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Chapter 3 : The Gut Microbiota: Ecology and Function

Authors: Benjamin P. Willing1, Janet K. Jansson2
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Affiliations: 1: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; 2: Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
Content Type: Monograph
Publication Year: 2011

Category: Applied and Industrial Microbiology; Environmental Microbiology

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Abstract:

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 and are representative of common interactions between and . 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.

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3

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Denaturing Gradient Gel Electrophoresis
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Restriction Fragment Length Polymorphism
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Microbial Ecology
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The Gut Microbiota: Ecology and Function
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Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
/content/10.1128/9781555816865.ch03.ch03fig01
FIGURE 1
Overview of “omics” approaches to study the gut microbiota.
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10.1128/9781555816865/f0041-01.gif
Image of FIGURE 1
FIGURE 1

Overview of “omics” approaches to study the gut microbiota.

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
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FIGURE 2
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. ( ), with permission.
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Image of FIGURE 2
FIGURE 2

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. ( ), with permission.

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
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FIGURE 3
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.
10.1128/9781555816865/f0046-01_thmb.gif
10.1128/9781555816865/f0046-01.gif
Image of FIGURE 3
FIGURE 3

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.

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
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FIGURE 4
Synergistic action of bacteria in degradation of carbohydrates. Different bacterial species work together in the metabolism of dietary carbohydrate, each contributing to the process.
10.1128/9781555816865/f0056-01_thmb.gif
10.1128/9781555816865/f0056-01.gif
Image of FIGURE 4
FIGURE 4

Synergistic action of bacteria in degradation of carbohydrates. Different bacterial species work together in the metabolism of dietary carbohydrate, each contributing to the process.

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
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FIGURE 5
A representation of and 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 for nutrients causes to stimulate the production of glycans from the host that it, but not can utilize. utilizes acetylCoA produced by 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 ( ).
10.1128/9781555816865/f0058-01_thmb.gif
10.1128/9781555816865/f0058-01.gif
Image of FIGURE 5
FIGURE 5

A representation of and 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 for nutrients causes to stimulate the production of glycans from the host that it, but not can utilize. utilizes acetylCoA produced by 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 ( ).

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
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Tables

The Gut Microbiota: Ecology and Function
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Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3
/content/10.1128/9781555816865.ch03.ch03tab01
Table 1
Representation of classified bacterial phyla from 60 mammalian species
Generic image for table
Table 1

Representation of classified bacterial phyla from 60 mammalian species

Citation: Willing B, Jansson J. 2011. The Gut Microbiota: Ecology and Function, p 39-65. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch3

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