Strain identifier

BacDive ID: 141064

Type strain: Yes

Species: Flavobacterium tyrosinilyticum

Strain Designation: THG-DN8.8

Strain history: <- Tae-Hoo Yi, Kyung Hee Univ.

NCBI tax ID(s): 1658740 (species)

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General

@ref: 43950

BacDive-ID: 141064

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Flavobacterium tyrosinilyticum THG-DN8.8 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from rhizosphere of a wild strawberry plant, located on Gyeryong Mountain, Daejeon, Republic of Korea.

NCBI tax id

  • NCBI tax id: 1658740
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Tae-Hoo Yi, Kyung Hee Univ.

doi: 10.13145/bacdive141064.20230509.8.1

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 tyrosinilyticum
  • full scientific name: Flavobacterium tyrosinilyticum Du and Yi 2016

@ref: 43950

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium tyrosinilyticum

strain designation: THG-DN8.8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43950negative1.4-2.7 µm0.3-0.5 µmrod-shapedyes
67771rod-shapedyes
67771negative

colony morphology

  • @ref: 43950
  • colony size: 0.5-1.5 mm
  • colony color: bright yellow
  • colony shape: circular
  • medium used: Nutrient agar

pigmentation

  • @ref: 43950
  • production: yes
  • name: Flexirubin-type pigments

Culture and growth conditions

culture medium

@refnamegrowth
43950LB (Luria-Bertani) MEDIUMyes
43950MacConkey agarno
43950Marine agar (MA)no
43950Nutrient agar (NA)yes
43950Reasoner's 2A agar (R2A)yes
43950Tryptone soya agaryes

culture temp

@refgrowthtypetemperaturerange
43950positivegrowth4-33
43950positiveoptimum24-28
67771positivegrowth28mesophilic

culture pH

  • @ref: 43950
  • ability: positive
  • type: growth
  • pH: 5.5-9.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43950facultative anaerobe
67771facultative anaerobe

halophily

  • @ref: 43950
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4395017128adipate-assimilation
4395027689decanoate-assimilation
4395016947citrate-assimilation
4395016899D-mannitol-assimilation
4395024265gluconate-assimilation
4395025115malate-assimilation
4395018401phenylacetate-assimilation
4395017234glucose-builds acid from
43950168082-dehydro-D-gluconate-carbon source
43950161933-hydroxybenzoate-carbon source
43950178794-hydroxybenzoate-carbon source
43950581435-dehydro-D-gluconate-carbon source
4395027689decanoate-carbon source
4395016899D-mannitol-carbon source
4395016988D-ribose-carbon source
4395017924D-sorbitol-carbon source
43950370543-hydroxybutyrate-carbon source
4395024996lactate-carbon source
4395017268myo-inositol-carbon source
4395017240itaconate-carbon source
43950L-alanine 4-nitroanilide-carbon source
4395015971L-histidine-carbon source
4395017272propionate-carbon source
4395053258sodium citrate-carbon source
4395062983sodium malonate-carbon source
439509300suberic acid-carbon source
4395017992sucrose-carbon source
4395031011valerate-carbon source
4395085146carboxymethylcellulose-hydrolysis
4395017029chitin-hydrolysis
4395016991dna-hydrolysis
4395028017starch-hydrolysis
4395053426tween 80-hydrolysis
4395017632nitrate-reduction
4395017634D-glucose+assimilation
4395016024D-mannose+assimilation
4395030849L-arabinose+assimilation
4395017306maltose+assimilation
43950506227N-acetylglucosamine+assimilation
4395017634D-glucose+carbon source
4395028087glycogen+carbon source
4395030849L-arabinose+carbon source
4395018287L-fucose+carbon source
4395017203L-proline+carbon source
4395062345L-rhamnose+carbon source
4395017115L-serine+carbon source
43950maltose hydrate+carbon source
4395028053melibiose+carbon source
43950506227N-acetylglucosamine+carbon source
4395017814salicin+carbon source
4395032954sodium acetate+carbon source
43950casein+hydrolysis
4395017895L-tyrosine+hydrolysis
4395053424tween 20+hydrolysis

metabolite production

  • @ref: 43950
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43950catalase+1.11.1.6
43950cytochrome oxidase+1.9.3.1
43950alkaline phosphatase+3.1.3.1
43950esterase (C 4)+
43950esterase Lipase (C 8)+
43950leucine arylamidase+3.4.11.1
43950valine arylamidase+
43950cystine arylamidase+3.4.11.3
43950alpha-chymotrypsin+3.4.21.1
43950acid phosphatase+3.1.3.2
43950naphthol-AS-BI-phosphohydrolase+
43950alpha-glucosidase+3.2.1.20
43950N-acetyl-beta-glucosaminidase+3.2.1.52
43950trypsin+/-3.4.21.4
43950lipase (C 14)-
43950alpha-galactosidase-3.2.1.22
43950alpha-mannosidase-3.2.1.24
43950beta-glucuronidase-3.2.1.31
43950alpha-fucosidase-3.2.1.51
43950beta-glucosidase+3.2.1.21
43950beta-galactosidase+3.2.1.23
43950arginine dihydrolase-3.5.3.6
43950urease-3.5.1.5
43950protease-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
43950rhizosphere of a wild strawberry plant, located on Gyeryong Mountain, Daejeon, Republic of KoreaGyeryong Mountain, DaejeonRepublic of KoreaKORAsiaNutrient agar3 days28
67771From rhizosphere of a wild strawberry plant in the forestDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_10581.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_207;97_5673;98_7880;99_10581&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: KR232271
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 27
  • aquatic counts: 36
  • animal counts: 7
  • plant counts: 8

Sequence information

16S sequences

  • @ref: 43950
  • description: 16S rRNA gene sequence
  • accession: KR232271
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Flavobacterium tyrosinilyticum KCTC 42726
  • accession: GCA_023656565
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1658740

GC content

@refGC-contentmethod
4395039.1high performance liquid chromatography (HPLC)
6777139.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.911no
gram-positiveno98.461yes
anaerobicno99.738yes
aerobicyes89.213yes
halophileno96.883no
spore-formingno92.727no
motileno78.977yes
glucose-fermentno89.595no
thermophileno99.697yes
glucose-utilyes91.9no

External links

@ref: 43950

culture collection no.: KCTC 42726, CCTCC AB 2015295

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27098975Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry.Du J, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0011042016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fragaria/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29464361Flavobacterium chungangensis sp. nov., a Bacterium Isolated from Soil of Chinese Cabbage Garden.Huq MA, Akter S, Lee SYCurr Microbiol10.1007/s00284-018-1456-62018Bacterial Typing Techniques, Base Composition, Brassica/*growth & development, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/classification/genetics/*isolation & purification/metabolism, Gardens, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil MicrobiologyMetabolism

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
43950Juan Du, Tae-Hoo YiFlavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry10.1099/ijsem.0.001104IJSEM 66: 2629-2634 201627098975
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
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/