Strain identifier

BacDive ID: 24514

Type strain: Yes

Species: Lutimaribacter saemankumensis

Strain Designation: SMK-117

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 490829 (species)

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General

@ref: 21193

BacDive-ID: 24514

DSM-Number: 28010

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped

description: Lutimaribacter saemankumensis SMK-117 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from sediment from tidal flat.

NCBI tax id

  • NCBI tax id: 490829
  • Matching level: species

strain history

@refhistory
21193<- KCTC <- J. H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; SMK-117
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive24514.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Lutimaribacter
  • species: Lutimaribacter saemankumensis
  • full scientific name: Lutimaribacter saemankumensis Yoon et al. 2009

@ref: 21193

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Lutimaribacter

species: Lutimaribacter saemankumensis

full scientific name: Lutimaribacter saemankumensis Yoon et al. 2009

strain designation: SMK-117

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28875negative5.5 µm0.6 µmrod-shapedno
67771negative
69480negative99

colony morphology

@refincubation period
211932-3 days
607192 days

pigmentation

  • @ref: 28875
  • production: no

Culture and growth conditions

culture medium

  • @ref: 21193
  • 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

@refgrowthtypetemperature
21193positivegrowth30
28875positivegrowth10-45
28875positiveoptimum30
60719positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepH
28875positivegrowth5.5-8.0
28875positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28875facultative anaerobe
60719aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no92.296
69481no100

halophily

@refsaltgrowthtested relationconcentration
28875NaClpositivegrowth>12 %
28875NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2887516947citrate+carbon source
2887537684mannose+carbon source
2887553424tween 20+carbon source
2887553423tween 40+carbon source
2887553425tween 60+carbon source
2887553426tween 80+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
21193catalase+1.11.1.6
21193cytochrome-c oxidase+1.9.3.1
28875catalase+1.11.1.6
28875cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21193-----------------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21193sediment from tidal flatSaemankum, Yellow SeaRepublic of KoreaKORAsia
60719Tidal flat sedimentSaemankum,Yellow SeaRepublic of KoreaKORAsia2006
67771From tidelandSaemankumRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_96589.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_6918;97_15003;98_18570;99_96589&stattab=map
  • Last taxonomy: Lutimaribacter saemankumensis subclade
  • 16S sequence: EU336981
  • Sequence Identity:
  • Total samples: 228
  • soil counts: 17
  • aquatic counts: 210
  • animal counts: 1

Safety information

risk assessment

  • @ref: 21193
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 28875
  • description: Lutimaribacter saemankumensis strain SMK-117 16S ribosomal RNA gene, partial sequence
  • accession: EU336981
  • length: 1420
  • database: nuccore
  • NCBI tax ID: 490829

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lutimaribacter saemankumensis DSM 28010GCA_900100005contigncbi490829
66792Lutimaribacter saemankumensis strain DSM 28010490829.3wgspatric490829
66792Lutimaribacter saemankumensis DSM 280102675903213draftimg490829

GC content

@refGC-contentmethod
2119363.5high performance liquid chromatography (HPLC)
2887563.5

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.813no
69480spore-formingspore-formingAbility to form endo- or exosporesno92.296no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.932no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.435yes
69480flagellatedmotile2+Ability to perform flagellated movementno81.677yes

External links

@ref: 21193

culture collection no.: DSM 28010, CCUG 55760, KCTC 22244

straininfo link

  • @ref: 88370
  • straininfo: 398622

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126722Lutimaribacter saemankumensis gen. nov., sp. nov., isolated from a tidal flat of the Yellow Sea.Yoon JH, Kang SJ, Lee JS, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.000109-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/*isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityPhenotype
Phylogeny27334981Lutimaribacter marinistellae sp. nov., isolated from a starfish.Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao YInt J Syst Evol Microbiol10.1099/ijsem.0.0012512016Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Starfish/*microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21193Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28010Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28010)
28875Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172531528776041
60719Curators of the CCUGhttps://www.ccug.se/strain?id=55760Culture Collection University of Gothenburg (CCUG) (CCUG 55760)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID398622.1