Strain identifier

BacDive ID: 132093

Type strain: Yes

Species: Lewinella marina

Strain Designation: MKG-38

Strain history: <- NCIMB <- <- Y. Nakagawa and S. T. Khan, NBRC, NITE, Chiba, Japan

NCBI tax ID(s): 438751 (species)

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General

@ref: 23883

BacDive-ID: 132093

DSM-Number: 104084

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

description: Lewinella marina MKG-38 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 438751
  • Matching level: species

strain history

  • @ref: 23883
  • history: <- NCIMB <- <- Y. Nakagawa and S. T. Khan, NBRC, NITE, Chiba, Japan

doi: 10.13145/bacdive132093.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Saprospiria
  • order: Saprospirales
  • family: Lewinellaceae
  • genus: Lewinella
  • species: Lewinella marina
  • full scientific name: Lewinella marina Khan et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Neolewinella marina

@ref: 23883

domain: Bacteria

phylum: Bacteroidetes

class: Saprospiria

order: Sphingobacteriales

family: Lewinellaceae

genus: Lewinella

species: Lewinella marina

full scientific name: Lewinella marina Khan et al. 2007

strain designation: MKG-38

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32322negative0.8 µm0.45 µmrod-shaped
69480no94.074
69480negative99.993

pigmentation

  • @ref: 32322
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 23883
  • 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
23883positivegrowth28mesophilic
32322positivegrowth4-42
32322positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
32322positivegrowth05-10alkaliphile
32322positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32322
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
32322NaClpositivegrowth01-07 %
32322NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3232222599arabinose+carbon source
3232217057cellobiose+carbon source
3232228757fructose+carbon source
3232233984fucose+carbon source
3232228260galactose+carbon source
3232217234glucose+carbon source
3232217716lactose+carbon source
3232217306maltose+carbon source
3232237684mannose+carbon source
3232228053melibiose+carbon source
32322506227N-acetylglucosamine+carbon source
3232216634raffinose+carbon source
3232226546rhamnose+carbon source
3232233942ribose+carbon source
3232217814salicin+carbon source
3232217992sucrose+carbon source
3232227082trehalose+carbon source
3232253424tween 20+carbon source
3232253423tween 40+carbon source
3232253426tween 80+carbon source
3232218222xylose+carbon source
323224853esculin+hydrolysis
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
32322catalase+1.11.1.6
32322gelatinase+
32322cytochrome oxidase+1.9.3.1
68368cytochrome oxidase+1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
23883+--------++---------+

Isolation, sampling and environmental information

isolation

  • @ref: 23883
  • sample type: marine sediment
  • geographic location: Kamogawa
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_32504.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_489;96_15718;97_19261;98_24049;99_32504&stattab=map
  • Last taxonomy: Lewinella
  • 16S sequence: AB301495
  • Sequence Identity:
  • Total samples: 697
  • soil counts: 69
  • aquatic counts: 556
  • animal counts: 71
  • plant counts: 1

Safety information

risk assessment

  • @ref: 23883
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23883
  • description: Lewinella marina gene for 16S rRNA, partial sequence, strain: MKG-38
  • accession: AB301495
  • length: 1446
  • database: ena
  • NCBI tax ID: 438751

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neolewinella marina MKG-38GCA_002631205contigncbi438751
66792Neolewinella marina DSM 104084GCA_011927705scaffoldncbi438751
66792Lewinella marina strain DSM 104084438751.4wgspatric438751
66792Lewinella marina DSM 1040842830012823draftimg438751
66792Lewinella marina MKG-382891513237draftimg438751

GC content

  • @ref: 32322
  • GC-content: 61

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno89.263no
flagellatedno96.51no
gram-positiveno96.389yes
anaerobicno99.195yes
aerobicyes90.16yes
halophileno60.496no
spore-formingno96.089no
glucose-utilyes89.476yes
thermophileno96.884yes
glucose-fermentno89.773yes

External links

@ref: 23883

culture collection no.: DSM 104084, NBRC 102633, NCIMB 14312

straininfo link

  • @ref: 90449
  • straininfo: 406345

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048755Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov.Khan ST, Fukunaga Y, Nakagawa Y, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.65308-02007Aerobiosis/physiology, Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Carboxymethylcellulose Sodium/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Organic Chemicals, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Starch/metabolismMetabolism
Phylogeny21993690Rubidimonas crustatorum gen. nov., sp. nov., a novel member of the family Saprospiraceae isolated from a marine crustacean.Yoon J, Katsuta A, Kasai HAntonie Van Leeuwenhoek10.1007/s10482-011-9653-32011Animals, Bacteroidetes/chemistry/classification/genetics/*isolation & purification/ultrastructure, Crustacea/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Alignment, Sequence Homology, Nucleic Acid, Species SpecificityGenetics
Phylogeny28875904Lewinella maritima sp. nov., and Lewinella lacunae sp. nov., novel bacteria from marine environments.Kang H, Kim H, Joung Y, Joh KInt J Syst Evol Microbiol10.1099/ijsem.0.0021762017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/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
23883Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104084Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104084)
32322Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172855828776041
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
68368Automatically annotated from API 20E
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
90449Reimer, 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-ID406345.1