Strain identifier

BacDive ID: 17719

Type strain: Yes

Species: Echinicola pacifica

Strain history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 6172

NCBI tax ID(s): 1121859 (strain), 346377 (species)

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General

@ref: 8343

BacDive-ID: 17719

DSM-Number: 19836

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

description: Echinicola pacifica DSM 19836 is a facultative anaerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from sea urchin Strongylocentrotus intermedius.

NCBI tax id

NCBI tax idMatching level
346377species
1121859strain

strain history

  • @ref: 8343
  • history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 6172

doi: 10.13145/bacdive17719.20230509.8.1

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 pacifica
  • full scientific name: Echinicola pacifica Nedashkovskaya et al. 2006

@ref: 8343

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Echinicola

species: Echinicola pacifica

full scientific name: Echinicola pacifica Nedashkovskaya et al. 2006 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
31738negative1.2-1.9 µm0.3-0.4 µmrod-shapedyesgliding
28014negative0.8-2.3 µm0.4-0.6 µmrod-shapedyesgliding

colony morphology

  • @ref: 28014
  • colony size: 2-3 mm
  • colony color: pink
  • colony shape: circular
  • medium used: marine agar

pigmentation

@refproductionname
31738yes
28014noFlexirubin type

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8343BACTO 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
28014Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
8343positivegrowth28mesophilic
31738positivegrowth06-41
31738positiveoptimum25-28mesophilic
28014positivegrowth42thermophilic
28014positiveoptimum25-28mesophilic
28014positivegrowth6-41

culture pH

@refabilitytypepH
31738positivegrowth7
31738positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31738
  • oxygen tolerance: facultative anaerobe

nutrition type

  • @ref: 28014
  • type: chemoorganotroph

spore formation

@refspore formationtype of spore
31738no
28014noendospore

halophily

@refsaltgrowthtested relationconcentration
31738NaClpositivegrowth0-12 %
31738NaClpositiveoptimum0-12 %
28014NaClpositivegrowth0-12 %

