The role of microbiota in animal health and productivity: misinterpretations and limitations.

The rise of sequencing technology brought about a surge of new methodologies that offered a new and deeper level of understanding of the role of the microbiome in the health and performance of livestock. This started a chain reaction in technology evolution, and a decade later, we have developed a new appreciation of a healthy gut and the role of early colonisation and nutrition in developing the microbiome, and its subsequent impact on animal productivity. An abundance of new products flooded the livestock supplement market with the promise of improving the health of intestinal microbiota. However, the impact of these products and any potential gains they might provide have not always been quantified or validated. Further to this, the potential interactions with the microbial community naturally occurring in the feed-base have not commonly been considered. We have recently shown that animal feed carries a complex microbial community that can have various impacts, including negating farm biosecurity measures. The ruminant animal provides an even greater level of complexity where physiological drivers act to maintain ruminal homeostasis. Despite many advances, numerous knowledge gaps remain, and the methodologies are not without their challenges with almost constant evolution in analysing and interpreting data. In this paper, we will discuss the benefits, challenges and shortfalls of microbiome science, its interfaces with multi-omics research and the strategies of its contribution to animal production science. With advances in sequencing technology, research of microbial communities has become more accessible and affordable. In livestock research, the roles of microbiota are associated with animal performance and welfare. Although universally accepted, amplicon-sequencing methodology has several issues that need to be considered in data interpretation. Here we review the main shortfalls, benefits and uses of the methodology in livestock research. [ABSTRACT FROM AUTHOR]