Factors Affecting the Gut Microbiome

Abstract

The recent boom in microbiome research, made possible by advances in sequencing technology, has revealed that the gut microbiome plays an important role in human health. A relatively stable community, gut microbes are essential in humans for the development of the immune system and processing of nutrients, such as vitamins. Changes to these communities have been observed in disease states, such as: inflammatory bowel disease, diabetes, obesity, colon cancer and even atherosclerosis. Factors such as antibiotic use and diet can alter the gut communities, and the microbiome has become a target of therapeutic interest for certain chronic inflammatory diseases. Here, we further examine factors affecting the gut microbiome, namely exercise, food supplements and probiotics. We have used deep sequencing methods to focus on the bacterial communities across three studies. Taxonomy was assigned to sequences and compared across samples using a bioinformatics approach. The first study examines the impact of exercise on the murine gut microbiome. Using a machine learning model, we identify moderate but measurable changes in gut bacteria as a result of moderate exercise. We identify previously associated and novel taxa associated with exercise. The second study examines the impact of fruit-derived antioxidants on the gut microbiome in a model of lung cancer. Anthocyanin-rich haskap berry extracts have a strong impact on gut bacteria and warrant further investigation as a dietary supplement to prevent lung cancer relapses. Lastly, we analyzed microbial succession in the production of a dairy-free, coconut kefir product. Kefir is made by fermenting coconut milk using traditional kefir grains containing bacteria and yeasts. We find that coconut kefir contains many of the same beneficial bacterial as traditional dairy kefir. The results illustrate that factors like exercise and dietary supplements have an impact on gut microbes in healthy subjects. While the effects of haskap extract were also seen in a model of murine lung cancer, these factors should be further examined in disease models. As research continues to unravel how the microbiome is related to various diseases, understanding how to shape the microbial community through exercise, diet and probiotics will become increasingly important. The research here provides a first glance at many of these systems using primarily murine animal models. Further studies in humans will extend these results further to better leverage the use of the microbiome to aid in human health.