Strain identifier

BacDive ID: 133319

Type strain: Yes

Species: Flavobacterium gilvum

Strain Designation: EM1308

Strain history: H. Yi; Korea Univ., South Korea; EM1308.

NCBI tax ID(s): 1492737 (species)

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General

@ref: 25165

BacDive-ID: 133319

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

description: Flavobacterium gilvum EM1308 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from stream water in Bukhansan National Park, Seoul.

NCBI tax id

  • NCBI tax id: 1492737
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Yi; Korea Univ., South Korea; EM1308.

doi: 10.13145/bacdive133319.20230509.8.1

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 gilvum
  • full scientific name: Flavobacterium gilvum Shin et al. 2017

@ref: 25165

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium gilvum

strain designation: EM1308

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25165negative0.5-1.2 µm0.3-0.7 µmrod-shapedno
69480negative99.995

colony morphology

  • @ref: 25165
  • colony size: 2.0-3.0 mm
  • colony color: cream-coloured
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A

pigmentation

  • @ref: 25165
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

  • @ref: 25165
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25165positivegrowth4-30
25165positiveoptimum28mesophilic
25165nogrowth37mesophilic
25165nogrowth42thermophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
25165positivegrowth5.5-8.0
25165positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25165
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

  • @ref: 25165
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2516516708adenine-hydrolysis
2516517128adipate-assimilation
2516527613amygdalin-carbon source
2516585146carboxymethylcellulose-hydrolysis
2516517634D-glucose-carbon source
2516516899D-mannitol-carbon source
2516516024D-mannose-carbon source
2516517924D-sorbitol-carbon source
2516527689decanoate-assimilation
251655291gelatin-hydrolysis
2516517234glucose-fermentation
2516517368hypoxanthine-hydrolysis
2516517268myo-inositol-carbon source
2516530849L-arabinose-carbon source
2516562345L-rhamnose-carbon source
2516517895L-tyrosine-hydrolysis
2516525115malate-assimilation
2516517306maltose-carbon source
2516528053melibiose-carbon source
25165506227N-acetylglucosamine-carbon source
2516518401phenylacetate-assimilation
2516532032potassium gluconate-assimilation
2516553258sodium citrate-assimilation
2516517992sucrose-carbon source
2516553424tween 20-hydrolysis
2516553423tween 40-hydrolysis
2516553425tween 60-hydrolysis
2516553426tween 80-hydrolysis
2516515318xanthine-hydrolysis
25165casein+hydrolysis
2516516991dna+hydrolysis
251654853esculin+hydrolysis
2516517632nitrate+reduction
2516528017starch+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2516516136hydrogen sulfideno
2516535581indoleno

enzymes

@refvalueactivityec
25165acid phosphatase+3.1.3.2
25165alkaline phosphatase+3.1.3.1
25165alpha-chymotrypsin+3.4.21.1
25165alpha-fucosidase+3.2.1.51
25165alpha-galactosidase-3.2.1.22
25165alpha-galactosidase+3.2.1.22
25165alpha-glucosidase+3.2.1.20
25165alpha-mannosidase-3.2.1.24
25165arginine dihydrolase-3.5.3.6
25165beta-galactosidase+3.2.1.23
25165beta-glucosidase-3.2.1.21
25165beta-glucuronidase-3.2.1.31
25165catalase+1.11.1.6
25165cystine arylamidase-3.4.11.3
25165cytochrome oxidase+1.9.3.1
25165esterase (C 4)+
25165esterase Lipase (C 8)+
25165gelatinase-
25165leucine arylamidase+3.4.11.1
25165lipase (C 14)-
25165N-acetyl-beta-glucosaminidase+3.2.1.52
25165naphthol-AS-BI-phosphohydrolase+
25165trypsin-3.4.21.4
25165urease-3.5.1.5
25165valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
25165stream water in Bukhansan National Park, SeoulBukhansan National Park, SeoulRepublic of KoreaKORAsia37.66126.99
67770Stream water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_4549.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2272;97_2753;98_3419;99_4549&stattab=map
  • Last taxonomy: Flavobacterium gilvum subclade
  • 16S sequence: KX037100
  • Sequence Identity:
  • Total samples: 1743
  • soil counts: 151
  • aquatic counts: 900
  • animal counts: 148
  • plant counts: 544

Sequence information

16S sequences

  • @ref: 25165
  • description: 16S rRNA gene sequence
  • accession: KX037100
  • length: 1470
  • database: ena
  • NCBI tax ID: 1492737

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium gilvum EM1308GCA_001761465completencbi1492737
66792Flavobacterium gilvum EM1308GCA_000735535contigncbi1492737
66792Flavobacterium gilvum EM13082718217955completeimg1492737
66792Flavobacterium gilvum EM13082609460187draftimg1492737

GC content

@refGC-contentmethod
2516535.2
6777035.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.088yes
gram-positiveno97.416no
anaerobicno99.437no
aerobicyes85.968no
halophileno98.489yes
spore-formingno94.863no
glucose-utilyes89.33no
thermophileno99.473no
motileno92.109no
glucose-fermentno90.53yes

External links

@ref: 25165

culture collection no.: KACC 18113, JCM 30144

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902216
  • title: Flavobacterium gilvum sp. nov., isolated from stream water.
  • authors: Shin SK, Ha Y, Cho YJ, Kwon S, Yong D, Yi H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001594
  • year: 2017

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
25165S.-K. H. Shin, Yongheon,Cho, Yong-Joon,Kwon, Soonsung,Yong, Dongeun,Yi, HanaFlavobacterium gilvum sp. nov., isolated from stream water10.1099/ijsem.0.001594IJSEM 67: 153-157 201727902216
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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