Strain identifier

BacDive ID: 140384

Type strain: Yes

Species: Echinicola sediminis

Strain Designation: 001-Na2

Strain history: <- Beom Seok Kim , Korea Univ.

NCBI tax ID(s): 1928082 (species)

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General

@ref: 42991

BacDive-ID: 140384

DSM-Number: 103729

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

description: Echinicola sediminis 001-Na2 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from beach sediment.

NCBI tax id

  • NCBI tax id: 1928082
  • Matching level: species

strain history

@refhistory
42991<- B. S. Kim, Korea Univ., Seoul; 001-Na2 <- D.-W. Lee and J.-J. Kim
67770B. S. Kim; Korea Univ., South Korea; 001-Na2.
67771<- Beom Seok Kim , Korea Univ.

doi: 10.13145/bacdive140384.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Echinicola
  • species: Echinicola sediminis
  • full scientific name: Echinicola sediminis Lee et al. 2017

@ref: 42991

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Echinicola

species: Echinicola sediminis

full scientific name: Echinicola sediminis Lee et al. 2017

strain designation: 001-Na2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
43484negative1-1.6 µm0.3-0.5 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative

colony morphology

  • @ref: 43484
  • colony size: 1.5 mm
  • colony color: darl-salmon
  • colony shape: circular
  • incubation period: 5 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43484ISP medium 2yes
43484Marine agar (MA)yes
43484Nutrient agar (NA)yes
43484Trypticase Soy Agar (TSA)yes
42991BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43484positivegrowth20-45
43484positiveoptimum28mesophilic
42991positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43484positivegrowth5-11alkaliphile
43484positiveoptimum8-9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43484aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
43484NaClpositivegrowth0-10 %(w/v)
43484NaClpositiveoptimum0-5 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4348417128adipate-assimilation
4348427689decanoate-assimilation
4348417108D-arabinose-assimilation
4348417634D-glucose-assimilation
4348416899D-mannitol-assimilation
4348416024D-mannose-assimilation
4348425115malate-assimilation
4348417306maltose-assimilation
43484506227N-acetylglucosamine-assimilation
4348418401phenylacetate-assimilation
4348432032potassium gluconate-assimilation
4348453258sodium citrate-assimilation
43484645522-hydroxybutyrate-carbon source
43484167632-oxobutanoate-carbon source
43484309162-oxoglutarate-carbon source
43484286442-oxopentanoate-carbon source
43484620642,3-butanediol-carbon source
43484370543-hydroxybutyrate-carbon source
43484167244-hydroxybutyrate-carbon source
43484181014-hydroxyphenylacetic acid-carbon source
4348415963ribitol-carbon source
4348473706bromosuccinate-carbon source
4348416383cis-aconitate-carbon source
4348416947citrate-carbon source
4348415570D-alanine-carbon source
4348418333D-arabitol-carbon source
4348415895D-galactonic acid lactone-carbon source
4348416899D-mannitol-carbon source
4348433801D-saccharate-carbon source
4348416523D-serine-carbon source
4348417126DL-carnitine-carbon source
4348416000ethanolamine-carbon source
4348415740formate-carbon source
4348416865gamma-aminobutyric acid-carbon source
4348417754glycerol-carbon source
4348414336glycerol 1-phosphate-carbon source
4348473804glycyl L-aspartic acid-carbon source
4348417596inosine-carbon source
4348417240itaconate-carbon source
4348429991L-aspartate-carbon source
4348415971L-histidine-carbon source
4348415603L-leucine-carbon source
4348417295L-phenylalanine-carbon source
4348417203L-proline-carbon source
4348418183L-pyroglutamic acid-carbon source
4348417115L-serine-carbon source
4348415792malonate-carbon source
4348475146monomethyl succinate-carbon source
4348417268myo-inositol-carbon source
4348450048phenylethylamine-carbon source
4348417272propionate-carbon source
4348417148putrescine-carbon source
4348426490quinate-carbon source
4348441865sebacic acid-carbon source
43484143136succinamate-carbon source
4348430031succinate-carbon source
4348417748thymidine-carbon source
4348453423tween 40-carbon source
4348453426tween 80-carbon source
4348416704uridine-carbon source
4348427248urocanic acid-carbon source
4348417151xylitol-carbon source
43484645522-hydroxybutyrate-energy source
43484167632-oxobutanoate-energy source
43484309162-oxoglutarate-energy source
43484286442-oxopentanoate-energy source
43484620642,3-butanediol-energy source
43484370543-hydroxybutyrate-energy source
43484167244-hydroxybutyrate-energy source
43484181014-hydroxyphenylacetic acid-energy source
4348415963ribitol-energy source
4348473706bromosuccinate-energy source
4348416383cis-aconitate-energy source
4348416947citrate-energy source
4348415570D-alanine-energy source
4348418333D-arabitol-energy source
