Strain identifier

BacDive ID: 132986

Type strain: Yes

Species: Flavobacterium aquicola

Strain Designation: TMd3a3

Strain history: K. Hatayama; Sagami Chem. Res. Inst., Japan; TMd3a3.

NCBI tax ID(s): 1682742 (species)

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General

@ref: 24774

BacDive-ID: 132986

DSM-Number: 100880

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

description: Flavobacterium aquicola TMd3a3 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from fresh water from a river.

NCBI tax id

  • NCBI tax id: 1682742
  • Matching level: species

strain history

@refhistory
24774<- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; TMd3a3 <- K. Hatayama and T. Kuno
67770K. Hatayama; Sagami Chem. Res. Inst., Japan; TMd3a3.

doi: 10.13145/bacdive132986.20250331.9.3

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 aquicola
  • full scientific name: Flavobacterium aquicola Hatayama et al. 2016

@ref: 24774

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium aquicola

full scientific name: Flavobacterium aquicola Hatayama et al. 2016

strain designation: TMd3a3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43092negative4-11 µm0.5-0.6 µmrod-shapedyesgliding
125439negative99.9
125438no91.5
125438negative96.727

colony morphology

  • @ref: 43092
  • colony color: light yellow
  • colony shape: irregular
  • incubation period: 3 days
  • medium used: R2A

pigmentation

  • @ref: 43092
  • production: yes
  • name: Flexirubin-type pigment

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43092Reasoner's 2A agar (R2A)yes
43092IPMyes0.5 g/l yeast extract, 0.5 g/l proteose peptone no. 3, 0.5 g/l tryptone, 0.5 g/l sucrose, 0.3 g/l sodium pyruvate, 0.3 g/l K2HPO4, 0.3 g/l MgSO4x7H2O, 0.3 g/l CaCl2x2H2O, 15 g/l gellan gum, pH 6.6
43092trypticase soy agar (TSA)yes
43092nutritient agar (NA)yes
43092Marine agar (MA)no
24774R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperature
43092positiveoptimum25
43092positivegrowth4-30
24774positivegrowth25
67770positivegrowth25

culture pH

@refabilitytypepH
43092positivegrowth6.0-8.0
43092positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43092facultative anaerobe
125439obligate aerobe95.6

spore formation

@refspore formationconfidence
43092no
125439no99.6
125438no90.945

halophily

@refsaltgrowthtested relationconcentration
43092NaClpositivegrowth0-1 %(w/v)
43092NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43092casein+hydrolysis
43092starch+hydrolysis28017
43092carboxymethylcellulose-hydrolysis85146
43092chitin-hydrolysis17029
43092pectin-hydrolysis17309
43092L-tyrosine-hydrolysis17895
43092dna-hydrolysis16991
43092egg yolk-hydrolysis
43092gelatin-hydrolysis5291
43092nitrate+reduction17632
43092D-glucose+assimilation17634
43092L-arabinose+assimilation30849
43092D-mannose+assimilation16024
43092maltose+assimilation17306
43092D-mannitol-assimilation16899
43092N-acetylglucosamine-assimilation506227
43092potassium gluconate-assimilation32032
43092decanoate-assimilation27689
43092adipate-assimilation17128
43092malate-assimilation25115
43092sodium citrate-assimilation53258
43092phenylacetate-assimilation18401
43092glucose-fermentation17234
43092citrate-assimilation16947
43092D-mannitol-fermentation16899
43092myo-inositol-fermentation17268
43092D-sorbitol-fermentation17924
43092L-rhamnose-fermentation62345
43092sucrose-fermentation17992
43092melibiose-fermentation28053
43092amygdalin-fermentation27613
43092L-arabinose-fermentation30849
43092alpha-cyclodextrin+oxidation40585
43092dextrin+oxidation23652
43092glycogen+oxidation28087
43092L-arabinose+oxidation30849
43092cellobiose+oxidation17057
43092D-galactose+oxidation12936
43092gentiobiose+oxidation28066
43092alpha-D-glucose+oxidation17925
43092alpha-lactose+oxidation36219
43092maltose+oxidation17306
43092D-mannose+oxidation16024
43092L-glutamate+oxidation29985
43092glycyl L-aspartic acid+oxidation73804
43092glycyl-l-glutamate+oxidation73784
43092tween 40-oxidation53423
43092tween 80-oxidation53426
43092N-acetylgalactosamine-oxidation28037
43092N-acetylglucosamine-oxidation506227
43092ribitol-oxidation15963
43092D-arabitol-oxidation18333
43092erythritol-oxidation17113
43092D-fructose-oxidation15824
43092L-fucose-oxidation18287
43092myo-inositol-oxidation17268
43092lactulose-oxidation6359
43092D-mannitol-oxidation16899
43092melibiose-oxidation28053
43092methyl beta-D-glucopyranoside-oxidation320055
43092D-psicose-oxidation27605
43092raffinose-oxidation16634
43092L-rhamnose-oxidation62345
43092D-sorbitol-oxidation17924
43092sucrose-oxidation17992
43092trehalose-oxidation27082
43092turanose-oxidation32528
43092xylitol-oxidation17151
43092methyl pyruvate-oxidation51850
43092monomethyl succinate-oxidation75146
43092acetate-oxidation30089
43092cis-aconitate-oxidation16383
43092citrate-oxidation16947
43092formate-oxidation15740
43092D-galactonic acid lactone-oxidation15895
43092D-galacturonic acid-oxidation18024
43092D-gluconate-oxidation8391
43092D-glucosaminic acid-oxidation17784
43092D-glucuronate-oxidation15748
430922-hydroxybutyrate-oxidation64552
43092beta-hydroxybutyrate-oxidation8295
430924-hydroxybutyrate-oxidation16724
430924-hydroxyphenylacetic acid-oxidation18101
43092itaconate-oxidation17240
430922-oxobutanoate-oxidation16763
430922-oxoglutarate-oxidation30916
430922-oxopentanoate-oxidation28644
43092lactate-oxidation24996
43092malonate-oxidation15792
43092propionate-oxidation17272
43092quinate-oxidation26490
43092D-saccharate-oxidation33801
43092sebacic acid-oxidation41865
43092succinate-oxidation30031
43092bromosuccinate-oxidation73706
43092succinamate-oxidation143136
43092glucuronamide-oxidation32323
43092L-alaninamide-oxidation21217
43092D-alanine-oxidation15570
43092L-alanine-oxidation16977
43092L-alanylglycine-oxidation73786
43092L-asparagine-oxidation17196
43092L-aspartate-oxidation29991
43092L-histidine-oxidation15971
430924-hydroxy-L-proline-oxidation18240
43092L-leucine-oxidation15603
43092L-ornithine-oxidation15729
43092L-phenylalanine-oxidation17295
43092L-proline-oxidation17203
43092L-pyroglutamic acid-oxidation18183
43092D-serine-oxidation16523
43092L-serine-oxidation17115
43092L-threonine-oxidation16857
43092DL-carnitine-oxidation17126
43092gamma-aminobutyric acid-oxidation16865
43092urocanic acid-oxidation27248
43092inosine-oxidation17596
43092uridine-oxidation16704
43092thymidine-oxidation17748
43092phenylethylamine-oxidation50048
43092putrescine-oxidation17148
43092ethanolamine-oxidation16000
430922,3-butanediol-oxidation62064
43092glycerol-oxidation17754
43092glucose 1-phosphate-oxidation29042
43092D-glucose 6-phosphate-oxidation14314

