Strain identifier

BacDive ID: 461

Type strain: Yes

Species: Marinobacterium litorale

Strain history: <- JC Cho, Inha Univ.

NCBI tax ID(s): 1122201 (strain), 404770 (species)

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General

@ref: 17276

BacDive-ID: 461

DSM-Number: 23545

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

description: Marinobacterium litorale DSM 23545 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from surface seawater collected near the coast of Deokjeok island ,.

NCBI tax id

NCBI tax idMatching level
1122201strain
404770species

strain history

@refhistory
17276<- KCTC <- J.-C. Cho, Inha University, Incheon, Korea
67771<- JC Cho, Inha Univ.

doi: 10.13145/bacdive461.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacterium
  • species: Marinobacterium litorale
  • full scientific name: Marinobacterium litorale Kim et al. 2007

@ref: 17276

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacterium

species: Marinobacterium litorale

full scientific name: Marinobacterium litorale Kim et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32057negative1.6 µm0.65 µmrod-shapedyes
67771negative
69480yes97.152
69480negative99.998

colony morphology

  • @ref: 60135
  • incubation period: 1 day

Culture and growth conditions

culture medium

  • @ref: 17276
  • 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
17276positivegrowth20psychrophilic
32057positivegrowth8.0-42
32057positiveoptimum30mesophilic
60135positivegrowth30-37mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32057positivegrowth5.0-12alkaliphile
32057positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32057facultative anaerobe
60135aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
32057NaClpositivegrowth1.0-7.5 %
32057NaClpositiveoptimum3.25 %

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3205730089acetate+carbon source
3205721217L-alaninamide+carbon source
3205716449alanine+carbon source
3205716947citrate+carbon source
3205715740formate+carbon source
3205724175galacturonate+carbon source
3205729987glutamate+carbon source
3205728087glycogen+carbon source
3205724996lactate+carbon source
3205715792malonate+carbon source
3205718257ornithine+carbon source
3205726271proline+carbon source
3205717272propionate+carbon source
3205717148putrescine+carbon source
3205751850methyl pyruvate+carbon source
3205726490quinate+carbon source
3205717822serine+carbon source
3205730031succinate+carbon source
3205753426tween 80+carbon source

enzymes

@refvalueactivityec
32057acid phosphatase+3.1.3.2
32057alkaline phosphatase+3.1.3.1
32057urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17276surface seawater collected near the coast of Deokjeok island (Yellow Sea),Yellow Sea, Deokjeok island, Korea.Republic of KoreaKORAsia
60135Seawaternear Deokjeok IslandRepublic of KoreaKORAsia
67771From seawaterRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_34475.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_16586;97_20354;98_25456;99_34475&stattab=map
  • Last taxonomy: Marinobacterium litorale subclade
  • 16S sequence: DQ917760
  • Sequence Identity:
  • Total samples: 94
  • soil counts: 1
  • aquatic counts: 93

Safety information

risk assessment

  • @ref: 17276
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17276
  • description: Marinobacterium litorale strain IMCC1877 16S ribosomal RNA gene, partial sequence
  • accession: DQ917760
  • length: 1508
  • database: ena
  • NCBI tax ID: 404770

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacterium litorale DSM 23545GCA_000428985scaffoldncbi1122201
66792Marinobacterium litorale DSM 235451122201.3wgspatric1122201
66792Marinobacterium litorale DSM 235452522572179draftimg1122201

GC content

@refGC-contentmethod
1727660.7high performance liquid chromatography (HPLC)
3205760.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes95.513yes
flagellatedyes93.627no
gram-positiveno99.092yes
anaerobicno97no
aerobicyes53.002no
halophileyes86.251no
spore-formingno95.179no
glucose-utilyes83.48no
thermophileno98.582yes
glucose-fermentno83.064no

External links

@ref: 17276

culture collection no.: DSM 23545, KCTC 12756, LMG 23872, CCUG 54309, IMCC 1877

straininfo link

  • @ref: 70140
  • straininfo: 293974

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625212Marinobacterium litorale sp. nov. in the order Oceanospirillales.Kim H, Choo YJ, Song J, Lee JS, Lee KC, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.64892-02007Aerobiosis, Alteromonadaceae/chemistry/*classification/genetics/*isolation & purification, Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolismGenetics
Phylogeny19189183Marinobacterium marisflavi sp. nov., isolated from a costal seawater.Kim H, Oh HM, Yang SJ, Lee JS, Hong JS, Cho JCCurr Microbiol10.1007/s00284-009-9355-52009Alteromonadaceae/chemistry/*classification/genetics/*isolation & purification, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny19767363Marinobacterium lutimaris sp. nov., isolated from a tidal flat.Kim JM, Lee SH, Jung JY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.016246-02009Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny25217624Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle.Alfaro-Espinoza G, Ullrich MSInt J Syst Evol Microbiol10.1099/ijs.0.067462-02014Alteromonadaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Seawater, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny27265099Marinobacterium zhoushanense sp. nov., isolated from surface seawater.Han SB, Wang RJ, Yu XY, Su Y, Sun C, Fu GY, Zhang CY, Zhu XF, Wu MInt J Syst Evol Microbiol10.1099/ijsem.0.0012132016Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Enzymology29499777Characterization of two styrene monooxygenases from marine microbes.Pu W, Cui C, Guo C, Wu ZLEnzyme Microb Technol10.1016/j.enzmictec.2018.02.0012018Alkenes/chemistry/metabolism, Alteromonadaceae/*enzymology/genetics, Amino Acid Sequence, Bacterial Proteins/genetics/*metabolism, Biocatalysis, Biotransformation, Hydrogen-Ion Concentration, Kinetics, Oceanospirillaceae/*enzymology/genetics, Oxygenases/genetics/*metabolism, Pseudomonas/enzymology/genetics, Recombinant Proteins/genetics/metabolism, Sequence Homology, Amino Acid, Stereoisomerism, Substrate Specificity, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17276Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23545)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23545
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
32057Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2830628776041
60135Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54309)https://www.ccug.se/strain?id=54309
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
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
70140Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293974.1StrainInfo: A central database for resolving microbial strain identifiers