Strain identifier

BacDive ID: 140632

Type strain: Yes

Species: Novosphingobium flavum

Strain Designation: UCM-28

NCBI tax ID(s): 1778672 (species)

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General

@ref: 43164

BacDive-ID: 140632

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

description: Novosphingobium flavum UCM-28 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1778672
  • Matching level: species

doi: 10.13145/bacdive140632.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium flavum
  • full scientific name: Novosphingobium flavum Nguyen et al. 2016

@ref: 43164

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Novosphingobium

species: Novosphingobium flavum

strain designation: UCM-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43164negative1.0-1.5 µm0.5-0.7 µmrod-shapedno
69480negative99.984

colony morphology

  • @ref: 43164
  • colony size: 0.8-1.2 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowth
43164Reasoner's 2A agar (R2A)yes
43164Trypticase Soy Agar (TSA)yes
43164MacConkey agarno
43164Nutrient agar (NA)no
43164LB (Luria-Bertani) MEDIUMno

culture temp

  • @ref: 43164
  • growth: positive
  • type: growth
  • temperature: 10-37

culture pH

  • @ref: 43164
  • ability: positive
  • type: growth
  • pH: 5.5-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43164
  • oxygen tolerance: obligate aerobe

spore formation

@reftype of sporespore formationconfidence
43164sporeno
69480no99.998

halophily

  • @ref: 43164
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4316417632nitrate+reduction
431645291gelatin-hydrolysis
43164milk-hydrolysis
4316428017starch-hydrolysis
4316416991dna-hydrolysis
4316453423tween 40-hydrolysis
4316453425tween 60-hydrolysis
4316453426tween 80-hydrolysis
4316462345L-rhamnose+carbon source
4316417992sucrose+carbon source
4316417634D-glucose+carbon source
4316417814salicin+carbon source
4316417924D-sorbitol+carbon source
4316430849L-arabinose+carbon source
43164506227N-acetylglucosamine-carbon source
4316416988D-ribose-carbon source
4316417268myo-inositol-carbon source
4316417306maltose-carbon source
4316417240itaconate-carbon source
431649300suberic acid-carbon source
4316462983sodium malonate-carbon source
4316432954sodium acetate-carbon source
4316424996lactate-carbon source
4316416977L-alanine-carbon source
43164potassium 5-dehydro-D-gluconate-carbon source
4316428087glycogen-carbon source
43164161933-hydroxybenzoate-carbon source
4316417115L-serine-carbon source
4316416899D-mannitol-carbon source
4316428053melibiose-carbon source
4316418287L-fucose-carbon source
4316417272propionate-carbon source
4316427689decanoate-carbon source
4316431011valerate-carbon source
4316453258sodium citrate-carbon source
4316415971L-histidine-carbon source
43164potassium 2-dehydro-D-gluconate-carbon source
4316417634D-glucose+assimilation
43164esculin ferric citrate+assimilation
431644-nitrophenyl beta-D-galactopyranoside hydrolysate+assimilation
4316432032potassium gluconate+assimilation
4316430849L-arabinose+assimilation
4316416828L-tryptophan-assimilation
4316416467L-arginine-assimilation
4316416024D-mannose-assimilation
4316417306maltose-assimilation
4316417128adipate-assimilation
4316425115malate-assimilation
4316453258sodium citrate-assimilation
4316418401phenylacetate-assimilation
4316416199urea-assimilation
4316417234glucose-fermentation
43164370543-hydroxybutyrate+assimilation
43164178794-hydroxybenzoate+assimilation
4316417203L-proline-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4316435581indoleno
4316416136hydrogen sulfideno

enzymes

@refvalueactivityec
43164catalase+1.11.1.6
43164cytochrome oxidase-1.9.3.1
43164urease-3.5.1.5
43164alkaline phosphatase+3.1.3.1
43164leucine arylamidase+3.4.11.1
43164acid phosphatase+3.1.3.2
43164naphthol-AS-BI-phosphohydrolase+
43164beta-galactosidase+3.2.1.23
43164beta-glucuronidase+3.2.1.31
43164alpha-glucosidase+3.2.1.20
43164esterase (C 4)-
43164esterase Lipase (C 8)-
43164lipase (C 14)-
43164valine arylamidase-
43164cystine arylamidase-3.4.11.3
43164trypsin-3.4.21.4
43164alpha-galactosidase-3.2.1.22
43164N-acetyl-beta-glucosaminidase-3.2.1.52
43164alpha-mannosidase-3.2.1.24
43164alpha-fucosidase-3.2.1.51
43164beta-glucosidase+3.2.1.21
43164alpha-chymotrypsin-3.4.21.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43164C12:0 2OH0.1
    43164C13:0 2OH0.3
    43164C14:0 2OH11.8
    43164C15:0 2OH1.7
    43164C16:1 2OH0.2
    43164C16:0 2OH0.4
    43164C16:0 iso 3OH0.5
    43164C14:00.1
    43164C16:03.9
    43164C17:00.5
    43164C18:00.3
    43164C15:1ω6c0.2
    43164C16:1ω5c1.2
    43164C16:1 iso H0.2
    43164C17:1ω6c4.7
    43164C17:1ω8c0.7
    43164C18:1 iso H0.6
    43164C18:1ω5c0.6
    43164C16:1ω7c / C16:1ω6c24.9
    43164C18:1ω7c / C18:1ω6c46.3
    43164C17:1 iso ω9c / C16:0 10-methyl0.3
    43164cyclo C19:0ω8c0.6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • incubation_oxygen: aerobic
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 43164
  • sample type: forest soil
  • geographic location: Suwon, Gyeonggi-Do province, South Korea
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43164
  • description: 16S rRNA gene sequences
  • accession: KT750339
  • length: 1436
  • database: ena
  • NCBI tax ID: 1778672

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium flavum NBRC 111647GCA_014230315contigncbi1778672
66792Novosphingobium flavum strain NBRC 1116471778672.4wgspatric1778672
66792Novosphingobium flavum NBRC 1116472921278680draftimg1778672

GC content

  • @ref: 43164
  • GC-content: 63.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes50no
motileno56.843yes
gram-positiveno98.021no
anaerobicno99.319no
aerobicyes91.506no
halophileno97.006no
spore-formingno95.232yes
thermophileno95.408no
glucose-utilyes91.597yes
flagellatedno83.883no
glucose-fermentno89.239yes

External links

@ref: 43164

culture collection no.: KACC 18571, NBRC 111647

literature

  • topic: Phylogeny
  • Pubmed-ID: 27306976
  • title: Description of Novosphingobiumflavum sp. nov., isolated from soil.
  • authors: Nguyen TM, Myung SW, Jang H, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001242
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/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
43164Tuan Manh Nguyen, Seung-Woon Myung, Hyein Jang and Jaisoo KimDescription of Novosphingobium flavum sp. nov., isolated from soil10.1099/ijsem.0.001242IJSEM 66: 3642-3650 201627306976
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