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Chapter 1 : The Fecal Environment, the Gut

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Abstract:

This chapter examines the ecology of the digestive tract of humans and animals with particular reference to the association between anatomical structures, their related physiologies, the mode of feeding, and the functional association of specific microbial communities in different gut compartments of the digestive tract. A section provides the reader who is not familiar with the digestive tract, a brief, nonexhaustive summary of the major features of the digestive tract. The combination model is one in which the inefficiencies of foregut fermentation are translocated to the hindgut. In the competition model, exemplified by the meat eater, there is little hindgut fermentation but, in the combination model (exemplified by the horse, rabbit, and dugong), extensive fermentation in the cecum and colon is possible. The development of pregastric fermentation in herbivores is a very successful adaptation for animals consuming diets dominated by forages. In the golden hamster (), the esophagus joins the pregastric chamber in close proximity to a sphincter-like muscular ring and most of the ingested food is deposited in this pregastric chamber. The rock hyrax () is unique in that it has three fermentation compartments that are completely separated from one another anatomically. In humans, the consumption of plant cell walls is not nearly as common as in herbivores, but complex carbohydrates in the form of starches are consumed and, in fact, encouraged because of the benefit to gut heath.

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1

Key Concept Ranking

Microbial Ecology
1.2599316
Viruses
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Small Intestine
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Large Intestine
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Chemicals
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Immune Systems
0.52527213
Bacteroides thetaiotaomicron
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Figures

Image of FIGURE 1
FIGURE 1

(A) Sequence of digestion in nonruminants. The simplest case (little or no cecal digestion) occurs in most carnivores and in humans. Cecal digestion occurs in large herbivores but is secondary to colon digestion (Stevens and Hume, 1988). (B) Sequence of digestion in rodents, most of which practice coprophagy; cecal fermentation is dominant over secondary colonic fermentation. Some rodents (hamsters and voles) exhibit pregastric digestion (see Fig. 2 ). Reprinted from Van Soest ( ) with permission from Cornell University Press.

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
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Image of FIGURE 2
FIGURE 2

(A) Sequence of digestion in nonruminants with pregastric digestion. (B) Sequence of digestion in ruminants. The sieving system of the omasum is much more developed in grazing species. Reprinted from Van Soest ( ) with permission from Cornell University Press.

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
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Image of FIGURE 3
FIGURE 3

Schematic showing the major pathways of carbohydrate fermentation by ruminal bacteria. “X” denotes alternative electron carrier (e.g., ferredoxin). In some ruminal bacteria, pyruvate decarboxylation is coupled to formate production, but most of this formate is converted to hydrogen and carbon dioxide by hydrogen formate lyase. The dashed lines show pathways that occur in other organisms. Reprinted from Russell and Rychlik ( ) with permission from AAAS.

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
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Image of FIGURE 4
FIGURE 4

The amount of microbial protein produced per unit of feed fermented in the rumen affects the rate of fermentation. Reprinted with permission from Van Soest et al. (1991).

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
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Image of FIGURE 5
FIGURE 5

Model relation in which release of nitrogen fractions parallels fermentation curves for respective fast-and slow-degrading carbohydrates and optimizes microbial protein output. Peptide production, which is important for the fast pool, depends on the presence of degradable true protein. Ammonia can come from the nonprotein nitrogen pool and from peptide degradation. The ammonia level does not rise much because it is competitively recycled into microbial protein. A: Nonprotein nitrogen and peptides; B1: true soluble protein; B2: neutral detergent soluble protein. Reprinted from Van Soest ( ) with permission from Cornell University Press.

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
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Tables

Generic image for table
Table 1

Mammals classified by gastrointestinal anatomy

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
Generic image for table
Table 2

Gastrointestinal volume of mammal species

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
Generic image for table
Table 3

Characteristics of predominant bacteria in human large intestine and in the rumen,

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1
Generic image for table
Table 4

Genome sequences concerned with plant polysaccharide breakdown in four species of gut bacteria

Citation: Krause D, Khafipour E. 2011. The Fecal Environment, the Gut, p 1-21. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch1

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