Chapter 11 : The Gastrointestinal Microbiome

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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.

Citation: Magee A, Versalovic J, Luna R. 2016. The Gastrointestinal Microbiome, p 126-137. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch11
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Image of FIGURE 1

The dynamic nature of the gut microbiome over the span of a lifetime. With initial seeding of the microbiome at birth, the bacterial community of the gut continues to evolve through the course of a lifetime. Various factors affect the specific composition of an individual's gut community, and in return, the gut microbiome contributes to health and disease. (Reproduced with permission from reference .)

Citation: Magee A, Versalovic J, Luna R. 2016. The Gastrointestinal Microbiome, p 126-137. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch11
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Image of FIGURE 2

Antibiotics, probiotics, and prebiotics in the gut. (A) While antibiotics successfully eliminate pathogenic bacteria, the diversity of the overall bacterial community is diminished and can leave the host susceptible to further disease. (B) Probiotics and prebiotics are effective at manipulating the microbial community and promoting a healthier microbiome profile in the gut. (Reproduced with permission from reference .)

Citation: Magee A, Versalovic J, Luna R. 2016. The Gastrointestinal Microbiome, p 126-137. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch11
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Fecal microbiome transplantation for the treatment of infection. Using material from a healthy donor, fecal transplants have successfully treated infection and restored a healthy gut microbiome. (Reproduced with permission from reference .)

Citation: Magee A, Versalovic J, Luna R. 2016. The Gastrointestinal Microbiome, p 126-137. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch11
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