The Microbiota of Freshwater Fish and Freshwater Niches Contain Omega-3 Fatty Acid-Producing Shewanella Species

Appl Environ Microbiol. 2015 Oct 23;82(1):218-31. doi: 10.1128/AEM.02266-15. Print 2016 Jan 1.


Approximately 30 years ago, it was discovered that free-living bacteria isolated from cold ocean depths could produce polyunsaturated fatty acids (PUFA) such as eicosapentaenoic acid (EPA) (20:5n-3) or docosahexaenoic acid (DHA) (22:6n-3), two PUFA essential for human health. Numerous laboratories have also discovered that EPA- and/or DHA-producing bacteria, many of them members of the Shewanella genus, could be isolated from the intestinal tracts of omega-3 fatty acid-rich marine fish. If bacteria contribute omega-3 fatty acids to the host fish in general or if they assist some bacterial species in adaptation to cold, then cold freshwater fish or habitats should also harbor these producers. Thus, we undertook a study to see if these niches also contained omega-3 fatty acid producers. We were successful in isolating and characterizing unique EPA-producing strains of Shewanella from three strictly freshwater native fish species, i.e., lake whitefish (Coregonus clupeaformis), lean lake trout (Salvelinus namaycush), and walleye (Sander vitreus), and from two other freshwater nonnative fish, i.e., coho salmon (Oncorhynchus kisutch) and seeforellen brown trout (Salmo trutta). We were also able to isolate four unique free-living strains of EPA-producing Shewanella from freshwater habitats. Phylogenetic and phenotypic analyses suggest that one producer is clearly a member of the Shewanella morhuae species and another is sister to members of the marine PUFA-producing Shewanella baltica species. However, the remaining isolates have more ambiguous relationships, sharing a common ancestor with non-PUFA-producing Shewanella putrefaciens isolates rather than marine S. baltica isolates despite having a phenotype more consistent with S. baltica strains.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA, Bacterial
  • Eicosapentaenoic Acid / biosynthesis
  • Fatty Acids, Omega-3 / biosynthesis*
  • Fishes / microbiology*
  • Fresh Water / microbiology
  • Gastrointestinal Tract / microbiology
  • Humans
  • Lakes / microbiology
  • Microbiota / physiology
  • Molecular Sequence Data
  • Phenotype
  • Phylogeny
  • RNA, Ribosomal, 16S
  • Shewanella / genetics
  • Shewanella / isolation & purification*
  • Shewanella / metabolism*
  • Water Microbiology*


  • DNA, Bacterial
  • Fatty Acids, Omega-3
  • RNA, Ribosomal, 16S
  • Eicosapentaenoic Acid

Associated data

  • GENBANK/KM347974
  • GENBANK/KM347975
  • GENBANK/KM357913
  • GENBANK/KM357914
  • GENBANK/KM363230
  • GENBANK/KM363231
  • GENBANK/KM386672
  • GENBANK/KM386674
  • GENBANK/KM396206
  • GENBANK/KM396214
  • GENBANK/KM407144
  • GENBANK/KM407146
  • GENBANK/KP164550
  • GENBANK/KP164551
  • GENBANK/KP890205
  • GENBANK/KP890209
  • GENBANK/KT183385
  • GENBANK/KT633940
  • GENBANK/KT633942
  • GENBANK/KT724967