Strain identifier

BacDive ID: 14046

Type strain: Yes

Species: Lewinella cohaerens

Strain Designation: II-2

Strain history: <- NBRC <- NCIMB <- R. A. Lewin, Scripps Inst. Oceanography, Univ. California, La Jolla, USA; II-2

NCBI tax ID(s): 1122176 (strain), 70995 (species)

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General

@ref: 16553

BacDive-ID: 14046

DSM-Number: 23179

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

description: Lewinella cohaerens II-2 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from mid-littoral mud.

NCBI tax id

NCBI tax idMatching level
70995species
1122176strain

strain history

  • @ref: 16553
  • history: <- NBRC <- NCIMB <- R. A. Lewin, Scripps Inst. Oceanography, Univ. California, La Jolla, USA; II-2

doi: 10.13145/bacdive14046.20230509.8.1

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 cohaerens
  • full scientific name: Lewinella cohaerens (Lewin 1970) Sly et al. 1998

  • synonyms

    • @ref: 20215
    • synonym: Herpetosiphon cohaerens

@ref: 16553

domain: Bacteria

phylum: Bacteroidetes

class: Saprospiria

order: Sphingobacteriales

family: Lewinellaceae

genus: Lewinella

species: Lewinella cohaerens

full scientific name: Lewinella cohaerens (Lewin 1970) Sly et al. 1998 emend. Khan et al. 2007

strain designation: II-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
28558negative1.2-2 µm0.3-0.5 µmrod-shaped
69480negative99.984

colony morphology

  • @ref: 28558
  • colony color: light orange
  • medium used: MA

multimedia

  • @ref: 16553
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23179.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16553BACTO 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
28558Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
16553positivegrowth25mesophilic
28558positiveoptimum25mesophilic
28558positivegrowth10-30
28558nogrowth4psychrophilic
28558nogrowth35-42

culture pH

@refabilitytypepH
28558nogrowth5
28558positivegrowth6-8
28558positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 28558
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 28558
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.981

halophily

@refsaltgrowthtested relationconcentration
28558NaClpositivegrowth2-4 %(w/v)
28558NaClnogrowth0 %(w/v)
28558NaClnogrowth1 %(w/v)
28558NaClnogrowth6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
285582509agar-degradation
2855828938ammonium-nitrogen source
2855827613amygdalin+/-builds acid from
2855818305arbutin+/-builds acid from
2855885146carboxymethylcellulose-degradation
285583435carrageenan-degradation
28558casamino acids+nitrogen source
28558casein+degradation
2855862968cellulose-degradation
2855817029chitin-degradation
2855817057cellobiose+builds acid from
2855828847D-fucose+/-builds acid from
2855817634D-glucose+builds acid from
2855817716lactose+builds acid from
2855862318D-lyxose+builds acid from
285586731melezitose+/-builds acid from
2855816443D-tagatose+/-builds acid from
2855832528turanose+builds acid from
2855816991dna+degradation
285584853esculin+builds acid from
285585291gelatin+degradation
2855828066gentiobiose+builds acid from
2855818287L-fucose+/-builds acid from
28558320061methyl alpha-D-glucopyranoside+/-builds acid from
2855817632nitrate-reduction
2855816301nitrite-reduction
28558peptone+nitrogen source
2855864243sodium L-glutamate-nitrogen source
2855863005sodium nitrate-nitrogen source
2855828017starch+degradation
2855816189sulfate-nitrogen source
2855853424tween 20+degradation
2855853423tween 40+degradation
2855853426tween 80+degradation
2855816199urea-degradation

metabolite production

  • @ref: 28558
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
28558catalase+1.11.1.6
28558cytochrome oxidase+1.9.3.1
28558beta-galactosidase+3.2.1.23
28558beta-glucosidase+3.2.1.21
28558arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

  • @ref: 16553
  • sample type: mid-littoral mud
  • geographic location: Biarritz
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4332.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_460;96_2173;97_2629;98_3259;99_4332&stattab=map
  • Last taxonomy: Lewinella cohaerens subclade
  • 16S sequence: AM295254
  • Sequence Identity:
  • Total samples: 1821
  • soil counts: 38
  • aquatic counts: 1591
  • animal counts: 177
  • plant counts: 15

Safety information

risk assessment

  • @ref: 16553
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lewinella cohaerens 16S ribosomal RNA gene, partial sequenceAF0392921425ena70995
20218Lewinella cohaerens partial 16S rRNA gene, type strain ATCC 23123TAM2952541413ena70995
16553Lewinella cohaerens gene for 16S ribosomal RNA, partial sequenceAB3016141446ena70995

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lewinella cohaerens DSM 23179GCA_000379805scaffoldncbi1122176
66792Lewinella cohaerens DSM 231791122176.3wgspatric1122176
66792Lewinella cohaerens DSM 231792515154030draftimg1122176

GC content

@refGC-contentmethod
1655345.0high performance liquid chromatography (HPLC)
1655344.9
2855845

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.53no
flagellatedno96.613no
gram-positiveno97.725yes
anaerobicno99.154yes
aerobicyes88.537yes
halophileno83.388no
spore-formingno93.044no
thermophileno97.338yes
glucose-utilyes87.985no
glucose-fermentno90.743no

External links

@ref: 16553

culture collection no.: DSM 23179, ATCC 23123, NBRC 102661, NCIMB 12855

straininfo link

  • @ref: 83215
  • straininfo: 37903

literature

  • topic: Phylogeny
  • Pubmed-ID: 18048730
  • title: Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment.
  • authors: Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65254-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16553Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23179)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23179
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2855810.1099/ijs.0.65308-018048755
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)
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
83215Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37903.1StrainInfo: A central database for resolving microbial strain identifiers