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Chapter 3 : The Gut Microbiota: Ecology and Function
Category: Applied and Industrial Microbiology; Environmental Microbiology
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This chapter focuses on the microbial ecology of the gut, with emphasis on information gleaned from recent molecular studies. Most attention has been devoted to bacterial components of the gut microbiota and, thus, they are the focus of this chapter. The first metagenomic study of the human gut resulted in 78 million base pairs of DNA sequences from two American individuals. This study cataloged the combined gene complement of the microbiome, including functional genes. A section discusses some dramatic differences that have been observed in the gut microbiota of infants that are fed formula compared to infants that are breast-fed. An interesting example of the importance of host physiology in shaping the composition of the microbiota was shown in reciprocal transplantations of gut microbiota between mice and zebrafish. The chapter primarily discusses Crohn's disease (CD) because of the large number of recent reports that have focused on the correlation of the gut microbiota to this particular disease. Therefore, the increased production of butyrate resulted in greater host responses to colonization. Although this model gave some new insights into the complex ecology of the gut microbiota, it is yet unclear whether the interactions observed between Eubacterium rectale and Bacteroides thetaiotaomicron are representative of common interactions between Bacteroidetes and Firmicutes. The study of genetically matched twins and defined model systems are examples of approaches that have promise to help define diagnostic targets and disease biomarkers.
Overview of “omics” approaches to study the gut microbiota.
Functional redundancy of the gut microbiota suggested by large variations in community composition between individuals: (a) compared to community functions or (b) categories of gene function. Reprinted from Turnbaugh et al. ( 2009 ), with permission.
Bacterial colonization of the GI tract. Bacterial numbers increase in abundance from proximal to distal regions. Bacteria reside in close proximity to the intestinal epithelium. A firmly adherent layer of mucous keeps bacteria at a safe distance so as to prevent continual mucosal stimulation and inflammation and a loosely adherent layer provides a habitat for abundant microbial colonization.
Synergistic action of bacteria in degradation of carbohydrates. Different bacterial species work together in the metabolism of dietary carbohydrate, each contributing to the process.
A representation of B. thetaiotaomicron and E. rectale colonizing the gastrointestinal tract of the mouse alone (A, B) or together (C). Interactions between bacteria result in changes in bacterial physiology and how they affect the host. Competition with E. rectale for nutrients causes B. thetaiotaomicron to stimulate the production of glycans from the host that it, but not E. rectale, can utilize. E. rectale utilizes acetylCoA produced by B. thetaiotaomicron resulting in an increased production of butyrate. The interactions between bacteria, including competition and synergistic interactions, result in an amplified host response. Adapted from Willing and Finlay ( 2009 ).
Representation of classified bacterial phyla from 60 mammalian species a