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Chapter 2 : Role of the Indigenous Microbiota in Health and Disease
Category: Clinical Microbiology
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This chapter focuses on the indigenous microbiota of the human large bowel, arguably the best-known ecosystem of the body. The study of microbial communities falls within the domain of microbial ecology—the study of the interrelationships that occur between populations within a community and between the community and the environment in which it is located. Microbial ecology is about how ecosystems work and therefore details the functions of populations, individually and collectively, in nature. The indigenous microbiota is a potent source of opportunistic infections that arise when the mechanisms that normally confine the microbes to a particular site are disrupted. Anaerobic infections following bowel surgery, urinary tract infections, chronic respiratory tract infections, dental/gingival diseases, and annoying skin conditions come into this category. Medical knowledge focuses on the pathogenesis of diseases and the derivation of intervention strategies. To understand health, one must learn about the mechanisms that operate in the healthy body by which stable ecosystems are sustained and maintained. Then, health might be guarded by reason, perhaps by interventions that would produce predictable outcomes on the basis of knowledge of molecular networks. Fortunately, the technological approaches to achieve these goals are at the fingertips of microbiologists: metagenomics to access and assess community genetics, and metabolomics to analyze functional attributes of the indigenous microbiota in concert with that of the host.