Species- and Level-Dependent Modulation of Growth and Skin and Intestinal Mucosal Microbiota in Rainbow Trout Fed Mushroom Stem Meals

Abstract

Mucosal microbiomes play key roles in fish physiology by supporting digestion, nutrient absorption, metabolism, immune modulation, and pathogen defense. This study evaluated the effects of mushroom stem meals from Agaricus bisporus (AB) and Pleurotus ostreatus (PO) as nutritional alternatives to soybean meal (SBM) on growth performance and mucosa-associated microbiota in rainbow trout (Oncorhynchus mykiss). A 60-day feeding trial was conducted with juveniles (22.1 ± 0.3 g) at 16.02 ± 0.19°C using isoproteic (47%) and isolipidic (23%) diets containing 50 or 100 g kg−1 AB or PO meals (AB5, AB10, PO5, and PO10), plus a control (CTRL) diet without mushroom meals. Microbial communities in feed, anterior and posterior intestine (PI), and skin mucus (SK) were analyzed by 16S rRNA (V3–V4) sequencing, and functional pathways were inferred. Growth responses were mushroom meal type- and level-dependent. Fish fed the AB5 diet showed similar growth to the CTRL group (p > 0.05), while those fed AB10, PO5, and PO10 diets grew 8%, 25%, and 60% less, respectively (p ≤ 0.05). Feed intake (FI) was unaffected by AB meal but reduced by PO5 and PO10 diets (3% and 40%, respectively). AB diets maintained intestinal alpha diversity and community structure, whereas PO diets increased alpha diversity and altered beta diversity, favoring fermentative and opportunistic taxa while reducing beneficial fermenters. Mycoplasma abundance correlated positively with growth performance in both intestinal regions, while Bradyrhizobium abundance and Shannon diversity index correlated negatively in the anterior intestine (AI). Functional predictions showed enrichment of lipid and xenobiotic metabolism pathways in PO10-fed fish, while AB10 enhanced carbohydrate-related functions. SK microbiota diversity remained stable despite compositional shifts, with increases in fermentative taxa and reductions in potential pathogens. Overall, AB meal showed greater compatibility with rainbow trout growth performance, feed efficiency, and gut microbial homeostasis, whereas high PO inclusion impaired growth by reducing FI and inducing marked changes in the gut community structure. These findings suggest that AB meal at low inclusion levels may be used as an alternative to SBM without substantial effects on key performance indicators and gut microbiota in rainbow trout.