With the rise in demand for commercial fisheries and marine invertebrate cultivation, understanding the biological needs of aquatic organisms for optimal health and growth has become critical. Sea urchins, valued for their biomedical research as model animals and cultured seafood, are increasingly studied for commercial and scientific purposes. The microbiomes - the living communities in the gut ecosystem of urchins, play a crucial role in echinoid health, influencing nutrition and metabolism.
While recent technological advancements have improved the accessibility of these microbiomes and made studying their effect on hosts logistically feasible, a lack of standardization has led to inconsistent methodologies in sample collection, dissection, experimental controls, genomic library preparation, and data analysis through informatic pipelines. Addressing these inconsistencies is essential to unlocking the full potential of microbiome research for enhancing urchin health and productivity.
At present, meaningful comparisons across urchin microbiome studies are challenging. This review aims to consolidate the current findings of the field, highlight differences in methodologies and reporting that contribute to variation across 16 studies involving 18 unique urchin species, and provide suggestions for standardizing methodologies and reporting for future studies. By focusing specifically on the gastrointestinal ecosystem and its associated microbiota, the standardization practices will help identify keystone and core taxa and their ecological roles in metabolic function, establishing a strong foundation for future ecological, biomedical, and nutritional sciences.