Strain identifier

BacDive ID: 158613

Type strain: Yes

Species: Flavobacterium foetidum

Strain Designation: CJ42

Strain history: C.-J. Cha; Chung-Ang Univ., South Korea; CJ42.

NCBI tax ID(s): 2026681 (species)

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General

@ref: 65335

BacDive-ID: 158613

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

description: Flavobacterium foetidum CJ42 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from ginseng soil.

NCBI tax id

  • NCBI tax id: 2026681
  • Matching level: species

strain history

  • @ref: 67770
  • history: C.-J. Cha; Chung-Ang Univ., South Korea; CJ42.

doi: 10.13145/bacdive158613.20230509.8.1

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 foetidum
  • full scientific name: Flavobacterium foetidum Bu and Cha 2018

@ref: 65335

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium foetidum

strain designation: CJ42

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65335negative1.6-1.7 µm0.6-0.75 µmrod-shapedyes
69480negative99.99

colony morphology

  • @ref: 65335
  • colony color: yellow
  • colony shape: circular
  • medium used: tryptic soy agar

pigmentation

  • @ref: 65335
  • production: yes
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65335
  • name: tryptic soy agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65335positivegrowth15-37
65335positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65335positivegrowth6-9alkaliphile
65335positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65335
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.99
69481no100

halophily

@refsaltgrowthtested relationconcentration
65335NaClpositivegrowth0-1 %
65335NaClpositiveoptimum0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6533540585alpha-cyclodextrin+carbon source
6533517925alpha-D-glucose+carbon source
6533527613amygdalin+builds acid from
6533518305arbutin-builds acid from
6533527689decanoate-assimilation
65335casein+hydrolysis
6533517057cellobiose+builds acid from
6533517057cellobiose+carbon source
6533562968cellulose+hydrolysis
6533515963ribitol-builds acid from
6533517108D-arabinose-builds acid from
6533518333D-arabitol-builds acid from
6533515824D-fructose+builds acid from
6533515824D-fructose+carbon source
6533528847D-fucose-builds acid from
6533512936D-galactose+builds acid from
6533512936D-galactose+carbon source
6533517634D-glucose+builds acid from
6533562318D-lyxose-builds acid from
6533516899D-mannitol-assimilation
6533516899D-mannitol-builds acid from
6533516024D-mannose+assimilation
6533516024D-mannose+builds acid from
6533516024D-mannose+carbon source
6533516988D-ribose-builds acid from
6533517924D-sorbitol-builds acid from
6533516443D-tagatose-builds acid from
6533565327D-xylose+builds acid from
6533523652dextrin+carbon source
6533516991dna+assimilation
6533516813galactitol-builds acid from
6533517113erythritol-builds acid from
65335esculin ferric citrate+builds acid from
6533528066gentiobiose+builds acid from
6533528066gentiobiose+carbon source
6533517234glucose+assimilation
6533517754glycerol-builds acid from
6533528087glycogen+builds acid from
6533528087glycogen+carbon source
6533517268myo-inositol-builds acid from
6533515443inulin-builds acid from
6533530849L-arabinose+assimilation
6533530849L-arabinose+builds acid from
6533530849L-arabinose+carbon source
6533518403L-arabitol-builds acid from
6533517196L-asparagine+carbon source
6533529991L-aspartate+carbon source
6533518287L-fucose+builds acid from
6533529985L-glutamate+carbon source
6533517203L-proline+carbon source
6533562345L-rhamnose-builds acid from
6533517266L-sorbose-builds acid from
6533565328L-xylose-builds acid from
6533517716lactose+builds acid from
6533517306maltose+assimilation
6533517306maltose+builds acid from
6533517306maltose+carbon source
6533528053melibiose-builds acid from
65335320061methyl alpha-D-glucopyranoside-builds acid from
6533543943methyl alpha-D-mannoside-builds acid from
65335506227N-acetylglucosamine+assimilation
65335506227N-acetylglucosamine+builds acid from
65335506227N-acetylglucosamine+carbon source
6533573784glycyl-l-glutamate+carbon source
6533517632nitrate-reduction
6533518401phenylacetate-assimilation
65335potassium 2-dehydro-D-gluconate-builds acid from
65335potassium 5-dehydro-D-gluconate-builds acid from
6533532032potassium gluconate-builds acid from
6533516634raffinose-builds acid from
6533517814salicin-builds acid from
6533553258sodium citrate-assimilation
6533528017starch-hydrolysis
6533528017starch+builds acid from
6533517992sucrose-builds acid from
6533527082trehalose-builds acid from
6533532528turanose-builds acid from
6533553426tween 80-hydrolysis
6533517151xylitol-builds acid from

