The exercise and diet-microbiome paradigm: influences of physical activity and dietary nutrition on the human gut microbiome

Introduction: Revolutionary insights of the human microbiome, the conglomeration of microorganisms that stably occupy an expansive array of anatomical locations of the human body, have certified the phenomenon as an integral component of human biology. As progress has been made in elucidating the various factors of influence that the microbiome imposes on human health, it has become apparent that modulation of the community structure and functional activity of the microbiome is an essential step in utilizing these microbes as an element of intervention in healthcare. Advancement in understanding of how the microbiome is manipulated is accordingly of great interest and importance. Methods: Physical activity is a recently emergent prospective modulator of the human intestinal microbiome. This development in microbiome-host interaction presents great potential, but has presently been investigated in limited depth. To expand the understanding of this biological dynamic we engaged the subject with focus on metabolic function of the microbiome, utilising advanced computation methods and molecular technologies. Our approach has sought to address multiple aspects of exercise induced microbiome alteration, and accordingly was conducted with randomized control trials and prospective observational study designs. Results: This work describes further evidence that physical exercise has a role in directing the community structure and metabolic activity of the gut microbiome. Our inspection of professional athletes, whose prolonged engagement in rigorous exercise grants perspective of the extreme end of the spectrum of physical activity, revealed a divergent microbiome from that of more sedentary controls. Metabolic pathways from the athletes were configured to offer enhanced energy recovery from the intestinal environment. Quantified metabolomic phenotyping of this system similarly revealed that the athlete microbiome had a favourable profile of SCFA enrichment. Examination of structured short-term exercise on exercise naïve individuals revealed subtle alterations of the microbiome, both in terms of phylogenetic composition and metabolic output. In our investigation it was also observed for the first time that supplementation of whey protein resulted in an alteration of the virome. Further sequencing of the supplement itself revealed a highly similar viral composition to the participants, suggesting that whey protein, a widely used supplement, is directly transmitting virus particles. To explore the implementation of exercise as a supportive intervention for health conditions related to the GI system, patients with inflammatory bowel disease (IBD) were recruited for a short-term exercise intervention study. While minimal changes in the composition of the IBD patients’ gut microbiome were identified, the patients were shown to undergo the treatment without insult to, or perturbation of their disease state. This important finding illustrates that sufferers of IBD can engage in physical exercise, reaping the well-known health benefits from the activity, without obvious influence on the gut microbiome. Elucidation of the longitudinal effects of exercise on the gut microbiome was achieved through the examination of two individuals engaging in exercise over the course of six months. Through this N of 1 style of study, resources were concentrated on the two participants, enabling the acquisition of much greater detail on the proposed question. Here again, it was observed that while the participants were rewarded with improvements in health parameters, changes of the gut microbiome were subtle. Complementing the impressive results produced from initial investigations of professional athletes, effort was put forth to apply advanced computational approaches to the previously generated data in order to advance understanding of the athlete microbiome. A novel algorithm designed to predict adherence to healthy dietary habits based on metabolomic profiling was used to better define dietary influence on the metabolomic dynamics of the gut environment. Separately, a computational modelling method centred on Flux Balance Analysis generated models of microbial metabolic exchange within the athletes and corresponding controls. Conclusions: The findings supporting this thesis have immediate relevance in the area of athleticism, with implications for professional athletes and individuals casually engaged in exercise. There is further impetus provided for continued investigation of the athlete microbiome, the influence of prolonged periods of exercise on populations with low fitness levels, and the impact of dietary supplement derived microbe transmission