4348415895D-galactonic acid lactone-energy source
4348416899D-mannitol-energy source
4348433801D-saccharate-energy source
4348416523D-serine-energy source
4348417126DL-carnitine-energy source
4348416000ethanolamine-energy source
4348415740formate-energy source
4348416865gamma-aminobutyric acid-energy source
4348417754glycerol-energy source
4348414336glycerol 1-phosphate-energy source
4348473804glycyl L-aspartic acid-energy source
4348417596inosine-energy source
4348417240itaconate-energy source
4348429991L-aspartate-energy source
4348415971L-histidine-energy source
4348415603L-leucine-energy source
4348417295L-phenylalanine-energy source
4348417203L-proline-energy source
4348418183L-pyroglutamic acid-energy source
4348417115L-serine-energy source
4348415792malonate-energy source
4348475146monomethyl succinate-energy source
4348417268myo-inositol-energy source
4348450048phenylethylamine-energy source
4348417272propionate-energy source
4348417148putrescine-energy source
4348426490quinate-energy source
4348441865sebacic acid-energy source
43484143136succinamate-energy source
4348430031succinate-energy source
4348417748thymidine-energy source
4348453423tween 40-energy source
4348453426tween 80-energy source
4348416704uridine-energy source
4348427248urocanic acid-energy source
4348417151xylitol-energy source
4348417234glucose-fermentation
434842509agar-hydrolysis
434845291gelatin-hydrolysis
4348417368hypoxanthine-hydrolysis
4348415318xanthine-hydrolysis
4348417632nitrate-reduction
4348430089acetate+carbon source
4348440585alpha-cyclodextrin+carbon source
4348417925alpha-D-glucose+carbon source
4348436219alpha-lactose+carbon source
4348417057cellobiose+carbon source
4348415824D-fructose+carbon source
4348412936D-galactose+carbon source
4348418024D-galacturonic acid+carbon source
434848391D-gluconate+carbon source
4348417784D-glucosaminic acid+carbon source
4348414314D-glucose 6-phosphate+carbon source
4348415748D-glucuronate+carbon source
4348416024D-mannose+carbon source
4348427605D-psicose+carbon source
4348417924D-sorbitol+carbon source
4348423652dextrin+carbon source
4348417113erythritol+carbon source
4348428066gentiobiose+carbon source
4348429042glucose 1-phosphate+carbon source
4348432323glucuronamide+carbon source
4348428087glycogen+carbon source
4348424741hydroxyproline+carbon source
4348421217L-alaninamide+carbon source
4348416977L-alanine+carbon source
4348473786L-alanylglycine+carbon source
4348430849L-arabinose+carbon source
4348417196L-asparagine+carbon source
4348418287L-fucose+carbon source
4348429985L-glutamate+carbon source
4348415729L-ornithine+carbon source
4348462345L-rhamnose+carbon source
4348416857L-threonine+carbon source
4348424996lactate+carbon source
434846359lactulose+carbon source
4348417306maltose+carbon source
4348428053melibiose+carbon source
4348437657methyl D-glucoside+carbon source
4348451850methyl pyruvate+carbon source
4348428037N-acetylgalactosamine+carbon source
43484506227N-acetylglucosamine+carbon source
4348473784glycyl-l-glutamate+carbon source
4348416634raffinose+carbon source
4348417992sucrose+carbon source
4348427082trehalose+carbon source
4348432528turanose+carbon source
434844853esculin+degradation
4348430089acetate+energy source
4348440585alpha-cyclodextrin+energy source
4348417925alpha-D-glucose+energy source
4348436219alpha-lactose+energy source
4348417057cellobiose+energy source
4348415824D-fructose+energy source
4348412936D-galactose+energy source
4348418024D-galacturonic acid+energy source
434848391D-gluconate+energy source
4348417784D-glucosaminic acid+energy source
4348414314D-glucose 6-phosphate+energy source
4348415748D-glucuronate+energy source
4348416024D-mannose+energy source
4348427605D-psicose+energy source
4348417924D-sorbitol+energy source
4348423652dextrin+energy source
4348417113erythritol+energy source
4348428066gentiobiose+energy source
4348429042glucose 1-phosphate+energy source
4348432323glucuronamide+energy source
4348428087glycogen+energy source
4348424741hydroxyproline+energy source
4348421217L-alaninamide+energy source
4348416977L-alanine+energy source
4348473786L-alanylglycine+energy source
4348430849L-arabinose+energy source
4348417196L-asparagine+energy source
4348418287L-fucose+energy source
4348429985L-glutamate+energy source
4348415729L-ornithine+energy source
4348462345L-rhamnose+energy source
4348416857L-threonine+energy source
4348424996lactate+energy source
434846359lactulose+energy source
4348417306maltose+energy source
4348428053melibiose+energy source
4348437657methyl D-glucoside+energy source
4348451850methyl pyruvate+energy source
4348428037N-acetylgalactosamine+energy source
43484506227N-acetylglucosamine+energy source
4348473784glycyl-l-glutamate+energy source
4348416634raffinose+energy source
4348417992sucrose+energy source
4348427082trehalose+energy source
4348432528turanose+energy source
4348418186tyrosine+hydrolysis