observation

  • @ref: 31738
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173816449alanine+carbon source
3173840585alpha-cyclodextrin+carbon source
3173822653asparagine+carbon source
3173835391aspartate+carbon source
3173816947citrate+carbon source
3173823652dextrin+carbon source
3173828757fructose+carbon source
3173833984fucose+carbon source
3173824175galacturonate+carbon source
3173817234glucose+carbon source
3173832323glucuronamide+carbon source
3173829987glutamate+carbon source
3173828087glycogen+carbon source
3173817716lactose+carbon source
3173837684mannose+carbon source
3173828053melibiose+carbon source
3173816634raffinose+carbon source
3173817992sucrose+carbon source
3173826986threonine+carbon source
3173827082trehalose+carbon source
317384853esculin+hydrolysis
28014645522-hydroxybutyrate-respiration
28014645522-hydroxybutyrate+respiration
28014309162-oxoglutarate-respiration
28014286442-oxopentanoate-respiration
28014620642,3-butanediol-respiration
28014370543-hydroxybutyrate-respiration
28014167244-hydroxybutyrate-respiration
28014181014-hydroxyphenylacetic acid-respiration
2801430089acetate-respiration
2801415963ribitol-builds acid from
2801415963ribitol-respiration
280142509agar+hydrolysis
280142509agar+/-degradation
2801440585alpha-cyclodextrin+respiration
2801417925alpha-D-glucose+respiration
2801436219alpha-lactose+respiration
2801427613amygdalin+builds acid from
2801473706bromosuccinate-respiration
2801485146carboxymethylcellulose-hydrolysis
28014casein-hydrolysis
2801462968cellulose-hydrolysis
2801417029chitin-hydrolysis
2801416383cis-aconitate-respiration
2801416947citrate-respiration
2801416947citrate+assimilation
2801415570D-alanine-respiration
2801417057cellobiose+builds acid from
2801415824D-fructose+respiration
2801412931D-galactonate-respiration
2801412936D-galactose+oxidation
2801412936D-galactose+respiration
2801418024D-galacturonic acid+respiration
280148391D-gluconate-respiration
2801417784D-glucosaminic acid-respiration
2801417634D-glucose+builds acid from
2801417634D-glucose+fermentation
2801414314D-glucose 6-phosphate-respiration
2801415748D-glucuronate+respiration
2801417716lactose+builds acid from
2801417306maltose+builds acid from
2801416899D-mannitol-respiration
2801416024D-mannose+builds acid from
2801416024D-mannose+respiration
2801428053melibiose+respiration
2801416634raffinose+respiration
2801433801D-saccharate-respiration
2801416523D-serine-respiration
2801417924D-sorbitol-respiration
2801416551D-trehalose+respiration
2801465327D-xylose+builds acid from
2801423652dextrin+respiration
2801417126DL-carnitine-respiration
2801416991dna-hydrolysis
2801416813galactitol-builds acid from
2801417113erythritol-respiration
280144853esculin+degradation
2801416000ethanolamine-respiration
2801415740formate-respiration
2801433984fucose-builds acid from
2801416865gamma-aminobutyric acid-respiration
280145291gelatin+hydrolysis
280145291gelatin+/-degradation
2801428066gentiobiose+respiration
2801429042glucose 1-phosphate-respiration
2801432323glucuronamide-respiration
2801417754glycerol-builds acid from
2801417754glycerol-respiration
2801414336glycerol 1-phosphate-respiration
2801428087glycogen+respiration
2801473804glycyl L-aspartic acid-respiration
2801424741hydroxyproline+respiration
2801417596inosine-respiration
2801417268myo-inositol-builds acid from
2801417240itaconate-respiration
2801421217L-alaninamide+respiration
2801416977L-alanine+respiration
2801473786L-alanylglycine+respiration
2801430849L-arabinose+builds acid from
2801418403L-arabitol-respiration
2801417196L-asparagine+respiration
2801429991L-aspartate+respiration
2801418287L-fucose+respiration
2801429985L-glutamate+respiration
2801415971L-histidine-respiration
2801415603L-leucine-respiration
2801415729L-ornithine-respiration
2801417295L-phenylalanine-respiration
2801417203L-proline-respiration
2801418183L-pyroglutamic acid-respiration
2801462345L-rhamnose+builds acid from
2801417115L-serine-respiration
2801416857L-threonine+respiration
2801465328L-xylose+builds acid from
2801424996lactate-respiration
280146359lactulose+respiration
2801415792malonate-respiration
2801429864mannitol-builds acid from
2801428053melibiose-builds acid from
2801437657methyl D-glucoside+respiration
2801451850methyl pyruvate-respiration
2801475146monomethyl succinate-respiration
2801417268myo-inositol-respiration
2801428037N-acetylgalactosamine-respiration
28014506227N-acetylglucosamine+builds acid from
2801473784glycyl-l-glutamate-respiration
2801417632nitrate-reduction
2801450048phenylethylamine-respiration
2801417272propionate-respiration
2801433951psicose+respiration
2801417148putrescine-respiration
2801426490quinate-respiration
2801416634raffinose-builds acid from
2801441865sebacic acid-respiration
2801427922sorbose-builds acid from
2801428017starch+degradation
2801428017starch+hydrolysis
28014143136succinamate-respiration
2801430031succinate-respiration
2801417992sucrose+oxidation
2801417992sucrose+respiration
2801417748thymidine-respiration
2801427897tryptophan-energy source
2801432528turanose+respiration
2801453424tween 20+degradation
2801453423tween 40+degradation
2801453426tween 80-respiration
2801453426tween 80+degradation
2801416704uridine-respiration
2801427248urocanic acid-respiration
2801417151xylitol-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
280146472lincomycinyesyes
2801428971ampicillinyesyes
280143393carbenicillinyesyes
2801417698chloramphenicolyesyes
2801450845doxycyclineyesyes
2801448923erythromycinyesyes
2801417833gentamicinyesyes
280146104kanamycinyesyes
280147507neomycinyesyes
2801416869oleandomycinyesyes
2801418208penicillin gyesyes
280148309polymyxin byesyes
2801417076streptomycinyesyes
2801427902tetracyclineyesyes

metabolite production

@refChebi-IDmetaboliteproduction
3173816136hydrogen sulfideyes
2801416136hydrogen sulfideyes
2801415688acetoinno
2801435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2801415688acetoin-
2801435581indole-

