Strain identifier

BacDive ID: 1369

Type strain: Yes

Species: Marinococcus halophilus

Strain Designation: HK 718

Strain history: CIP <- 1996, JCM <- M.V. Hao: strain HK 718 <- CCM <- T.J. Novitsky

NCBI tax ID(s): 1371 (species)

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General

@ref: 8794

BacDive-ID: 1369

DSM-Number: 20408

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive

description: Marinococcus halophilus HK 718 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from salted mackerel.

NCBI tax id

  • NCBI tax id: 1371
  • Matching level: species

strain history

@refhistory
8794<- D.J. Kushner <- NRCC <- ?
67770M. V. Hao HK 718 <-- CCM 2706 <-- T. J. Novitsky 14033.
119816CIP <- 1996, JCM <- M.V. Hao: strain HK 718 <- CCM <- T.J. Novitsky

doi: 10.13145/bacdive1369.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Marinococcus
  • species: Marinococcus halophilus
  • full scientific name: Marinococcus halophilus (Novitsky and Kushner 1976) Hao et al. 1985

  • synonyms

    • @ref: 20215
    • synonym: Planococcus halophilus

@ref: 8794

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Marinococcus

species: Marinococcus halophilus

full scientific name: Marinococcus halophilus (Novitsky and Kushner 1976) Hao et al. 1985

strain designation: HK 718

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119816positivecoccus-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8794BACTO 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
39106MEDIUM 204 - for Halorubrum, Marinococcus and NatrialbayesDistilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (5.000 g);Ferrous chloride tetrahydrate
119816CIP Medium 204yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=204
119816CIP Medium 240yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=240

culture temp

@refgrowthtypetemperaturerange
8794positivegrowth30mesophilic
39106positivegrowth37mesophilic
67770positivegrowth30mesophilic
119816positivegrowth22-41
119816nogrowth5psychrophilic
119816nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119816
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 91

halophily

  • @ref: 119816
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 8794
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119816citrate-carbon source16947
119816esculin-hydrolysis4853
119816nitrate-reduction17632
119816nitrite-reduction16301
119816nitrate-respiration17632

antibiotic resistance

  • @ref: 119816
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119816
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11981615688acetoin-
11981617234glucose-

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
119816oxidase-
119816alcohol dehydrogenase-1.1.1.1
119816gelatinase-
119816catalase+1.11.1.6
119816tween esterase-
119816gamma-glutamyltransferase-2.3.2.2
119816lysine decarboxylase-4.1.1.18
119816ornithine decarboxylase-4.1.1.17
119816phenylalanine ammonia-lyase-4.3.1.24
119816tryptophan deaminase-
119816urease-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
119816-+++--------++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119816-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119816+--+---+-++---+-+-----+------------------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8794salted mackerel
67770Salted mackerel
119816Salted mackerel

isolation source categories

Cat1Cat2
#Host#Fishes
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_6855.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_605;96_3225;97_3957;98_5046;99_6855&stattab=map
  • Last taxonomy: Marinococcus
  • 16S sequence: X90835
  • Sequence Identity:
  • Total samples: 2817
  • soil counts: 176
  • aquatic counts: 1141
  • animal counts: 1431
  • plant counts: 69

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87941Risk group (German classification)
1198161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Marinococcus halophilus 16S rRNA gene, strain DSM 20408X908351520ena1371
20218Marinococcus halophilus gene for 16S ribosomal RNA, partial sequence, strain: JCM 2479AB7694811495ena1371
20218Marinococcus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 102359AB6817511498ena1371

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinococcus halophilus strain KCTC 28431371.6wgspatric1371
66792Marinococcus halophilus strain NBRC 1023591371.9wgspatric1371
66792Marinococcus halophilus KCTC 28432832122235draftimg1371
67770Marinococcus halophilus NBRC 102359GCA_007989565contigncbi1371
67770Marinococcus halophilus KCTC 2843GCA_002265875contigncbi1371

GC content

@refGC-contentmethod
879446.4
6777050-51thermal denaturation, midpoint method (Tm)
6777049.7-51.1fluorimetric
6777046.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
motileyes86.225no
gram-positiveyes92.994no
anaerobicno99.189no
halophileyes96.294no
spore-formingno74.025no
thermophileno98.163yes
glucose-utilyes88.879no
aerobicyes95.975no
flagellatedyes58.798no
glucose-fermentno85.095no

External links

@ref: 8794

culture collection no.: DSM 20408, ATCC 27964, CCM 2706, JCM 2479, NRCC 14033, CIP 104819, IAM 12844, KCTC 2843, LMG 17439, NBRC 102359, NCIMB 13496, VKM Ac-1985

straininfo link

  • @ref: 71020
  • straininfo: 66132

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism14872322Marinococcus halophilus DSM 20408T encodes two transporters for compatible solutes belonging to the betaine-carnitine-choline transporter family: identification and characterization of ectoine transporter EctM and glycine betaine transporter BetM.Vermeulen V, Kunte HJExtremophiles10.1007/s00792-004-0375-62004Amino Acid Sequence, Amino Acids, Diamino/*metabolism, Bacterial Proteins/*genetics/*metabolism, Betaine/*metabolism, Biological Transport, Active, Cloning, Molecular, DNA, Bacterial/genetics, Escherichia coli/genetics/growth & development/metabolism, Genes, Bacterial, Gram-Positive Bacteria/*genetics/*metabolism, Kinetics, Membrane Transport Proteins/*genetics/*metabolism, Molecular Sequence Data, Osmotic Pressure, Plasmids/genetics, Recombinant Proteins/genetics/metabolism, Restriction Mapping, Sequence Homology, Amino AcidEnzymology
Phylogeny16166669Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west China.Li WJ, Schumann P, Zhang YQ, Chen GZ, Tian XP, Xu LH, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63596-02005Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Genes, rRNA, Gram-Positive Bacteria/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, *Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny19628611Marinococcus luteus sp. nov., a halotolerant bacterium isolated from a salt lake, and emended description of the genus Marinococcus.Wang Y, Cao LL, Tang SK, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009670-02009Bacillaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Salt Tolerance, Sodium Chloride/metabolism, *Water MicrobiologyGenetics
Phylogeny23504966Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine.Balderrama-Subieta A, Guzman D, Minegishi H, Echigo A, Shimane Y, Hatada Y, Quillaguaman JInt J Syst Evol Microbiol10.1099/ijs.0.045401-02013Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bolivia, DNA, Bacterial/genetics, Fatty Acids/analysis, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27349661Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh.Vishnuvardhan Reddy S, Thirumala M, Farooq M, Sasikala C, Venkata Ramana CArch Microbiol10.1007/s00203-016-1263-z2016Bacillaceae/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8794Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20408)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20408
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
39106Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16770
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/
68371Automatically annotated from API 50CH acid
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
71020Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID66132.1StrainInfo: A central database for resolving microbial strain identifiers
119816Curators of the CIPCollection of Institut Pasteur (CIP 104819)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104819