Abstract
Researchers have adjusted dietary lipid:protein ratios and n-3 long-chain polyunsaturated fatty acids (LC-PUFA) to optimize the growth performance of Atlantic salmon. However, dietary impacts on the gut microbiome are lacking, especially under varying environmental conditions. To examine this response, post-smolt salmon (184 ± 5 g) were fed diets with lipid:protein ratios considered low (180, 570 g/kg) and high (230, 460 g/kg) along with low and high levels of n-3 LC-PUFA (7 or 14 g/kg) while fish were reared under low and high levels of dissolved oxygen (6.7 or 8.0 mg/L). At day 0, 35 and 116, digesta in the distal intestine were collected and analyzed for viable counts and 16S ribosomal RNA (rRNA) genes (V4 region) using Illumina MiSeq. The reduction in oxygen had negligible effects, except on viable plate counts of total bacteria and an initial effect on beta-diversity. In contrast, the high lipid (HL) diets had an increased alpha-diversity (e.g., Shannon and Chao-1) at day 0 and day 35 whereas high n-3 diets suppressed these indices at day 116. Generally, a reduction in alpha-diversity was observed over time and an interaction between lipid:protein ratio x n-3 was found. Between diets, beta-diversity and phyla abundance were similar as both Proteobacteria (44%) and Firmicutes (21%) dominated. However, at the genus level Aliivibrio, Streptococcus, Weissella, and Lactobacillus, were associated with low lipid (LL) diets while the high lipid diets were associated with less abundant bacteria, e.g., Chromohalobacter. At day 116, the relative abundance of the Tenericutes phylum increased 10-fold (36%). Fish fed the high lipid diet with high n-3 had reduced alpha-diversity, lowest abundance of lactic acid bacteria, and highest abundance of Mycoplasma, which may indicate a less healthy gut microbiome. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed that saturated and unsaturated fatty acid biosynthesis pathways were several folds higher in fish fed the high lipid diet, possibly to compensate for the lack of dietary n-3. In summary, our results show that the viable plate counts, alpha-diversity, beta-diversity, and predictive function of gut bacteria in Atlantic salmon post-smolts are influenced by dietary lipid:protein ratio and n-3 LC-PUFA over several time points with little effect by dissolved oxygen.
Highlights
The gut microbiota play a vital role in fermenting dietary carbohydrates and producing short chain fatty acids (SCFA), such as acetate, propionate, and butyrate, which can be utilized in energy metabolism and enhance gut health (Kihara and Sakata, 1997; Asaduzzaman et al, 2018)
Total viable counts of aerobic bacteria cultured on typtone soya agar (TSA) significantly decreased (p = 0.029) by approximately 3-logs over the course of the experiment from 3.7 ± 2.2 × 106 (6.6 log) colony forming units (CFUs) ml−1 at day 21 compared to 4.2 ± 1.0 × 103 (3.6 log) CFU ml−1 at day 116 (Figure 1A)
There has been a spike in the number of studies using highthroughput sequencing to characterize the gut microbes of salmonids including farmed species of Atlantic salmon (Zarkasi et al, 2014, 2016; Gajardo et al, 2016, 2017; Dehler et al, 2017; Rudi et al, 2018; Villasante et al, 2019), rainbow trout (Huyben et al, 2017, 2018, 2019; Lyons et al, 2017a,b,c; Michl et al, 2017; Bruce et al, 2018 ) and Arctic charr (Nyman et al, 2017)
Summary
The gut microbiota (e.g., bacteria and fungi) play a vital role in fermenting dietary carbohydrates and producing short chain fatty acids (SCFA), such as acetate, propionate, and butyrate, which can be utilized in energy metabolism and enhance gut health (Kihara and Sakata, 1997; Asaduzzaman et al, 2018). Abundance of different phyla in the gut (e.g., Firmicutes) has been found to increase lipid deposition in zebrafish (Danio rerio; Semova et al, 2012). Two studies have used next-generation sequencing to determine the influence of dietary lipids on the salmon gut microbiota (Zarkasi et al, 2016; Rudi et al, 2018). Feeding high lipid:protein diets was found to increase the diversity and abundance of lactic acid bacteria in the gut of Atlantic salmon (Zarkasi et al, 2016). Energy levels were not equal between diets and the gut bacteria were not associated with any functional role, e.g., using a predictive metagenomic approach
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