Dear Colleagues,

The communities of microorganisms found in and on animals play vital roles not only in the health of their hosts but also in shaping the hosts’ physiological, immunological, developmental and hormonal states. This microbiota includes bacteria, archaea, fungi, protists and viruses. Exploring the totality of an organism’s microbiota—the whole microbiome—is critical to understanding its role in all aspects of host biology. Molecular genetic technologies for studying host and microorganism interactions have provided a wealth of information about the roles of microorganisms in animal physiology and development. The microbiomes of a large group of organisms that have only recently been the focus of these studies are those of the finfish and shellfish, found in freshwater and marine environments. Finfish include nearly half of all existing vertebrates, representing a broad range of ecologies and physiologies. Together, finfish and shellfish are, therefore, an important group for understanding host–microbiota interactions from ecological, evolutionary and genetic perspectives.

Understanding the relationships between finfish and shellfish hosts and their resident microbial communities as well as the interactions within the microbial community provides insight into important biological characteristics ranging from development to systems biology. Their microbiomes are shaped by the hosts’ environments and the microenvironments provided by the hosts, e.g., the gastrointestinal tract and gills. In addition, colonization by members possessing new genetic characteristics can alter the community structure to either the benefit or detriment of the host. Benefits might result in the stimulation of the host’s immune system, the removal of pathogens by competition or phage infection, or the introduction of new metabolic pathways to assist in nutrition or the development or evolution of new dietary strategies. Conversely, microbiome alterations may result in disease and, in the case of aquaculture-raised species, the enrichment of members that cannot be eliminated by chemotherapeutic approaches with antimicrobial agents.

This Special Issue will focus on the molecular genetic factors that shape the microbiomes of finfish and shellfish and how those factors affect the host. We envision an emphasis on microbiome genetics research including the genetics of antimicrobial resistance; probiotics; microbial virulence; viral, bacterial, archaeal and fungal diversity; dysbiosis; the adaptation of microbiomes to diet; and finfish and shellfish microbiomes in anthropogenically impacted environments.

Dr. Harold J. Schreier
Dr. Eric J. Schott
Guest Editors

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• Antimicrobial resistance
• Probiotics mechanisms
• Microbial virulence
• Viral, bacterial, archaeal, protistan and fungal diversity
• Microbiome adaptation to diet
• Microbiome adaptation in anthropogenically impacted environments
• Aquaculture
• Dysbiosis