Strain identifier

BacDive ID: 158777

Type strain: Yes

Species: Flavobacterium naphthae

Strain Designation: Brt-M

Strain history: J. Kim; Kyonggi Univ., South Korea; Brt-M.

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General

@ref: 65531

BacDive-ID: 158777

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

description: Flavobacterium naphthae Brt-M is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from oil-contaminated soil.

strain history

  • @ref: 67770
  • history: J. Kim; Kyonggi Univ., South Korea; Brt-M.

doi: 10.13145/bacdive158777.20230509.8.1

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 naphthae
  • full scientific name: Flavobacterium naphthae Chaudhary and Kim 2018

  • synonyms

    • @ref: 20215
    • synonym: Paenimyroides naphthae

@ref: 65531

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium naphtae

strain designation: Brt-M

type strain: yes

Morphology

cell morphology

  • @ref: 65531
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65531
  • colony size: 1.0-1.5 mm
  • colony color: yellow
  • colony shape: circular
  • medium used: TSA

pigmentation

  • @ref: 65531
  • production: yes
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
65531Reasoner's 2A agar (R2A)yes
65531Nutrient agar (NA)yes
65531LB (Luria-Bertani) MEDIUMyes
65531VIAyes
65531Marine agar (MA)no
65531Trypticase Soy Agar (TSA)yes
65531SMAno

culture temp

@refgrowthtypetemperaturerange
65531positivegrowth15-45
65531positiveoptimum25-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65531positivegrowth5.5-9.0alkaliphile
65531positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 65531
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65531
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65531NaClpositivegrowth0-1 %
65531NaClpositiveoptimum0 %non-halophilic

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65531161933-hydroxybenzoate-assimilation
65531370543-hydroxybutyrate-assimilation
65531178794-hydroxybenzoate-assimilation
6553117128adipate-assimilation
6553127689decanoate-assimilation
6553185146carboxymethylcellulose-hydrolysis
65531casein-hydrolysis
6553117029chitin-hydrolysis
6553117634D-glucose-assimilation
6553116899D-mannitol-assimilation
6553116024D-mannose-assimilation
6553116988D-ribose-assimilation
6553117924D-sorbitol-assimilation
6553116991dna-hydrolysis
655314853esculin+/-hydrolysis
655315291gelatin+/-hydrolysis
6553117234glucose-fermentation
6553128087glycogen-assimilation
6553117268myo-inositol-assimilation
6553117240itaconate-assimilation
6553116977L-alanine-assimilation
6553130849L-arabinose-assimilation
6553118287L-fucose-assimilation
6553115971L-histidine-assimilation
6553117203L-proline-assimilation
6553162345L-rhamnose-assimilation
6553117115L-serine-assimilation
6553124996lactate-assimilation
6553125115malate-assimilation
6553117306maltose-assimilation
6553128053melibiose-assimilation
65531506227N-acetylglucosamine-assimilation
6553117632nitrate-reduction
6553118401phenylacetate-assimilation
65531potassium 2-dehydro-D-gluconate-assimilation
65531potassium 5-dehydro-D-gluconate-assimilation
6553132032potassium gluconate-assimilation
6553117272propionate-assimilation
6553117814salicin-assimilation
6553132954sodium acetate-assimilation
6553153258sodium citrate-assimilation
6553162983sodium malonate-assimilation
6553128017starch-hydrolysis
655319300suberic acid-assimilation
6553117992sucrose+/-assimilation
6553153423tween 40-hydrolysis
6553153426tween 80-hydrolysis
6553118186tyrosine+/-hydrolysis
6553131011valerate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6553115688acetoinno
6553116136hydrogen sulfideno
6553135581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6553117234glucose-
6553115688acetoin-

enzymes

@refvalueactivityec
65531catalase+1.11.1.6
65531cytochrome oxidase+1.9.3.1
65531alkaline phosphatase+3.1.3.1
65531esterase (C 4)+
65531esterase Lipase (C 8)+
65531lipase (C 14)+
65531leucine arylamidase+3.4.11.1
65531valine arylamidase+
65531naphthol-AS-BI-phosphohydrolase+/-
65531cystine arylamidase-3.4.11.3
65531trypsin-3.4.21.4
65531alpha-chymotrypsin-3.4.21.1
65531acid phosphatase-3.1.3.2
65531alpha-galactosidase-3.2.1.22
65531beta-galactosidase-3.2.1.23
65531alpha-glucosidase-3.2.1.20
65531beta-glucuronidase-3.2.1.31
65531beta-glucosidase-3.2.1.21
65531N-acetyl-beta-glucosaminidase-3.2.1.52
65531alpha-mannosidase-3.2.1.24
65531arginine dihydrolase-3.5.3.6
65531urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65531C16:00.8
    65531C15:0 anteiso0.8
    65531C17:0 anteiso0.6
    65531C13:0 iso0.3
    65531C15:0 iso52.2
    65531C17:0 iso0.5
    65531C18:1ω5c0.6
    65531C15:0 2OH0.2
    65531C15:0 iso 3OH5.7
    65531C16:0 3OH0.3
    65531C17:0 2OH0.2
    65531C17:0 iso 3OH13.1
    65531C16:1ω7c / C16:1ω6c9.2
    65531C17:1 iso ω9c / C16:0 10-methyl14.5
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • incubation temperature: 28
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture
65531oil-contaminated soilBiratnagar, MorangNepalNPLAsiaTSA
67770Oil-contaminated soil of BiratnagarMorangNepalNPLAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 65531
  • description: 16S rRNA gene sequence
  • accession: MF405102
  • database: nuccore

GC content

  • @ref: 67770
  • GC-content: 37.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65531

culture collection no.: KEMB 9005-692, KACC 19393, JCM 32171

literature

  • topic: Phylogeny
  • Pubmed-ID: 29185939
  • title: Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil.
  • authors: Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002504
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, 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
65531Dhiraj Kumar Chaudhary and Jaisoo KimFlavobacterium naphthae sp. nov., isolated from oil-contaminated soil10.1099/ijsem.0.002504IJSEM 68: 305-309 201829185939
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/