Strain identifier

BacDive ID: 158772

Type strain: Yes

Species: Antarcticibacterium flavum

Strain Designation: JB01H24

Strain history: <- Anzhang Li, Guangdong Institute of Microbiology

NCBI tax ID(s): 2058175 (species)

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General

@ref: 65526

BacDive-ID: 158772

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

description: Antarcticibacterium flavum JB01H24 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from From marine sediment.

NCBI tax id

  • NCBI tax id: 2058175
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Anzhang Li, Guangdong Institute of Microbiology

doi: 10.13145/bacdive158772.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Antarcticibacterium
  • species: Antarcticibacterium flavum
  • full scientific name: Antarcticibacterium flavum Li et al. 2018

@ref: 65526

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Antarcticibacterium

species: Antarcticibacterium flavum

strain designation: JB01H24

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
65526negative1-2 µm0.6-0.9 µmrod-shaped
69480negative99.963

colony morphology

  • @ref: 65526
  • colony size: 1 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: MA

Culture and growth conditions

culture medium

  • @ref: 65526
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65526positivegrowth4-40
65526positiveoptimum25-30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
65526positivegrowth7.0-9.0alkaliphile
65526positiveoptimum7.5-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65526aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no99.988
69481no100

halophily

@refsaltgrowthtested relationconcentration
65526NaClpositivegrowth0-8 %(w/v)
65526NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6552616651(S)-lactate-carbon source
65526645522-hydroxybutyrate-carbon source
65526167632-oxobutanoate-carbon source
65526309162-oxoglutarate-carbon source
65526739183-O-methyl-D-glucose-carbon source
65526181014-hydroxyphenylacetic acid-carbon source
6552630089acetate+carbon source
6552613705acetoacetate+carbon source
6552617128adipate-growth
6552617925alpha-D-glucose+carbon source
6552627613amygdalin-builds acid from
6552622599arabinose+/-builds acid from
6552673706bromosuccinate-carbon source
6552627689decanoate-growth
65526casein-hydrolysis
6552617057cellobiose+/-carbon source
6552662968cellulose-hydrolysis
6552616947citrate-carbon source
6552618333D-arabitol-carbon source
6552629990D-aspartate-carbon source
6552615824D-fructose+carbon source
6552678697D-fructose 6-phosphate-carbon source
6552628847D-fucose-carbon source
6552612936D-galactose+carbon source
6552618024D-galacturonic acid-carbon source
655268391D-gluconate-carbon source
6552614314D-glucose 6-phosphate-carbon source
6552615748D-glucuronate-carbon source
6552615588D-malate-carbon source
6552616899D-mannitol+/-carbon source
6552616024D-mannose+carbon source
6552633801D-saccharate-carbon source
6552616523D-serine-carbon source
6552617924D-sorbitol-carbon source
6552623652dextrin+carbon source
65526370543-hydroxybutyrate-carbon source
6552615740formate-carbon source
6552616537galactarate-carbon source
6552616865gamma-aminobutyric acid-carbon source
655265291gelatin-hydrolysis
655265291gelatin+carbon source
6552628066gentiobiose+carbon source
6552617234glucose-builds acid from
6552632323glucuronamide-carbon source
6552617754glycerol-carbon source
6552670744glycine-proline-carbon source
6552617596inosine-carbon source
6552617268myo-inositol-builds acid from
6552617268myo-inositol-carbon source
6552616977L-alanine-carbon source
6552630849L-arabinose-growth
6552616467L-arginine+/-carbon source
6552629991L-aspartate+carbon source
6552618287L-fucose-carbon source
6552617464L-galactonic acid gamma-lactone-carbon source
6552629985L-glutamate+/-carbon source
6552615971L-histidine-carbon source
6552615589L-malate-carbon source
65526L-pyroglutamic acid-carbon source
6552662345L-rhamnose-carbon source
6552617115L-serine-carbon source
6552617895L-tyrosine-hydrolysis
6552617716lactose+/-carbon source
6552625115malate-growth
6552617306maltose+carbon source
6552629864mannitol-builds acid from
6552628053melibiose+/-builds acid from
6552628053melibiose+/-carbon source
6552674611methyl (R)-lactate-carbon source
6552637657methyl D-glucoside-carbon source
6552651850methyl pyruvate-carbon source
6552663154N-acetyl-beta-D-mannosamine+/-carbon source
6552628037N-acetylgalactosamine+/-carbon source
65526506227N-acetylglucosamine-carbon source
65526506227N-acetylglucosamine-growth
6552635418n-acetylneuraminate-carbon source
6552617632nitrate+reduction
6552617309pectin-carbon source
6552618401phenylacetate-growth
6552632032potassium gluconate-growth
6552617272propionate-carbon source
6552626490quinate-carbon source
6552616634raffinose+/-carbon source
6552626546rhamnose-builds acid from
6552617814salicin+carbon source
6552653258sodium citrate-growth
6552630911sorbitol-builds acid from
6552617164stachyose+carbon source
6552628017starch-hydrolysis
6552617992sucrose-builds acid from
6552617992sucrose+carbon source
6552627082trehalose+carbon source
6552632528turanose-carbon source
6552653424tween 20+hydrolysis
6552653423tween 40+carbon source
6552653426tween 80+hydrolysis
6552637166xylan-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6552615688acetoinno
6552616136hydrogen sulfideno
6552635581indoleno

