Chapter 11 : The Gastrointestinal Microbiome

Abstract:

Through the years, the individual microbes that reside in the human gastrointestinal (GI) tract have been labeled as pathogens, commensals, uncultivable, or unidentifiable. While exploration of particular species in the discovery and diagnosis of disease remains paramount, it is the landscape of the microbial community that continues to offer greater clues to the role of microbes in human health and quality of life. In contrast to other body systems, the human GI microbiome is ecologically diverse and complex and plays an active role in digestion, metabolism, behavior, heart size, and the development of the mucosal immune system, among other associations (1, 2). The composition of the gut microbiota is influenced by diet, age, host genetics, antibiotic treatment, and the environment (e.g., psychological stress, hygiene, climate, and allergies) (3). The microbial communities found in the gut have also been shown to contribute, both negatively and positively, not only to health issues rooted in the GI tract, but also to those of the respiratory and central nervous systems. An imbalance or shift of the gut microbiome has been linked to the development of a variety of disorders including inflammatory bowel disease (4–6), gastric ulcers and cancer (7–10), autism spectrum disorder (11–15), and obesity and diabetes (16–19). Because of the implications related to these changes and the development of “unhealthy” microbiomes, research is ongoing to continue to refine the definition and composition of a “healthy” gut microbiome.