68261alpha-galactosidase-3.2.1.22
68261beta-galactosidase-3.2.1.23
68261beta-glucuronidase-3.2.1.31
68261alpha-glucosidase-3.2.1.20
68261beta-glucosidase-3.2.1.21
68261N-acetyl-beta-glucosaminidase-3.2.1.52
68261alpha-mannosidase-3.2.1.24
68261alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68261C14:01.2
    68261C16:02.2
    68261C12:0 iso1.1
    68261C13:0 iso3.4
    68261C14:0 iso2.9
    68261C15:0 iso16
    68261C16:0 iso6.7
    68261C15:1 iso G4.3
    68261C16:1 iso H3.7
    68261C13:0 anteiso2.1
    68261C15:0 anteiso6.7
    68261C15:1 anteiso A1.5
    68261C17:1 anteiso w9c1.7
    68261C15:1 w6c1.7
    68261C17:1 w6c1.6
    68261C16:0 3OH2.1
    68261C15:0 iso 3OH3.6
    68261C16:0 iso 3OH7.8
    68261C17:0 iso 3OH4.1
    68261C16:1 w7c/C16:1 w6c19.1
    68261C17:1 iso w9c / C16:0 10-methyl1.7
  • type of FA analysis: whole cell analysis
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
67770Sediment of a branch of the Nackdong River in SangjuRepublic of KoreaKORAsia
68261sediment of a branch of the Nackdong RiverRepublic of KoreaKORAsiaSangju36.471128.154R2A agar7 days25

Sequence information

16S sequences

  • @ref: 67770
  • description: Flavobacterium nackdongense 16S ribosomal RNA gene, complete sequence
  • accession: MH168565
  • length: 1513
  • database: ena
  • NCBI tax ID: 2547394

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium nackdongense GS13GCA_004355225completencbi2547394
66792Flavobacterium nackdongense GS132848968057completeimg2547394

GC content

  • @ref: 67770
  • GC-content: 36.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.238yes
flagellatedno97.059yes
gram-positiveno98.162no
anaerobicno98.528yes
aerobicyes83.082yes
halophileno98.252yes
spore-formingno95.175no
glucose-utilyes90.272no
thermophileno98.859yes
glucose-fermentno87.217no

External links

@ref: 67770

culture collection no.: JCM 32765, KCTC 62569

literature

  • topic: Phylogeny
  • Pubmed-ID: 31745602
  • title: Flavobacterium nackdongense sp. nov., a cellulose-degrading bacterium isolated from sediment.
  • authors: Kim H, Yu SM
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-019-01770-5
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, Cellulose/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/classification/genetics/*isolation & purification/*metabolism, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA
  • 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/
68261Hyangmi Kim & Sang Mi YuFlavobacterium nackdongense sp. nov., a cellulose-degrading bacterium isolated from sediment10.1007/s00203-019-01770-5Arch Microbiol 202: 591-595 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