Strain identifier

BacDive ID: 6034

Type strain: Yes

Species: Halomonas alimentaria

Strain Designation: YKJ-16

Strain history: CIP <- 2002, JCM <- 2000, Y. H. Park: strain YKJ-16

NCBI tax ID(s): 147248 (species)

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General

@ref: 5871

BacDive-ID: 6034

DSM-Number: 15356

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Halomonas alimentaria YKJ-16 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seafood jeotgal.

NCBI tax id

  • NCBI tax id: 147248
  • Matching level: species

strain history

@refhistory
5871<- JCM <- Y.-H. Park; YKJ-16
67770Y.-H. Park YKJ-16.
67771<- JCM <- Y-H Park YKJ-16
116234CIP <- 2002, JCM <- 2000, Y. H. Park: strain YKJ-16

doi: 10.13145/bacdive6034.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas alimentaria
  • full scientific name: Halomonas alimentaria Yoon et al. 2002

@ref: 5871

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas alimentaria

full scientific name: Halomonas alimentaria Yoon et al. 2002

strain designation: YKJ-16

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771negative
69480negative99.996
116234negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5871BACTO 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
33783Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116234CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5871positivegrowth30mesophilic
33783positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
116234positivegrowth5-45

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
116234NaClpositivegrowth4-10 %
116234NaClnogrowth0 %
116234NaClnogrowth2 %

observation

@refobservation
67770quinones: Q-9
67771quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11623416947citrate-carbon source
1162344853esculin-hydrolysis
116234606565hippurate+hydrolysis
11623417632nitrate+reduction
11623416301nitrite-reduction
11623415792malonate-assimilation
11623417632nitrate+respiration

metabolite production

  • @ref: 116234
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
116234oxidase+
116234beta-galactosidase-3.2.1.23
116234alcohol dehydrogenase-1.1.1.1
116234gelatinase-
116234amylase-
116234caseinase-3.4.21.50
116234catalase+1.11.1.6
116234tween esterase-
116234gamma-glutamyltransferase+2.3.2.2
116234lecithinase-
116234lipase-
116234lysine decarboxylase-4.1.1.18
116234ornithine decarboxylase-4.1.1.17
116234phenylalanine ammonia-lyase-4.3.1.24
116234tryptophan deaminase-
116234urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116234-+---+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116234--------------------------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5871seafood jeotgalKoreaRepublic of KoreaKORAsia
67770Jeotgal, Korean traditional fermented seafoodRepublic of KoreaKORAsia
67771From jeotgal (Korean traditional fermented seafood)Republic of KoreaKORAsia
116234Food, Jeotgal, korean traditinal fermented seafoodRepublic of KoreaKORAsia1999

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_111858.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_996;98_6007;99_111858&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AF211860
  • Sequence Identity:
  • Total samples: 406
  • soil counts: 49
  • aquatic counts: 297
  • animal counts: 54
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58711Risk group (German classification)
1162341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas alimentaria genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1256AB3672271256ena147248
5871Halomonas alimentaria 16S ribosomal RNA gene, partial sequenceAF2118601493ena147248

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas alimentaria DSM 15356GCA_009902005scaffoldncbi147248
66792Halomonas alimentaria strain DSM 15356147248.4wgspatric147248

GC content

@refGC-contentmethod
587163high performance liquid chromatography (HPLC)
6777163.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno65.524no
flagellatedno83.441no
gram-positiveno98.9yes
anaerobicno98.17no
aerobicyes81.456no
halophileyes91.931no
spore-formingno97.2no
glucose-utilyes70.773no
thermophileno98.954yes
glucose-fermentno82.523no

External links

@ref: 5871

culture collection no.: DSM 15356, JCM 10888, KCCM 41042, KCTC 12950, CGMCC 1.3500, CIP 107381

straininfo link

@refstraininfo
75520100675
75521317591

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11837294Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ, Park YHInt J Syst Evol Microbiol10.1099/00207713-52-1-1232002Animals, Base Composition, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fermentation, Food Handling/*methods, Halomonas/chemistry/*classification/genetics/isolation & purification/physiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny17551033Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium.Wang YN, Cai H, Chi CQ, Lu AH, Lin XG, Jiang ZF, Wu XLInt J Syst Evol Microbiol10.1099/ijs.0.64973-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Halomonas/*classification/genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Nitrogen/*metabolism, Nucleic Acid Hybridization, Petroleum/*metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Phylogeny18398185Halomonas nitroreducens sp. nov., a novel nitrate- and nitrite-reducing species.Gonzalez-Domenech CM, Bejar V, Martinez-Checa F, Quesada EInt J Syst Evol Microbiol10.1099/ijs.0.65415-02008Base Composition, Chile, DNA, Bacterial/chemistry/genetics, Genes, Bacterial, Halomonas/*classification/genetics/*metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Nitrates/metabolism, Nitrites/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Homology, Nucleic Acid, Species Specificity, Terminology as TopicMetabolism
Phylogeny18984697Halomonas korlensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from saline and alkaline soil.Li HB, Zhang LP, Chen SFInt J Syst Evol Microbiol10.1099/ijs.0.65711-02008Bacterial Typing Techniques, China, DNA Fingerprinting, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Halomonas/*classification/genetics/isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Soil Microbiology, Species SpecificityGenetics
Phylogeny27380915Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.Lee JC, Kim SJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0012782016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny28005522Halomonas alkalicola sp. nov., isolated from a household product plant.Tang X, Zhai L, Lin Y, Yao S, Wang L, Ge Y, Liu Y, Zhang X, Zhang T, Zhang L, Liu J, Cheng CInt J Syst Evol Microbiol10.1099/ijsem.0.0017572017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genotype, Halomonas/*classification/genetics/isolation & purification, *Household Products, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny32748161Halomonas marinisediminis sp. nov., A Moderately Halophilic Bacterium Isolated from the Bohai Gulf.Zhao H, Wang C, Tian Y, Zhang Y, Wu Y, Zhang Y, Du Z, Li B, Ji XCurr Microbiol10.1007/s00284-020-02147-42020Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, *Halomonas/genetics, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny33351740Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India.Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AKInt J Syst Evol Microbiol10.1099/ijsem.0.0046112020Bacterial Typing Techniques, Base Composition, Bathing Beaches, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/isolation & purification, India, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5871Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15356)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15356
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33783Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4810
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75520Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100675.1StrainInfo: A central database for resolving microbial strain identifiers
75521Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID317591.1StrainInfo: A central database for resolving microbial strain identifiers
116234Curators of the CIPCollection of Institut Pasteur (CIP 107381)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107381