Mushroom stem-based diets elicit region-specific shifts in rainbow trout gut microbiota

The intestinal microbiota of fish plays a crucial role in host condition and health, exhibiting region-specific functions influenced by dietary components. This study evaluated the effects of mushroom stem meals from Agaricus bisporus (AB), Lentinula edodes (LE), and Pleurotus ostreatus (PO), used as sustainable ingredients on the intestinal microbiota and histomorphology of rainbow trout (Oncorhynchus mykiss). Experimental diets containing 30% mushroom stem meals were tested for 42 days under standard conditions in juvenile rainbow trout (120.1 ± 0.4 g). Mushroom stem meals did not affect the integrity of the intestinal mucosa while inducing a subtle region-specific shift in the intestinal microbial communities. These changes were reflected in intra-individual and inter-individual diversity differences among diets. Specifically, Shannon index decreased in the pyloric caeca (PC), anterior (AI) and posterior intestine (PI) of fish fed the AB diet, while the observed richness and Faith's phylogenetic diversity showed a reduction in the AI and PI regions of fish fed the LE diet. Regarding composition, a consistent pattern found across the three intestinal regions was the high abundance of Desulfobacterota in fish fed the control diet (0% mushroom stem meals). Regarding the mushroom stem-based diets, the AB diet promoted an increase in the abundance of potentially beneficial bacteria, such as Mycoplasma in the PC and AI, Legionella exclusively in the AI, and Weissella in the PI. In contrast, the PO diet increased the abundance of Paenibacillus in the PC, while the LE diet did not markedly alter genus-level abundances. Region-specific patterns suggested microbial shifts in the PC were related to digestion and nutrient metabolism, while changes in the AI may reflect transient colonization by diet-derived bacteria linked to niche specialization. The PI microbiota was comparatively conserved and associated with carbohydrate fermentation. These findings provide insights into the region-specific effects of circular dietary ingredients and highlight the potential use of mushroom stem meals as functional ingredients due to prebiotic effect as they beneficially modulate the intestinal microbiota and support gut health in rainbow trout.