metabolite production

  • @ref: 43484
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43484alkaline phosphatase+3.1.3.1
43484esterase (C 4)+
43484esterase Lipase (C 8)+
43484leucine arylamidase+3.4.11.1
43484valine arylamidase+
43484acid phosphatase+3.1.3.2
43484naphthol-AS-BI-phosphohydrolase+
43484alpha-galactosidase+3.2.1.22
43484beta-galactosidase+3.2.1.23
43484alpha-glucosidase+3.2.1.20
43484beta-glucosidase+3.2.1.21
43484N-acetyl-beta-glucosaminidase+3.2.1.52
43484alpha-mannosidase+3.2.1.24
43484alpha-fucosidase+3.2.1.51
43484lipase (C 14)-
43484cystine arylamidase-3.4.11.3
43484trypsin-3.4.21.4
43484alpha-chymotrypsin-3.4.21.1
43484beta-glucuronidase-3.2.1.31
43484arginine dihydrolase-3.5.3.6
43484urease-3.5.1.5
43484cytochrome oxidase+1.9.3.1
43484catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43484C15:0 anteiso3.2
    43484anteiso-C17:1B / iso-C17:1I3.8
    43484C15:1ω6c2.3
    43484C16:02.3
    43484C16:1ω5c4.3
    43484C16:1ω6c / C16:1ω7c10
    43484C17:1ω6c9.4
    43484C17:1ω8c1.7
    43484C18:01
    43484C14:0 iso1.8
    43484C15:0 iso35.1
    43484C15:0 iso 3OH3.3
    43484C16:0 iso3.5
    43484C16:1 iso H1.4
    43484C17:0 iso 3OH2.6
    43484iso-C17:1ω9c / 10-methylC16:07.4
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
42991beach sedimentSindu-ri, Wonbuk-myeon, Taean-gun, Chungcheongnam-doRepublic of KoreaKORAsia
43484coastal sediment/beach sand-soil of the Yellow Sea in Sindu-riSindu-ri, Yellow SeaRepublic of KoreaKORAsia
67770Coastal sediment of the Yellow Sea in Sindu-riRepublic of KoreaKORAsia
67771From beach sand-soilSindu-ri Coastal Sand Hills, Wonbok-Myeon, Taean-gun, North Chungcheong ProvinceRepublic of KoreaKORAsia35.9833126.6

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_54570.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_505;96_4463;97_28284;98_39006;99_54570&stattab=map
  • Last taxonomy: Echinicola sediminis subclade
  • 16S sequence: KX774280
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 14
  • aquatic counts: 53
  • animal counts: 10
  • plant counts: 1

Safety information

risk assessment

  • @ref: 42991
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42991
  • description: Echinicola sediminis 16S ribosomal RNA gene, partial sequence
  • accession: KX774280
  • length: 1431
  • database: ena
  • NCBI tax ID: 1928082

GC content

@refGC-contentmethod
4299144.6high performance liquid chromatography (HPLC)
6777144.6

External links

@ref: 42991

culture collection no.: DSM 103729, KCTC 52495, JCM 31786

straininfo link

  • @ref: 96675
  • straininfo: 397295

literature

  • topic: Phylogeny
  • Pubmed-ID: 28857020
  • title: Echinicola sediminis sp. nov., a marine bacterium isolated from coastal sediment.
  • authors: Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002118
  • year: 2017
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/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
42991Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103729Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103729)
43484Dong Wan Lee, Aslan Hwanhwi Lee, Hanbyul Lee, Jae-Jin Kim, Jong Seong Khim, Un Hyuk Yim, Beom Seok KimEchinicola sediminis sp. nov., a marine bacterium isolated from coastal sediment10.1099/ijsem.0.002118IJSEM 67: 3351-3357 201728857020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
96675Reimer, 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-ID397295.1