Strain identifier

BacDive ID: 455

Type strain: Yes

Species: Marinimicrobium koreense

Strain Designation: M9

Strain history: <- CJ Kim, KRIBB <- JM Lim, KRIBB

NCBI tax ID(s): 306545 (species)

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General

@ref: 6589

BacDive-ID: 455

DSM-Number: 16974

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

description: Marinimicrobium koreense M9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 306545
  • Matching level: species

strain history

@refhistory
6589<- C.-J. Kim, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); M9 <- J.-M. Lim
67771<- CJ Kim, KRIBB <- JM Lim, KRIBB

doi: 10.13145/bacdive455.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Cellvibrionaceae
  • genus: Marinimicrobium
  • species: Marinimicrobium koreense
  • full scientific name: Marinimicrobium koreense Lim et al. 2006

@ref: 6589

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Cellvibrionaceae

genus: Marinimicrobium

species: Marinimicrobium koreense

full scientific name: Marinimicrobium koreense Lim et al. 2006

strain designation: M9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31698negative0.9-1.5 µm0.5-0.8 µmrod-shapedyes
67771negative
69480yes95.976
69480negative99.995

pigmentation

  • @ref: 31698
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6589
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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
6589positivegrowth28mesophilic
31698positivegrowth10-45
31698positiveoptimum35-40
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
31698positivegrowth6-10.5alkaliphile
31698positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31698aerobe
67771aerobe

spore formation

@refspore formationconfidence
31698no
69481no100
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
31698NaClpositivegrowth0-15 %
31698NaClpositiveoptimum01-03 %

observation

  • @ref: 31698
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169822599arabinose+carbon source
3169828757fructose+carbon source
3169817716lactose+carbon source
3169817306maltose+carbon source
3169837684mannose+carbon source
3169828053melibiose+carbon source
3169833942ribose+carbon source
3169817992sucrose+carbon source
3169827082trehalose+carbon source
3169818222xylose+carbon source
316984853esculin+hydrolysis

enzymes

  • @ref: 31698
  • value: alkaline phosphatase
  • activity: +
  • ec: 3.1.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6589tidal flat sedimentJeonnam province in the South Sea of Korea (the Korea Strait)Republic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6561.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_3108;97_3809;98_4841;99_6561&stattab=map
  • Last taxonomy: Marinimicrobium koreense subclade
  • 16S sequence: AY839869
  • Sequence Identity:
  • Total samples: 1293
  • soil counts: 137
  • aquatic counts: 806
  • animal counts: 339
  • plant counts: 11

Safety information

risk assessment

  • @ref: 6589
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6589
  • description: Marinimicrobium koreense strain M9 16S ribosomal RNA gene, partial sequence
  • accession: AY839869
  • length: 1454
  • database: ena
  • NCBI tax ID: 306545

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinimicrobium koreense DSM 16974GCA_003762925contigncbi306545
66792Marinimicrobium koreense strain DSM 16974306545.3wgspatric306545
66792Marinimicrobium koreense DSM 169742786546140draftimg306545

GC content

@refGC-content
658957.0
3169857

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.443yes
anaerobicno99.04yes
halophileyes60.092no
spore-formingno96.259yes
glucose-utilyes90.599no
motileyes90.43yes
flagellatedyes76.82no
aerobicyes91.483no
thermophileno98.455no
glucose-fermentno79.437no

External links

@ref: 6589

culture collection no.: DSM 16974, KCTC 12356, CIP 109193

straininfo link

  • @ref: 70134
  • straininfo: 232833

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514044Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea.Lim JM, Jeon CO, Lee JC, Song SM, Kim KY, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.64075-02006Base Composition, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Geologic Sediments/*microbiology, Korea, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny19620360Marinimicrobium locisalis sp. nov., isolated from a marine solar saltern, and emended description of the genus Marinimicrobium.Yoon JH, Kang SJ, Jung YT, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.008458-02009Alteromonadaceae/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Sodium Chloride, Temperature, Ubiquinone/analysisGenetics
Phylogeny30566073Marinimicrobium alkaliphilum sp. nov., an alkaliphilic bacterium isolated from soil and emended description of the genus Marinimicrobium.Song L, Liu H, Cai S, Zhou YInt J Syst Evol Microbiol10.1099/ijsem.0.0031832018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6589Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16974)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16974
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
31698Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.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
70134Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232833.1StrainInfo: A central database for resolving microbial strain identifiers