metabolite production

@refChebi-IDmetaboliteproduction
4309235581indoleno
4309216136hydrogen sulfideno
4309215688acetoinno

metabolite tests

  • @ref: 43092
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
43092catalase+1.11.1.6
43092cytochrome oxidase+1.9.3.1
43092arginine dihydrolase-3.5.3.6
43092urease-3.5.1.5
43092beta-glucosidase+3.2.1.21
43092beta-galactosidase+3.2.1.23
43092lysine decarboxylase-4.1.1.18
43092ornithine decarboxylase-4.1.1.17
43092tryptophan deaminase-4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43092C13:0 iso2.9
    43092C14:0 iso2.7
    43092iso C15:1 G5.8
    43092C15:0 iso23.3
    43092C15:0 anteiso5.7
    43092C15:1ω6c5
    43092C16:1 iso H1.2
    43092C16:0 iso2.4
    43092C16:01.5
    43092C15:0 iso 3OH3.8
    43092C15:0 3OH1.1
    43092C17:1ω6c1.9
    43092C16:0 iso 3OH6.8
    43092C16:0 3OH2.2
    43092C17:0 iso 3OH7.6
    43092C16:1ω6c / C16:1ω7c17.7
    43092C17:1 iso ω9c / C16:0 10-methyl2.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: liquid
  • incubation temperature: 25
  • incubation time: 1
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24774fresh water from a riverKanagawa, Atsugi, Tamagawa RiverJapanJPNAsia
43092freshwater sampleTamagawa River, Atsugi, KanagawaJapanJPNAsiaIPM plates2-7 days25
67770Freshwater sample collected from the Tamagawa RiverJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#River (Creek)

Safety information

risk assessment

  • @ref: 24774
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24774Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequenceLC0656621436nuccore1682742
24774Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C1LC1208181436nuccore1682742
24774Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C2LC1208191436nuccore1682742
24774Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C3LC1208201436nuccore1682742

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium aquicola DSM 100880GCA_003385115scaffoldncbi1682742
66792Flavobacterium aquicola strain DSM 1008801682742.3wgspatric1682742
66792Flavobacterium aquicola DSM 100880 (v2)2739367662draftimg1682742

GC content

  • @ref: 24774
  • GC-content: 36.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.727yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.194yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes71.388yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.945yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.972no
125438motile2+flagellatedAbility to perform flagellated movementno91.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125439BacteriaNetmotilityAbility to perform movementyes50
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.6

External links

@ref: 24774

culture collection no.: DSM 100880, JCM 30987, BCRC 81042

straininfo link

  • @ref: 91262
  • straininfo: 406973

literature

  • topic: Phylogeny
  • Pubmed-ID: 27045592
  • title: Flavobacterium aquicola sp. nov., isolated from river water.
  • authors: Hatayama K, Ushida A, Kuno T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001057
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Japan, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24774Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100880Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100880)
43092Kouta Hatayama, Ayako Ushida, Teruaki KunoFlavobacterium aquicola sp. nov., isolated from river water10.1099/ijsem.0.001057IJSEM 66: 2789-2796 201627045592
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
91262Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406973.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG