High throughput next generation sequencing has propelled advances in genomic inquiry, including discoveries on the composition of the host gut microbiota. Research on mammals has demonstrated critical ways through which the gut microbiota influences host health and fitness, but applications involving fisheries are in their infancy. Given the breadth of research interests and importance of hatcheries in fisheries management and aquaculture in food production, studies investigating the gut microbiome of fish will play an integral role in promoting fish growth and health in all settings. This perspective highlights what is currently known about the fish gut microbiome, and how research can apply next generation sequencing and related methods to address emerging questions in fisheries and aquaculture. With continuing advances in sequencing technologies, gut microbiome research will change our understanding of the microbiota's role in fisheries and aquaculture through inquiry into the mutualistic relationship between microbes and fish hosts.

Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good’s Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray–Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.

No abstract