2011 and 2012 Early Careers Achievement Awards: use of genomic biology to study companion animal intestinal microbiota.

Although dogs and cats are quite different than many livestock species in that they have evolved by eating diets high in fat and protein and low in carbohydrates, the gastrointestinal microbiota still play a key role in the gut and overall host health of these species. Early experiments in this field used culture-based techniques to evaluate the effects of dietary ingredients, such as fibers and prebiotics, on microbiota and indices of gut health (e.g., fecal scores, pH, fermentative end products). Such studies, however, were limited in scope and lacked precision as it pertained to the microbiota. The DNA-based techniques that have become available over the past decade have greatly upgraded research capabilities and have provided a more encompassing view of the canine and feline gastrointestinal microbiomes. High-throughput sequencing techniques that are much cheaper and faster than Sanger sequencing have been a key development in this progress. Sequence data not only allow for the identification of all microbial taxa but also provide information regarding functional capacity when a shotgun sequencing approach is used. The few canine and feline studies that have used 454 pyrosequencing have identified the predominant microbial taxa and metabolic functions present in healthy populations, differences between healthy and diseased dog and cat populations, and the effects of diet (e.g., dietary fibers, prebiotics, protein to carbohydrate ratio) on gastrointestinal microbiota. Although these studies have provided a foundation from which to work, more research is needed to increase our general understanding of the gastro-intestinal microbiome, how it impacts host health, how its composition and activity may be altered by age, genetic, or environmental factors, and test whether specific pathogens or disease signatures can be identified and used in diagnosis and/or treatment of disease.