enzymes

@refvalueactivityec
65526catalase+1.11.1.6
65526cytochrome oxidase+1.9.3.1
65526alkaline phosphatase+3.1.3.1
65526esterase (C 4)+
65526esterase Lipase (C 8)+
65526lipase (C 14)+
65526leucine arylamidase+3.4.11.1
65526valine arylamidase+
65526cystine arylamidase+3.4.11.3
65526trypsin+3.4.21.4
65526alpha-chymotrypsin+3.4.21.1
65526acid phosphatase+3.1.3.2
65526naphthol-AS-BI-phosphohydrolase+
65526alpha-glucosidase+3.2.1.20
65526N-acetyl-beta-glucosaminidase+/-3.2.1.52
65526alpha-galactosidase-3.2.1.22
65526beta-galactosidase-3.2.1.23
65526beta-glucuronidase-3.2.1.31
65526beta-glucosidase-3.2.1.21
65526alpha-mannosidase-3.2.1.24
65526alpha-fucosidase-3.2.1.51
65526arginine dihydrolase-3.5.3.6
65526lysine decarboxylase-4.1.1.18
65526ornithine decarboxylase-4.1.1.17
65526urease-3.5.1.5
65526tryptophan deaminase-4.1.99.1
65526gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65526C15:0 iso20
    65526C16:0 iso4
    65526C15:0 anteiso12.4
    65526C15:1ω6c3.7
    65526C16:1ω6c / C16:1ω7c13.8
    65526C17:1ω6c2.4
    65526C15:1 iso G10.4
    65526C16:1 iso H2.7
    65526C15:1 anteiso A1.2
    65526C17:1 iso I /C17:1 anteiso B6.9
    65526iso-C16:1ω9c / 10-methyl C18:09.5
    65526C15:0 2OH3.8
    65526C15:0 iso 3OH4.6
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation temperature: 25
  • incubation time: 5
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
67771From marine sedimentRoss sea, AntarcticaAntarcticaATAAustralia and Oceania
65526surface sedimentRoss SeaAntarcticaATAAustralia and Oceania2015-02-77.5883165.569MA20 days4standard dilution plating

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

Sequence information

16S sequences

  • @ref: 65526
  • description: 16S rRNA gene sequence
  • accession: KY985393
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Antarcticibacterium flavum JB01H24GCA_006159205completencbi2058175
66792Antarcticibacterium flavum strain KCTC 52984 strain JB01H242058175.3completepatric2058175
66792Antarcticibacterium flavum JB01H242883447522completeimg2058175

GC content

  • @ref: 65526
  • GC-content: 42.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.233no
flagellatedno94.478no
gram-positiveno98.31yes
anaerobicno98.691yes
aerobicyes82.267yes
halophileno57.252no
spore-formingno95.388no
glucose-utilyes85.998yes
thermophileno99.582no
glucose-fermentno89.257no

External links

@ref: 65526

culture collection no.: GDMCC 1.1229, KCTC 52984

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29205128Antarcticibacterium flavum gen. nov., sp. nov., isolated from marine sediment.Li AZ, Lin LZ, Zhang MX, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0024892017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32213252Antarcticibacterium arcticum sp. nov., a bacterium isolated from marine sediment of the Canadian Beaufort Sea.Lee YM, Baek K, Lee DH, Park Y, Shin SC, Jin YKInt J Syst Evol Microbiol10.1099/ijsem.0.0041222020Bacterial Typing Techniques, Base Composition, Canada, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
65526An-Zhang Li, Long-Zhen Lin, Ming-Xia Zhang and Hong-Hui ZhuAntarcticibacterium flavum gen. nov., sp. nov., isolated from marine sediment10.1099/ijsem.0.002489IJSEM 68: 254-259 201829205128
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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