Strain identifier

BacDive ID: 159807

Type strain: Yes

Species: Flavobacterium crocinum

Strain Designation: HYN0056

NCBI tax ID(s): 2183896 (species)

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General

@ref: 66771

BacDive-ID: 159807

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

description: Flavobacterium crocinum HYN0056 is an aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from freshwater.

NCBI tax id

  • NCBI tax id: 2183896
  • Matching level: species

doi: 10.13145/bacdive159807.20230509.8.1

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 crocinum
  • full scientific name: Flavobacterium crocinum Baek et al. 2018

@ref: 66771

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium crocinum

strain designation: HYN0056

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
66771negative1.2 µm0.4-0.44 µmrod-shapedyesgliding
69480negative99.994

colony morphology

  • @ref: 66771
  • colony color: pale yellow
  • colony shape: irregular
  • medium used: R2A medium

pigmentation

  • @ref: 66771
  • production: yes
  • name: flexirubin-type pigment

Culture and growth conditions

culture medium

@refnamegrowth
66771MacConkey agarno
66771Nutrient agar (NA)yes
66771Reasoner's 2A agar (R2A)yes
66771tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
66771positiveoptimum30mesophilic
66771positivegrowth4-40

culture pH

@refabilitytypepHPH range
66771positiveoptimum7.5
66771positivegrowth5-11.5alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.998
69481no100

halophily

@refsaltgrowthtested relationconcentration
66771NaClpositivegrowth0-2 %(w/v)
66771NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6677127897tryptophan-assimilation
6677117634D-glucose-builds acid from
6677116899D-mannitol-carbon source
6677117128adipate-carbon source
6677118401phenylacetate-carbon source
6677125115malate-carbon source
6677127689decanoate-carbon source
6677132032potassium gluconate-carbon source
6677153258sodium citrate-carbon source
6677116024D-mannose+carbon source
6677117306maltose+carbon source
6677117634D-glucose+carbon source
6677130849L-arabinose+carbon source
6677159640N-acetylglucosamine+carbon source
667713557154-nitrophenyl beta-D-galactopyranoside+carbon source
667715291gelatin-hydrolysis
6677115318xanthine-hydrolysis
6677116708adenine-hydrolysis
6677117029chitin-hydrolysis
6677117368hypoxanthine-hydrolysis
6677153426tween 80-hydrolysis
6677158187alginate-hydrolysis
66771crystalline cellulose-hydrolysis
667714853esculin+hydrolysis
6677116991dna+hydrolysis
6677117895L-tyrosine+hydrolysis
6677128017starch+hydrolysis
6677153423tween 40+hydrolysis
6677153424tween 20+hydrolysis
6677153425tween 60+hydrolysis
66771casein+hydrolysis

metabolite production

  • @ref: 66771
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
66771alpha-chymotrypsin-3.4.21.1
66771alpha-fucosidase-3.2.1.51
66771alpha-galactosidase-3.2.1.22
66771alpha-glucosidase-3.2.1.20
66771alpha-mannosidase-3.2.1.24
66771arginine dihydrolase-3.5.3.6
66771beta-galactosidase-3.2.1.23
66771beta-glucosidase-3.2.1.21
66771beta-glucuronidase-3.2.1.31
66771cystine arylamidase-3.4.11.3
66771esterase (C 4)-
66771esterase Lipase (C 8)-
66771lipase (C 14)-
66771naphthol-AS-BI-phosphohydrolase-
66771nitrate reductase-1.7.99.4
66771trypsin-3.4.21.4
66771urease-3.5.1.5
66771acid phosphatase+3.1.3.2
66771alkaline phosphatase+3.1.3.1
66771catalase+1.11.1.6
66771cytochrome oxidase+1.9.3.1
66771leucine arylamidase+3.4.11.1
66771N-acetyl-beta-glucosaminidase+3.2.1.52
66771valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66771C16:0 iso1
    66771C17:1 w8c1.1
    66771C13:11.2
    66771C14:01.2
    66771C15:0 3OH1.5
    66771C17:0 iso 3OH10.2
    66771C17:1 w6c2.3
    66771C15:0 anteiso2.5
    66771C15:1 w6c2.6
    66771C16:0 iso 3OH2.8
    66771C15:0 iso22.3
    66771C15:1 iso G5.4
    66771C16:06.5
    66771C16:0 3OH6.9
    66771C15:0 iso 3OH8.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6 6.10
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 66771
  • sample type: freshwater
  • geographic location: Jinyangho Lake
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 35.1675
  • longitude: 128.032
  • enrichment culture: R2A
  • enrichment culture temperature: 25
  • isolation procedure: A standard plating technique on R2A agar (BD) was used for isolation.

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

Sequence information

16S sequences

  • @ref: 66771
  • description: Flavobacterium ginsengisoli strain HYN0056 16S ribosomal RNA gene, partial sequence
  • accession: KY077156
  • length: 1444
  • database: ena
  • NCBI tax ID: 871694

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium crocinum HYN0056GCA_003122385completencbi2183896
66792Flavobacterium crocinum HYN00562844330942completeimg2183896

GC content

  • @ref: 66771
  • GC-content: 34
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.256no
gram-positiveno98.636no
anaerobicno99.643no
halophileno96.434yes
spore-formingno92.789no
glucose-utilyes90.339yes
aerobicyes88.781yes
thermophileno99.554yes
motileno82.975no
glucose-fermentno88.323no

External links

@ref: 66771

culture collection no.: KACC 19182, NBRC 112743

literature

  • topic: Phylogeny
  • Pubmed-ID: 30320543
  • title: Flavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and Flavobacterium album sp. nov.
  • authors: Baek C, Shin SK, Yi H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003067
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification, Lakes/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Water Microbiology
  • 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
66771Chaeyun Baek, Su-Kyoung Shin and Hana YiFlavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and Flavobacterium album sp. nov10.1099/ijsem.0.003067IJSEM 68: 3837-3843 201830320543
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
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