Effect of Dietary Carbohydrate-to-Protein Ratio on Gut Microbiota in Atlantic Salmon (Salmo salar)

Abstract

Atlantic salmon (Salmo salar) is a carnivorous fish species whose productive performance tends to be suboptimal when fed low-cost carbohydrate rich meals. It is of interest to study the dynamics of gut microbiota communities in salmonids fed high carbohydrate diets since gut microbes are referred to as key players that influence the metabolism and physiology of the host. A study was conducted to determine the effect of feeding a high carbohydrate diet to Atlantic salmon in gut microbiota communities. A medium carbohydrate (15% wheat starch)/medium protein (MC/MP) diet or a high carbohydrate (30% wheat starch)/low protein (HC/LP) diet was fed to triplicate tanks (28 fish each) during four weeks. We conducted an in-depth characterization of the distal intestine digesta microbiota using high-throughput sequencing of the V4 region of the 16S rRNA gene. Firmicutes, Actinobacteria and Proteobacteria were the major phyla determined in either experimental group. Phylum Planctomycetes, class Planctomycetia, order Planctomycetales and genus Lactococcus were significantly more abundant in fish fed the HC/LP diet compared with fish fed the MC/MP diet. Our study suggests feeding a carbohydrate rich meal to salmon exerts a low impact on the structure of gut microbial communities, affecting mostly low-abundance bacteria capable of metabolizing anaerobically carbohydrates as a major energy-yielding substrate.

Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets

“…The overall microbial composition of the European seabass gut was similar to that recently described in other teleosts 20 , 41 – 43 and in particular in other studies on European seabass 56 , 60 . Gut microbiota was dominated by Proteobacteria, Firmicutes, Acidobacteria, and Actinobacteria and their relative abundances were not significantly different between digesta and mucosa intestinal samples.…”

“…Although Clostridium was not one of the prevalent genera in our study, its significant increase upon plants incorporation into European seabass diets might indicate that they play a key role in helping carnivorous fish to tolerate plant feedstuffs. A similar trend was seen in salmon 41 , where increasing dietary carbohydrates mostly affected low-abundance bacteria, favoring those groups with carbohydrolytic potential. Altogether this study details how plant-based diets affect the gut microbiota of European seabass and elucidate the predominant bacterial taxa that might inform culture-based studies to isolate novel strains with carbohydrolytic potential.…”

“…Contaminant sequences of chloroplasts, common in NGS studies, in particular in those analyzing herbivores guts or plants-associated microbiota, due to their 16S high homology to that of bacteria, were removed from the downstream analysis, as previously reported in similar studies [41][42][43] .…”

Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions

“…There has been a spike in the number of studies using high-throughput 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 ). Of these, most dietary studies have investigated replacing fishmeal with vegetable, insect, or microbial protein sources.…”

High-throughput sequencing of the 16S rRNA gene to analyze the gut microbiome in juvenile and adult tropical gar (Atractosteus tropicus)

“…The majority of the most abundant OTUs present in CGMBiom of the cultivated A. tropicus juvenile samples were from the Staphylococcus (2.62%), Plesiocystis (2.56%) and Myroides (2.36%) genera. Staphylococcus is the only genus exclusive for the distal gut digesta of fish fed a median carbohydrate and protein diet (Villasante et al, 2019) or is associated with the gut immune system, which is known as gutassociated lymphoid tissues (GALT, Nayak, 2010). Plesiocystis is a genus of Myxobacteria and a monotypic taxon containing only its type species, Plesiocystis pacifica.…”