Effects of mushroom stem meals on the microbiota of rainbow trout (Oncorhynchus mykiss)
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 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 5% or 10% AB or PO meals (AB5, AB10, PO5, and PO10). Microbial communities were characterized in feed, anterior and posterior intestine, and skin mucus by 16S rRNA (V3–V4) sequencing, and functional pathways were inferred. Growth responses were species- and dose-dependent: AB diets caused negligible effects at 5% and moderate impairments at 10%, whereas PO diets induced clear, dose-dependent growth reductions, particularly at 10% inclusion. Consistent patterns were observed in intestinal microbiota: AB5 and AB10 did not significantly affect alpha diversity or community structure, while PO5 and PO10 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, Shewanella), secondary consumers of fermentation products (Pelomonas, Bradyrhizobium, Legionella), and opportunistic taxa (Vibrio), while beneficial fermenters (Mycoplasma, Brevinema) declined. Functional analysis in PO10-fed fish revealed enrichment of lipid and xenobiotic metabolism pathways, whereas AB10 enhanced carbohydrate-related functions. In contrast, the skin microbiota showed no significant differences in alpha or beta diversity, although mushroom-based diets enriched fermentative genera (Anoxybacillus, Veillonella) and reduced potential pathogens (Pseudomonas, Candidatus Piscichlamydia). Overall, AB meal appeared more compatible with trout performance and gut microbial balance, whereas high PO inclusion impaired growth and intestinal stability, likely due to its higher ß-glucan content and structural complexity. These findings suggest that AB meal, particularly at 5% inclusion, is a promising functional ingredient, while PO meal could be better suited for use at lower inclusion levels or after fermentation processing.