Species- and dose-dependent modulation of growth and skin and intestinal mucosal microbiota in rainbow trout fed mushroom stem meals
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 alternative protein sources 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 15.7 ± 0.2 °C using isoproteic (47%) and isolipidic (23%) diets containing 50 or 100 g kg-1 AB or PO meals (AB5, AB10, PO5, and PO10), a control (CTRL) diet was devoid of mushroom meals and contained 100 and 120 g kg-1 of fishmeal and SBM, respectively. Microbial communities were characterized in feed, anterior and posterior intestine, and skin mucus by 16S rRNA (V3–V4) sequencing, and functional pathways (KEGG) were inferred. Growth responses to diet were mushroom meal type- and dose-dependent; in particular, at the end of the feeding trial, the growth of fish fed the AB5 diet was similar to that of the CTRL group (p > 0.05).  In contrast, rainbow trout fed the AB10, PO5, and PO10 diets grew 8%, 25%, and 60% less than fish fed the CTRL diet (p < 0.05), respectively. Feed intake (FI) was not affected by the inclusion of the AB meal (p > 0.05), while in PO groups, this parameter was reduced by 3% and 40% compared to the CTRL group (p < 0.05). Consistent patterns were observed in intestinal microbiota, AB5 and AB10 diets did not significantly affect alpha diversity or community structure, while PO5 and PO10 diets increased alpha diversity and showed distinct beta diversity profiles relative to AB and CTRL groups. Microbiota shifts were driven by host–diet interactions rather than direct transfer from feed. PO diets promoted fermentative genera (Cutibacterium and Shewanella), secondary consumers of fermentation products (Pelomonas, Bradyrhizobium and Legionella), and opportunistic taxa (Vibrio), while beneficial fermenters (Mycoplasma and Brevinema) declined. Functional analysis of PO10-fed fish revealed enrichment of lipid and xenobiotic metabolism pathways, whereas AB10 enhanced carbohydrate-related functions. In contrast, the skin mucus microbiota showed no significant differences in alpha or beta diversity, although mushroom-based diets enriched fermentative genera (Anoxybacillus and Veillonella) and reduced potential pathogens (Pseudomonas and Candidatus Piscichlamydia). Overall, the AB meal was more compatible with rainbow trout growth performance, feed efficiency, and gut microbial homeostasis, whereas high PO inclusion levels (100 g kg-1) impaired somatic growth by reducing FI and inducing gut dysbiosis. 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.