Core, Resident, and Transient Members of the Trout Gut Microbiome: Dietary, Environmental, Stress and Pathogen/Antibiotic Modulation.

The gut microbiome of rainbow trout plays a crucial role in fish nutrition, immune function and stress resistance, making it a key factor in aquaculture sustainability. This review systematizes metagenomic data that enable the distinction between resident and transient microbial communities and the identification of a core microbiome. At the phylum level, the core is predominantly composed of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Mycoplasmatota, with additional phyla detected depending on the gut region and methodological approach. Diet-induced changes are often rapid and reversible: insect meal and certain probiotics increase the abundance of beneficial Bacillota and suppress opportunists. Unlike dietary shifts, chronic stressors-particularly elevated temperatures and antibiotic treatment-can override these benefits, causing a persistent alpha diversity reduction, overgrowth of Pseudomonadata, and depletion of key commensals. The autochthonous mucosal microbial community is more resilient to short-term fluctuations but can be irreversibly altered by prolonged stress or antimicrobial therapy, leading to dysbiosis and reduced colonization resistance. A holistic understanding of host-microbe-environment interactions is essential for establishing dynamic reference ranges for a "healthy" microbiome. Such knowledge would enable early detection of dysbiosis and support the rational development of functional feeds and probiotics in commercial trout farming.