Host, its microbiota and their interactions

The development of sequencing technologies has advanced the field of host-associated microbiology by showing the huge diversity and functionality of the omnipresent microbes of all multicellular life. With these advances, new interesting questions have been raised with regards to microbial community composition, pollutants that can interact with the host microbial community, the factors that can affect the host microbial community and the processes that determine the enormous variety of the microbiota among hosts of the same species or genotype. However, conceptual disagreement regarding the ecology, genetics and evolutionary concepts regulating microbial diversity are frequently occurring in this field. Concepts such as symbiont, holobiont, and hologenome are generating discordances in the scientific community regarding microbial host associations and microbial communities. Then it is important to take into account the definitions and clarify the bases of these concepts: the holobiont refers to the host and their symbiotic microbes. Therefore, the hologenome are the genes of host plus the genes of their symbionts. However, the symbiont definition is wide open and when we use it at the holobiont level it can be misinterpreted as all microbes in a host. To separate symbionts from non-symbionts, it is necessary to search at the functional level for the emergence or enhancement of traits at the holobiont level. For that reason, not all of the microbiota are symbionts and, therefore the holobiont should only include the host and all the microbial symbionts that inhabit it. Consequently, host-associated microbes are part of the amalgam in the complex organisation of an organism and can also be explained by ecological associations. Understanding these complex interactions between host and its microbiota can, for instance, give us insight into how this community can influence the host’s regulatation of pollutants as stress factors. More important, to understand synergistic effects of pollutants such as microplastics and metals on the host and their microorganisms, constitute one of the new frontiers in toxicology. Finally, it is important to take into account how stress factors such as competition, environmental changes, pollution, and diet can influence the fitness, genome dynamics and diversification between organisms.