Strain identifier

BacDive ID: 158745

Type strain: Yes

Species: Flavobacterium limi

Strain Designation: THG-AG6.4

NCBI tax ID(s): 2045105 (species)

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General

@ref: 65495

BacDive-ID: 158745

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

description: Flavobacterium limi THG-AG6.4 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest mud.

NCBI tax id

  • NCBI tax id: 2045105
  • Matching level: species

doi: 10.13145/bacdive158745.20230509.8.1

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 limi
  • full scientific name: Flavobacterium limi Moya et al. 2017

@ref: 65495

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium limi

strain designation: THG-AG6.4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65495negative1.7-2.0 µm0.4-0.5 µmrod-shapedno
69480negative99.996

colony morphology

  • @ref: 65495
  • colony size: 1.5-4.0 mm
  • colony color: bright yellow
  • colony shape: circular
  • medium used: NA

pigmentation

  • @ref: 65495
  • production: yes
  • name: flexirubin

Culture and growth conditions

culture medium

@refnamegrowth
65495Reasoner's 2A agar (R2A)yes
65495Trypticase Soy Agar (TSA)yes
65495LB (Luria-Bertani) MEDIUMno
65495MacConkeyno
65495Nutrient agar (NA)yes
65495Marine agar (MA)no

culture temp

@refgrowthtypetemperaturerange
65495positivegrowth10-35
65495positiveoptimum25-35mesophilic

culture pH

@refabilitytypepHPH range
65495positivegrowth6.0-9.5alkaliphile
65495positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 65495
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.994
69481no100

halophily

@refsaltgrowthtested relationconcentration
65495NaClpositivegrowth0-1.5 %(w/v)
65495NaClpositiveoptimum1.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65495168082-dehydro-D-gluconate-assimilation
65495161933-hydroxybenzoate-assimilation
65495370543-hydroxybutyrate-assimilation
65495178794-hydroxybenzoate-assimilation
65495581435-dehydro-D-gluconate-assimilation
6549527613amygdalin+assimilation
6549518305arbutin+assimilation
6549571422beta-gentiobiose+assimilation
6549527689decanoate-assimilation
6549585146carboxymethylcellulose+hydrolysis
65495casein-hydrolysis
6549517057cellobiose+assimilation
6549517029chitin-hydrolysis
6549515824D-fructose+assimilation
6549517634D-glucose+assimilation
6549517306maltose+assimilation
6549516899D-mannitol-assimilation
6549516024D-mannose+assimilation
6549528053melibiose-assimilation
6549516988D-ribose-assimilation
6549517924D-sorbitol-assimilation
6549565327D-xylose+assimilation
65495dipic acid-assimilation
6549524996lactate-assimilation
6549516991dna-hydrolysis
654954853esculin+hydrolysis
6549528260galactose+assimilation
654955291gelatin-hydrolysis
6549524265gluconate-assimilation
6549517234glucose+/-builds acid from
6549528087glycogen-assimilation
6549517268myo-inositol-assimilation
6549517240itaconate-assimilation
6549516977L-alanine-assimilation
6549530849L-arabinose+assimilation
6549518287L-fucose-assimilation
6549515971L-histidine-assimilation
6549517203L-proline-assimilation
6549562345L-rhamnose+assimilation
6549517115L-serine-assimilation
6549517895L-tyrosine-hydrolysis
6549517716lactose+assimilation
6549525115malate-assimilation
65495506227N-acetylglucosamine+/-assimilation
6549517632nitrate+reduction
6549564681phenyl beta-D-glucuronide+hydrolysis
6549518401phenylacetate-assimilation
6549517272propionate-assimilation
6549517814salicin-assimilation
6549532954sodium acetate-assimilation
6549553258sodium citrate-assimilation
6549562983sodium malonate-assimilation
6549528017starch-hydrolysis
6549528017starch+assimilation
654959300suberic acid-assimilation
6549517992sucrose+/-assimilation
6549553424tween 20-hydrolysis
6549553426tween 80-hydrolysis
6549516199urea-hydrolysis
6549531011valerate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6549516136hydrogen sulfideno
6549535581indoleno

enzymes

@refvalueactivityec
65495catalase+1.11.1.6
65495cytochrome oxidase+1.9.3.1
65495alkaline phosphatase+3.1.3.1
65495esterase (C 4)+
65495esterase Lipase (C 8)+
65495leucine arylamidase+3.4.11.1
65495valine arylamidase+
65495cystine arylamidase+3.4.11.3
65495trypsin+3.4.21.4
65495alpha-chymotrypsin+3.4.21.1
65495naphthol-AS-BI-phosphohydrolase+
65495alpha-galactosidase+3.2.1.22
65495beta-galactosidase+3.2.1.23
65495alpha-glucosidase+3.2.1.20
65495beta-glucosidase+3.2.1.21
65495N-acetyl-beta-glucosaminidase+3.2.1.52
65495lipase (C 14)-
65495acid phosphatase-3.1.3.2
65495beta-glucuronidase-3.2.1.31
65495alpha-mannosidase-3.2.1.24
65495alpha-fucosidase-3.2.1.51
65495arginine dihydrolase+3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65495C10:01
    65495C12:0 anteiso2.6
    65495C14:03.6
    65495C16:034.4
    65495C17:0 10-methyl1.1
    65495C17:1ω8c1.5
    65495C17:1ω5c1
    65495C18:09.8
    65495C18:0 10-methyl13
    65495C18:1ω9c10
    65495C18:3ω6c (6, 9, 12)2
    65495C19:03.1
    65495C20:01.5
    65495C16:1ω7c / C16:1ω6c12.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 28
  • incubation time: 2
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 65495
  • sample type: forest mud
  • geographic location: Kyung Hee University, Yongin, Gyeonggi
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37.2758
  • longitude: 127.178
  • enrichment culture: NA
  • enrichment culture duration: 2 days
  • enrichment culture temperature: 28
  • isolation procedure: One gram of sample was suspended in 10 ml sterile water containing 0.85 % NaCl (w/v). Serial dilutions of up to 10-5 were prepared using the same solution. Consequently, 100 µl of each dilution was plated onto nutrient agar plates.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Mud (Sludge)

Sequence information

16S sequences

  • @ref: 65495
  • description: 16S rRNA gene sequence
  • accession: KX263321
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium limi THG-AG6.4GCA_010645075contigncbi2045105
66792Flavobacterium limi CGMCC 1.16060GCA_014644395scaffoldncbi2045105
66792Flavobacterium limi strain CGMCC 1.160602045105.4wgspatric2045105
66792Flavobacterium limi strain THG-AG6.42045105.3wgspatric2045105
66792Flavobacterium limi THG-AG6.42906870539draftimg2045105

GC content

  • @ref: 65495
  • GC-content: 30.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.669yes
gram-positiveno98.497yes
anaerobicno99.642yes
aerobicyes87.616yes
halophileno96.835no
spore-formingno93.972no
glucose-utilyes92.041yes
thermophileno99.238no
motileno88.527yes
glucose-fermentno89.817no

External links

@ref: 65495

culture collection no.: KACC 18851, CGMCC 1.16060

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984563
  • title: Flavobacterium limi sp. nov., isolated from forest mud.
  • authors: Moya G, Yan ZF, Won KH, Yang JE, Kook MC, Yi TH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002354
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/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
65495Gabriela Moya, Zheng-Fei Yan, Kyung-Hwa Won, Jung-Eun Yang, Moo-Chang Kook and Tae-Hoo YiFlavobacterium limi sp. nov., isolated from forest mud10.1099/ijsem.0.002354IJSEM 67: 4667-4673 201728984563
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
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