enzymes

@refvalueactivityec
31738alkaline phosphatase+3.1.3.1
31738catalase+1.11.1.6
31738cytochrome oxidase+1.9.3.1
28014arginine dihydrolase-3.5.3.6
28014lysine decarboxylase-4.1.1.18
28014ornithine decarboxylase-4.1.1.17
28014alpha-galactosidase+3.2.1.22
28014beta-galactosidase+3.2.1.23
28014alkaline phosphatase+3.1.3.1
28014acid phosphatase+3.1.3.2
28014esterase (C 4)+
28014esterase Lipase (C 8)+
28014leucine arylamidase+3.4.11.1
28014valine arylamidase+
28014cystine arylamidase+3.4.11.3
28014trypsin+3.4.21.4
28014alpha-chymotrypsin+3.4.21.1
28014naphthol-AS-BI-phosphohydrolase+
28014alpha-glucosidase+3.2.1.20
28014beta-glucosidase+3.2.1.21
28014N-acetyl-beta-glucosaminidase+3.2.1.52
28014alpha-mannosidase+3.2.1.24
28014alpha-fucosidase+3.2.1.51
28014lipase (C 14)-
28014beta-glucuronidase-3.2.1.31
28014tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8343sea urchin Strongylocentrotus intermediusStrongylocentrotus intermediusSea of Japan, Gulf of Peter the Great, Troitsa BayRussiaRUSAsia
28014Troitsa Bay, Gulf of Peter the GreatEast Sea, Troitsa Bay, Gulf of Peter the Great

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Echinodermata
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_52344.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_505;96_23508;97_29398;98_37531;99_52344&stattab=map
  • Last taxonomy: Echinicola pacifica subclade
  • 16S sequence: DQ185611
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 4
  • aquatic counts: 23
  • animal counts: 2
  • plant counts: 1

Safety information

risk assessment

  • @ref: 8343
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8343
  • description: Echinicola pacifica strain KMM 6172 16S ribosomal RNA gene, partial sequence
  • accession: DQ185611
  • length: 1363
  • database: ena
  • NCBI tax ID: 346377

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Echinicola pacifica KCTC 12368GCA_014651455contigncbi346377
66792Echinicola pacifica DSM 19836GCA_000373245scaffoldncbi1121859
66792Echinicola pacifica DSM 198361121859.3wgspatric1121859
66792Echinicola pacifica strain KCTC 12368346377.3wgspatric346377
66792Echinicola pacifica DSM 198362515154083draftimg1121859

GC content

@refGC-contentmethod
3173844-45
2801444-45thermal denaturation, midpoint method (Tm)
834343.8sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno85.858no
flagellatedno96.889no
gram-positiveno97.907yes
anaerobicno99.397no
aerobicyes87.68yes
halophileno62.536no
spore-formingno95.164no
thermophileno98.948no
glucose-utilyes89.154yes
glucose-fermentno87.117yes

External links

@ref: 8343

culture collection no.: DSM 19836, KCTC 12368, KMM 6172, LMG 23350

straininfo link

  • @ref: 86710
  • straininfo: 138410

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627637Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius.Nedashkovskaya OI, Kim SB, Vancanneyt M, Lysenko AM, Shin DS, Park MS, Lee KH, Jung WJ, Kalinovskaya NI, Mikhailov VV, Bae KS, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.64156-02006Animals, Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strongylocentrotus/*microbiologyEnzymology
Phylogeny20851907Echinicola jeungdonensis sp. nov., isolated from a solar saltern.Kim H, Joung Y, Ahn TS, Joh KInt J Syst Evol Microbiol10.1099/ijs.0.026765-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Enzymology27015142Structure of the O-specific polysaccharide from a marine bacterium Echinicola pacifica capital KA, Cyrilliccapital EM, Cyrilliccapital EM, Cyrillic 6172(capital TE, Cyrillic) containing 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid.Tomshich SV, Kokoulin MS, Kalinovsky AI, Nedashkovskaya OI, Komandrova NACarbohydr Res10.1016/j.carres.2016.03.0032016Carbohydrate Conformation, Cytophagaceae/*chemistry, Glucuronates/analysis/*chemistry, Polysaccharides/*chemistry/isolation & purificationPhylogeny
Phylogeny27902316Echinicola strongylocentroti sp. nov., isolated from a sea urchin Strongylocentrotus intermedius.Jung YJ, Yang SH, Kwon KK, Bae SSInt J Syst Evol Microbiol10.1099/ijsem.0.0016912017Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Strongylocentrotus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28857020Echinicola sediminis sp. nov., a marine bacterium isolated from coastal sediment.Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BSInt J Syst Evol Microbiol10.1099/ijsem.0.0021182017Bacterial 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/chemistryTranscriptome
34946153The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172(T) and Echinicola vietnamensis KMM 6221(T).Pither MD, Mantova G, Scaglione E, Pagliuca C, Colicchio R, Vitiello M, Chernikov OV, Hua KF, Kokoulin MS, Silipo A, Salvatore P, Molinaro A, Di Lorenzo FMicroorganisms10.3390/microorganisms91225522021

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_reference
8343Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19836)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19836
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
2801410.1099/ijs.0.64156-016627637
31738Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128014
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86710Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138410.1StrainInfo: A central database for resolving microbial strain identifiers