enzymes

@refvalueactivityec
65335cytochrome oxidase+1.9.3.1
65335catalase+1.11.1.6
65335alkaline phosphatase+3.1.3.1
65335esterase (C 4)+
65335esterase Lipase (C 8)+
65335leucine arylamidase+3.4.11.1
65335valine arylamidase+
65335trypsin+3.4.21.4
65335acid phosphatase+3.1.3.2
65335naphthol-AS-BI-phosphohydrolase+
65335beta-galactosidase+3.2.1.23
65335alpha-glucosidase+3.2.1.20
65335beta-glucosidase+3.2.1.21
65335N-acetyl-beta-glucosaminidase+3.2.1.52
65335lipase (C 14)-
65335cystine arylamidase-3.4.11.3
65335alpha-chymotrypsin-3.4.21.1
65335beta-glucuronidase-3.2.1.31
65335alpha-mannosidase-3.2.1.24
65335beta-D-fucosidase-3.2.1.38

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65335C13:00.5
    65335C14:01.3
    65335C16:07.6
    65335C14:0 iso0.5
    65335C15:0 iso22.3
    65335C16:0 iso0.8
    65335C17:0 iso0.5
    65335C15:1 iso G4.2
    65335C17:1 iso ω9c2.4
    65335C15:0 anteiso2.1
    65335C15:1ω6c2.9
    65335C16:1ω5c1
    65335C17:1ω6c2.7
    65335C17:1ω8c1.4
    65335C18:1ω9c0.5
    65335C15:0 3OH2.1
    65335C16:0 3OH6.3
    65335C17:0 3OH0.7
    65335C15:0 iso 3OH43652
    65335C16:0 iso 3OH1
    65335C17:0 iso 3OH8.3
    65335C14:0 3OH and/or C16:1 iso I1.1
    65335C16:1ω7c and/or C16:1ω6c18.7
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy agar
  • incubation temperature: 30
  • incubation time: 1
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureisolation procedure
65335ginseng soil2012-12AnseongRepublic of KoreaKORAsia37.0651127.484R2Aserial dilution
67770Ginseng soil in AnseongRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 65335
  • description: 16S rRNA gene sequence
  • accession: KY056226
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium foetidum JCM 32085GCA_004634245contigncbi2026681
66792Flavobacterium foetidum strain JCM 320852026681.3wgspatric2026681
66792Flavobacterium foetidum JCM 320852882034188draftimg2026681

GC content

  • @ref: 65335
  • GC-content: 30.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno82.883yes
gram-positiveno98.481no
anaerobicno99.64no
aerobicyes85.497yes
halophileno96.727yes
spore-formingno93.407no
glucose-utilyes89.366no
flagellatedno94.031no
thermophileno99.548no
glucose-fermentno88.469no

External links

@ref: 65335

culture collection no.: KACC 19302, JCM 32085

literature

  • topic: Phylogeny
  • Pubmed-ID: 29303696
  • title: Flavobacterium foetidum sp. nov., isolated from ginseng soil.
  • authors: Bu JH, Cha CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002553
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Panax/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, 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
65335Ji-Hye Bu, Chang-Jun ChaFlavobacterium foetidum sp. nov., isolated from ginseng soil10.1099/ijsem.0.002553IJSEM 68: 616-622 201829303696
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/
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