Strain identifier

BacDive ID: 158612

Type strain: Yes

Species: Sphingobacterium terrae

Strain Designation: Brt-F

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

NCBI tax ID(s): 2070451 (species)

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

@ref: 65334

BacDive-ID: 158612

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

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

NCBI tax id

  • NCBI tax id: 2070451
  • Matching level: species

strain history

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

doi: 10.13145/bacdive158612.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium terrae
  • full scientific name: Sphingobacterium terrae Chaudhary and Kim 2018

@ref: 65334

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium terrae

strain designation: Brt-F

type strain: yes

Morphology

cell morphology

  • @ref: 65334
  • gram stain: negative
  • cell length: 0.8-1 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65334
  • colony size: 1-1.5 mm
  • colony color: cream
  • colony shape: circular
  • medium used: tryptic soy agar

Culture and growth conditions

culture medium

@refnamegrowth
65334tryptic soy agaryes
65334Reasoner's 2A agar (R2A)yes
65334Nutrient agar (NA)yes
65334LB (Luria-Bertani) MEDIUMyes
65334veal infusion agaryes
65334Marine agar (MA)yes
65334sorbitol MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
65334positivegrowth15-45
65334positiveoptimum25-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65334positivegrowth6.5-10.5alkaliphile
65334positiveoptimum7-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65334
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65334
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65334NaClpositivegrowth0-4.5 %
65334NaClpositiveoptimum0 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65334161933-hydroxybenzoate-assimilation
65334370543-hydroxybutyrate-assimilation
65334178794-hydroxybenzoate-assimilation
6533417128adipate-assimilation
6533427689decanoate-assimilation
6533485146carboxymethylcellulose+hydrolysis
65334casein-hydrolysis
6533417029chitin-hydrolysis
6533417634D-glucose+assimilation
6533416899D-mannitol-assimilation
6533416024D-mannose+assimilation
6533416988D-ribose+assimilation
6533417924D-sorbitol-assimilation
6533416991dna-hydrolysis
653344853esculin+hydrolysis
653345291gelatin-fermentation
653345291gelatin-hydrolysis
6533417234glucose-fermentation
6533428087glycogen+assimilation
6533417268myo-inositol-assimilation
6533417240itaconate-assimilation
6533416977L-alanine-assimilation
6533430849L-arabinose+assimilation
6533416467L-arginine-fermentation
6533418287L-fucose-assimilation
6533415971L-histidine-assimilation
6533417203L-proline-assimilation
6533462345L-rhamnose+assimilation
6533417115L-serine-assimilation
6533416828L-tryptophan-assimilation
6533424996lactate-assimilation
6533425115malate-assimilation
6533417306maltose+assimilation
6533428053melibiose+assimilation
65334506227N-acetylglucosamine+assimilation
6533417632nitrate-reduction
6533418401phenylacetate-assimilation
65334potassium 2-dehydro-D-gluconate-assimilation
65334potassium 5-dehydro-D-gluconate-assimilation
6533432032potassium gluconate-assimilation
6533417272propionate-assimilation
6533417814salicin+assimilation
6533432954sodium acetate-assimilation
6533453258sodium citrate-assimilation
6533462983sodium malonate-assimilation
6533428017starch-hydrolysis
653349300suberic acid-assimilation
6533417992sucrose+assimilation
6533453423tween 40-hydrolysis
6533453426tween 80-hydrolysis
6533418186tyrosine-hydrolysis
6533416199urea-fermentation
6533431011valerate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6533415688acetoinno
6533416136hydrogen sulfideno
6533435581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6533417234glucose-
6533415688acetoin-

enzymes

@refvalueactivityec
65334catalase+1.11.1.6
65334cytochrome oxidase+1.9.3.1
65334alkaline phosphatase+3.1.3.1
65334leucine arylamidase+3.4.11.1
65334trypsin+3.4.21.4
65334acid phosphatase+3.1.3.2
65334naphthol-AS-BI-phosphohydrolase+
65334alpha-glucosidase+3.2.1.20
65334beta-glucosidase+3.2.1.21
65334alpha-mannosidase+3.2.1.24
65334alpha-fucosidase+3.2.1.51
65334valine arylamidase+
65334cystine arylamidase+3.4.11.3
65334alpha-galactosidase+3.2.1.22
65334esterase (C 4)-
65334esterase Lipase (C 8)-
65334lipase (C 14)-
65334alpha-chymotrypsin-3.4.21.1
65334beta-galactosidase-3.2.1.23
65334beta-glucuronidase-3.2.1.31
65334N-acetyl-beta-glucosaminidase-3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65334C14:00.3
    65334C16:04.8
    65334C15:0 anteiso0.6
    65334C15:0 iso27.8
    65334iso-C15:0 F0.2
    65334C17:0 iso0.4
    65334C16:1ω5c0.8
    65334C14:0 2OH0.2
    65334C15:0 iso 3OH3.1
    65334C16:0 2OH0.3
    65334C16:0 3OH1
    65334C16:0 iso 3OH0.2
    65334C17:0 iso 3OH19.1
    65334C16:1ω7c and/or C16:1ω6c36.3
    65334C17:1 iso I and/or C17:1 anteiso B0.4
    65334C18:1ω7c and/or C18:1ω6c1.3
    65334iso-C17:1ω9c and/or C16:010-methyl2.1
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy agar
  • incubation temperature: 28
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65334oil-contaminated soilpetroleum distribution center of Biratnagar, MorangNepalNPLAsia26.492287.2767tryptic soy broth15 daysroomtemperaturemodified culture technique with six-well polycarbonate Transwell plates
67770Oil-contaminated soil sample of BiratnagarMorangNepalNPLAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 65334
  • description: 16S rRNA gene sequence
  • accession: MF405100
  • database: nuccore

GC content

  • @ref: 65334
  • GC-content: 43.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65334

culture collection no.: KEMB 9005-691, KACC 19392, JCM 32159

literature

  • topic: Phylogeny
  • Pubmed-ID: 29303695
  • title: Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil.
  • authors: Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002552
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nepal, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, 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
65334Dhiraj Kumar Chaudhary, Jaisoo KimSphingobacterium terrae sp. nov., isolated from oil-contaminated soil10.1099/ijsem.0.002552IJSEM 68: 609-615 201829303695
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/