Comparative Physiological Profiling of Abalone (Haliotis iris): Insights from Wild and Aquaculture Broodstock

New Zealand abalone (Haliotis iris) holds ecological, economic, and cultural value, with wild stocks supporting fisheries and an emerging aquaculture industry. Wild-caught adult abalone are often used as broodstock, but captivity can affect spawning and offspring quality. This study is the first to profile wild and farmed H. iris broodstock using histology, proximate composition, microbiome, and metabolomics analyses. Histology showed higher gonadal abnormalities in farmed abalone, while wild abalone exhibited increased ciliates in their gills, indicating richer marine–microorganism interactions. Microbiome analyses revealed a higher microbial richness and diversity in the buccal cavity of wild abalone. The core microbiota phyla across both groups included Proteobacteria, Bacteroidota, Campylobacterota, Fusobacteria, and Firmicutes. Proximate analyses showed higher muscle protein in farmed abalone, while gonadal tissue partitioned by sex showed higher fat in females and higher protein in males. Metabolomics revealed altered amino acid metabolism in the adductor muscle, carboxylic acid metabolism in the gonad, and fatty acid metabolism in the foot. This investigation expands our understanding of the physiological and microbial differences between wild and farmed abalone, showing altered gonad and muscle conditions from prolonged captivity and highlighting the need for greater microbial diversity in cultured stocks.