Strain identifier

BacDive ID: 158706

Type strain: Yes

Species: Aequorivita todarodis

Strain Designation: MYP2-2

Strain history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

NCBI tax ID(s): 2036821 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 8.1 (current version)

General

@ref: 65448

BacDive-ID: 158706

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

description: Aequorivita todarodis MYP2-2 is an aerobe, psychrophilic, Gram-negative bacterium that forms circular colonies and was isolated from the intestinal tract of a squid .

NCBI tax id

  • NCBI tax id: 2036821
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Jung-Hoon YOON, Sungkyunkwan Univ.

doi: 10.13145/bacdive158706.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aequorivita
  • species: Aequorivita todarodis
  • full scientific name: Aequorivita todarodis (Kim et al. 2018) Zhang et al. 2020

  • synonyms

    @refsynonym
    20215Aequorivita todarodis
    20215Vitellibacter todarodis

@ref: 65448

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Vitellibacter

species: Vitellibacter todarodis

strain designation: MYP2-2

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
65448negative0.2-0.4 µmrod-shapedno
67771rod-shaped
67771ovoid-shaped
67771negative

colony morphology

  • @ref: 65448
  • colony size: 1-1.5 mm
  • colony color: vivid orange yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: marine agar

pigmentation

  • @ref: 65448
  • production: yes
  • name: Flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65448
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65448positivegrowth4psychrophilic
65448positivegrowth40thermophilic
65448positiveoptimum30-35mesophilic
65448nogrowth45thermophilic
67771positivegrowth30-35mesophilic

culture pH

@refabilitytypepH
65448positiveoptimum7-8
65448positivegrowth5.5
65448nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65448aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
65448NaClpositivegrowth1-8 %(w/v)
65448NaClpositiveoptimum2.0 %(w/v)

observation

@refobservation
65448Mg 2+ ions are not required for growth
65448the predominant menaquinone is MK-6
65448the major polar lipids are phosphatidylethanolamine and one unidentified lipid
67771quinones: MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
65448casein+hydrolysis
65448cellobiose-builds acid from17057
65448D-fructose-builds acid from15824
65448D-galactose-builds acid from12936
65448D-glucose-builds acid from17634
65448D-mannitol-builds acid from16899
65448D-mannose-builds acid from16024
65448D-ribose-builds acid from16988
65448D-sorbitol-builds acid from17924
65448D-xylose-builds acid from65327
65448esculin-hydrolysis4853
65448gelatin+hydrolysis5291
65448hypoxanthine-hydrolysis17368
65448L-arabinose-builds acid from30849
65448L-rhamnose-builds acid from62345
65448L-tyrosine+hydrolysis17895
65448lactose-builds acid from17716
65448maltose-builds acid from17306
65448melezitose-builds acid from6731
65448melibiose-builds acid from28053
65448myo-inositol-builds acid from17268
65448nitrate-reduction17632
65448raffinose-builds acid from16634
65448starch-hydrolysis28017
65448sucrose-builds acid from17992
65448trehalose-builds acid from27082
65448tween 80+hydrolysis53426
65448urea-hydrolysis16199
65448xanthine-hydrolysis15318

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
6544828971ampicillinyesyes10 µg (disc)
6544816869oleandomycinyesyes15 µg (disc)
6544818208penicillin gyesyes20 Unit (disc)
6544817833gentamicinyesyes30 µg (disc)
654486104kanamycinyesyes30 µg (disc)
654487507neomycinyesyes30 µg (disc)
6544817076streptomycinyesyes50 µg (disc)
654488309polymyxin byesyes100 Unit (disc)
6544828368novobiocinyesyes5 µg (disc)
654486472lincomycinyesyes15 µg (disc)
654483542cephalothinyesyes30 µg (disc)
6544827902tetracyclineyesyes30 µg (disc)
654483393carbenicillinyesyes100 µg (disc)
6544817698chloramphenicolyesyes100 µg (disc)

enzymes

@refvalueactivityec
65448catalase+1.11.1.6
65448cytochrome oxidase+1.9.3.1
65448alkaline phosphatase+3.1.3.1
65448esterase (C 4)+
65448esterase Lipase (C 8)+
65448leucine arylamidase+3.4.11.1
65448valine arylamidase+
65448naphthol-AS-BI-phosphohydrolase+
65448alpha-chymotrypsin+3.4.21.1
65448acid phosphatase+3.1.3.2
65448lipase (C 14)-
65448cystine arylamidase-3.4.11.3
65448trypsin-3.4.21.4
65448alpha-galactosidase-3.2.1.22
65448beta-galactosidase-3.2.1.23
65448beta-glucuronidase-3.2.1.31
65448alpha-glucosidase-3.2.1.20
65448beta-glucosidase-3.2.1.21
65448N-acetyl-beta-glucosaminidase-3.2.1.52
65448alpha-mannosidase-3.2.1.24
65448alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65448C16:01.8
    65448C15:0 iso34.1
    65448C16:0 iso1.8
    65448C17:0 iso1
    65448iso-C15:1G*5.1
    65448C15:0 anteiso3.4
    65448C17:1 iso ω9c11.7
    65448C15:0 2OH0.7
    65448C17:0 2OH0.8
    65448C17:0 3OH0.7
    65448C15:0 iso 3OH3.9
    65448C16:0 iso 3OH1.1
    65448C17:0 iso 3OH22.2
    65448C16:1ω7c and/or C16:1ω6c8.1
  • type of FA analysis: whole cell analysis
  • incubation medium: marine broth 2216
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
65448the intestinal tract of a squid (Todarodes pacificus)East Sea near DonghaeRepublic of KoreaKORAsia37.5511129.114marine agar 221610 days20the content from its intestinal tract was scraped and used as a source for the isolation of bacterial strains, about 1 g of the intestinal content was serially diluted using 0.85 % (w/v) NaCl solution
67771From stomach of squid, `Todarodes pacificus`the East Sea near DonghaeRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract

Sequence information

16S sequences

  • @ref: 65448
  • description: 16S rRNA gene sequence
  • accession: MF962575
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Aequorivita todarodis KCTC 62141
  • accession: GCA_028561335
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2036821

GC content

  • @ref: 67771
  • GC-content: 41.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.38yes
flagellatedno96.172yes
gram-positiveno98.563yes
anaerobicno99.085yes
aerobicyes88.591yes
halophileyes53.491no
spore-formingno96.468no
glucose-fermentno89.964no
thermophileno99.007no
glucose-utilyes76.508no

External links

@ref: 65448

culture collection no.: KCTC 62141, NBRC 113025

literature

  • topic: Phylogeny
  • Pubmed-ID: 32375986
  • title: Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov.
  • authors: Wang Q, Cai SD, Liu J, Zhang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004174
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • 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
65448Hyun Chul Kim, Young-Ok Kim, Sooyeon Park, Bo-Hye Nam, Dong-Gyun Kim, Ji-Min Park ,Jung-Hoon YoonVitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus)10.1099/ijsem.0.002655IJSEM 68: 1233-1237 201829480794
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