Strain identifier

BacDive ID: 456

Type strain: Yes

Species: Marinimicrobium agarilyticum

Strain Designation: M18, 27.101

Strain history: CIP <- 2006, KCTC <- C.J. Kim, KRIBB <- J.M. Lim, KRIBB

NCBI tax ID(s): 1122194 (strain), 306546 (species)

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General

@ref: 6597

BacDive-ID: 456

DSM-Number: 16975

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

description: Marinimicrobium agarilyticum M18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

NCBI tax idMatching level
1122194strain
306546species

strain history

@refhistory
6597<- C.-J. Kim, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); M18 <- J.-M. Lim
67771<- CJ Kim, KRIBB <- JM Lim, KRIBB
116151CIP <- 2006, KCTC <- C.J. Kim, KRIBB <- J.M. Lim, KRIBB

doi: 10.13145/bacdive456.20230509.8.1

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 agarilyticum
  • full scientific name: Marinimicrobium agarilyticum Lim et al. 2006

@ref: 6597

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Cellvibrionaceae

genus: Marinimicrobium

species: Marinimicrobium agarilyticum

full scientific name: Marinimicrobium agarilyticum Lim et al. 2006

strain designation: M18, 27.101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31698negative0.9-1.5 µm0.5-0.8 µmrod-shapedyes
67771negative
69480yes97.143
69480negative99.996
116151negativerod-shapedyes

colony morphology

  • @ref: 116151

pigmentation

  • @ref: 31698
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6597BACTO 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
116151CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6597positivegrowth28mesophilic
31698positivegrowth12-40
31698positiveoptimum35mesophilic
67771positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
31698positivegrowth6-10.5alkaliphile
31698positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31698aerobe
67771aerobe
116151obligate aerobe

spore formation

@refspore formationconfidence
31698no
69481no100
69480no99.906
116151no

halophily

@refsaltgrowthtested relationconcentration
31698NaClpositivegrowth0-13 %
31698NaClpositiveoptimum0-1 %

observation

  • @ref: 31698
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169822599arabinose+carbon source
3169828757fructose+carbon source
3169817234glucose+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
11615117632nitrate+reduction
11615116301nitrite+reduction

metabolite production

  • @ref: 116151
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31698alkaline phosphatase+3.1.3.1
31698cytochrome oxidase+1.9.3.1
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
116151oxidase+
116151catalase+1.11.1.6
116151urease-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
116151-++++++-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6597tidal flat sedimentJeonnam province in the South Sea of Korea (the Korea Strait)Republic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
116151Environment, Tidal flat sedimentJeonnam province in the South Sea of Korea (the Korea Strait)Republic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2787.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_235;96_1480;97_1766;98_2160;99_2787&stattab=map
  • Last taxonomy: Marinimicrobium agarilyticum
  • 16S sequence: AY839870
  • Sequence Identity:
  • Total samples: 118
  • soil counts: 13
  • aquatic counts: 85
  • animal counts: 15
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65971Risk group (German classification)
1161511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6597
  • description: Marinimicrobium agarilyticum strain M18 16S ribosomal RNA gene, partial sequence
  • accession: AY839870
  • length: 1455
  • database: ena
  • NCBI tax ID: 306546

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinimicrobium agarilyticum DSM 16975GCA_000423345scaffoldncbi1122194
66792Marinimicrobium agarilyticum DSM 169751122194.5wgspatric1122194
66792Marinimicrobium agarilyticum DSM 169752524023067draftimg1122194

GC content

@refGC-content
659758.0
3169858

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.598yes
flagellatedyes63.159no
gram-positiveno98.123yes
anaerobicno99.124yes
aerobicyes91.221yes
halophileno64.614yes
spore-formingno95.34no
glucose-utilyes90.712yes
thermophileno97.886yes
glucose-fermentno82.04no

External links

@ref: 6597

culture collection no.: DSM 16975, KCTC 12357, CIP 109192

straininfo link

  • @ref: 70135
  • straininfo: 232847

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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6597Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16975)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16975
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)
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
70135Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232847.1StrainInfo: A central database for resolving microbial strain identifiers
116151Curators of the CIPCollection of Institut Pasteur (CIP 109192)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109192