Effect of yeast species and processing on intestinal microbiota of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater

Abstract

Background Yeasts are gaining attention as alternative ingredients in aquafeeds. However, the impact of yeast inclusion on modulation of intestinal microbiota of fish fed plant-based ingredients is limited. Thus, the present study investigates the effects of yeast and processing on composition, diversity and predicted metabolic capacity of gut microbiota of Atlantic salmon smolt fed soybean meal (SBM)-based diet. Two yeasts, Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA), were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 °C for 16 h, followed by spray-drying (ACJ and AWA). In a 42-day feeding experiment, fish were fed one of six diets: a fishmeal (FM)-based diet, a challenging diet with 30% SBM and four other diets containing 30% SBM and 10% of each of the four yeast products (i.e., ICJ, ACJ, IWA and AWA). Microbial profiling of digesta samples was conducted using 16S rRNA gene sequencing, and the predicted metabolic capacities of gut microbiota were determined using genome-scale metabolic models. Results The microbial composition and predicted metabolic capacity of gut microbiota differed between fish fed FM diet and those fed SBM diet. The digesta of fish fed SBM diet was dominated by members of lactic acid bacteria, which was similar to microbial composition in the digesta of fish fed the inactivated yeasts (ICJ and IWA diets). Inclusion of autolyzed yeasts (ACJ and AWA diets) reduced the richness and diversity of gut microbiota in fish. The gut microbiota of fish fed ACJ diet was dominated by the genus Pediococcus and showed a predicted increase in mucin O-glycan degradation compared with the other diets. The gut microbiota of fish fed AWA diet was highly dominated by the family Bacillaceae. Conclusions The present study showed that dietary inclusion of FM and SBM differentially modulate the composition and predicted metabolic capacity of gut microbiota of fish. The inclusion of inactivated yeasts did not alter the modulation caused by SBM-based diet. Fish fed ACJ diet increased relative abundance of Pediococcus, and mucin O-glycan degradation pathway compared with the other diets.

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages

“…Metabolic reaction analysis of intestinal microbiota was performed in Python 3.9.1 according to the method previously described [ 65 ]. The ASVs for the intestinal samples were mapped to metabolic reactions using available Genome-Scale Metabolic Models (GSMMs) of human gut microbiota [ 66 ] as recently described [ 67 ].…”

How Do Alternative Protein Resources Affect the Intestine Morphology and Microbiota of Atlantic Salmon?

“…The authors also described that soybean protein concentrate could have an effect on raising the bacterial diversity of the intestinal tract, leading to the presence of unusual bacteria, like Escherichia and Propionibacterium, that are not usually associated with marine fish. The impact of yeast inclusion on the modulation of the intestinal microbiota of fish fed SBM was studied by Agboola et al [ 77 ], and it was concluded that the addition of inactivated yeasts did not lead to an alteration in the modulation caused by the SBM diet.…”