Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

SIMPLE SUMMARY: The relentless capacity of sequencing every bit of DNA at low cost has been fueling major advances in several research areas. This also applies to the animal sciences, which witnessed unprecedented progresses in fields such as animal nutrition, health, and breeding. Particular attention has been paid to the gut microbiome, the community of microorganisms inhabiting the digestive tract of livestock species, and unforeseen developments have arisen. Nonetheless, such efforts have not been equal for the different livestock species, and the vast majority rely on widely-used standard techniques through which taxonomically useful genetic data are generated rather than more informative—yet computationally demanding—organismal genome-wide variation data. This review offers a glimpse of the gut microbiome research on five emblematic livestock species touching on the limitations regarding (i) the major methodological frameworks, (ii) species or breed, (iii) and spatial reach of these studies, thus providing valuable indications to fill current knowledge gaps and hopefully lay the basis for the planning of concerted research efforts. In this respect, we conclude that future studies should extend shotgun sequencing and transcriptomic approaches primarily to largely neglected ovicaprine and chicken breeds from rural areas of developing countries and microbial groups other than bacteria. ABSTRACT: The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.