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

Abstract

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.

Genotypic diversity among Shewanella spp. collected from freshwater fish

“…A6 from ice‐storage common carp ( Cyprinus carpio L.) (Beaz‐Hidalgo et al, ). Another one (W9) was similar to previously described isolate from walleye ( Sander vitreus ) with no definite identification (Castillo, Gram, & Dailey, ; Dailey et al, ). Isolates currently described were quite different from Shewanella reported mainly from environmental and food samples.…”

“…We took into consideration sequences of reference strains as well as bacteria previously collected from freshwater fish. Comparison of S. putrefaciens 16S rRNA genes of tested isolates with the ones described by other authors (Beaz-Hidalgo et al, 2015;Dailey et al, 2016;Qin et al, 2012) showed high similarity (≥99.5%) between all isolates (Supporting Information Table S1; Figure 1). Despite that in some cases, the 16S rRNA gene sequence was insufficient for reliable species identification (Beaz-Hidalgo et al, 2015;Dailey et al, 2016;Janda & Abbott, 2014).…”

“…Comparison of S. putrefaciens 16S rRNA genes of tested isolates with the ones described by other authors (Beaz-Hidalgo et al, 2015;Dailey et al, 2016;Qin et al, 2012) showed high similarity (≥99.5%) between all isolates (Supporting Information Table S1; Figure 1). Despite that in some cases, the 16S rRNA gene sequence was insufficient for reliable species identification (Beaz-Hidalgo et al, 2015;Dailey et al, 2016;Janda & Abbott, 2014). Some of the currently described isolates described isolate from walleye (Sander vitreus) with no definite identification (Castillo, Gram, & Dailey, 2018;Dailey et al, 2016) were isolated from independent healthy fish.…”

“…Despite that in some cases, the 16S rRNA gene sequence was insufficient for reliable species identification (Beaz-Hidalgo et al, 2015;Dailey et al, 2016;Janda & Abbott, 2014). Some of the currently described isolates described isolate from walleye (Sander vitreus) with no definite identification (Castillo, Gram, & Dailey, 2018;Dailey et al, 2016) were isolated from independent healthy fish. Further studies are needed to clarify the relationship between genotype and pathogenicity of the isolates, as well as possible application of the method for outbreak investigation.…”

“…Furthermore, S. oneidensis and S. xiamenensis were included in group III (Huang, Sun, & Zhang, ; Venkateswaran et al, ). The most recent studies focused on analysis of 16S rRNA or gyrB genes (Beaz‐Hidalgo, Agüeria, Latif‐Eugenín, Yeannes, & Figueras, ; Dailey et al, ; Jung‐Schroers et al, ; Pękala et al, ). The other methods such as random amplified polymorphic DNA (RAPD‐PCR), enterobacterial repetitive intergenic consensus (ERIC‐PCR) and pulsed‐field gel electrophoresis (PFGE) were also used to characterize Shewanella (Beaz‐Hidalgo et al, ; Kim et al, ; Oh et al, ; Roh et al, ; Ziemke, Brettar, & Hofle, ).…”