Bacterial Diversity in the Human Gut

Publisher Summary

The human digestive tract is colonized by highly complex microbial ecosystem containing vast numbers of bacteria that could be assigned to several hundred bacterial species. Bacterial colonization of the gut is affected by a wide variety of host, microbiological, environmental and dietary factors, as indicated in the chapter. Until recently, our knowledge of bacterial diversity in the large intestine was derived by using classical viable counting techniques. However, the advent of molecular methods of analysis has led to renewed interest in the structure and composition of the gut ecosystem. The advantages of culturing techniques are that they are relatively inexpensive, widely available, and quantitative. On the other hand molecular techniques are rapid and have the potential for high throughput analysis. Biological samples can be frozen, while DNA is easily transported among laboratories. They also allow so-called unculturable species to be detected. The disadvantages of these technologies are that they tend to be expensive, while some bacteria are more susceptible to lysis than others and can therefore be detected more easily.

Introduction

The human digestive tract is colonized by microorganisms to varying degrees throughout its length. Because of acid pH, and the short retention time of gastric contents, numbers of viable bacterial cells in the stomach are usually <10² per ml, with aciduric Gram-positive species such as lactobacilli and streptococci predominating, although numbers can increase 1000-fold postprandially. While the rapid passage of digestive materials through the upper small bowel does not allow time for significant bacterial growth to occur, their numbers increase considerably to >10⁸ per ml in the distal ileum (Macfarlane and Cummings, 1991). The rate of movement of intestinal contents slows markedly in the large bowel, which facilitates the development of large complex bacterial communities (Cummings 1978, Cummings 1993). Indeed, the vast majority of cells associated with the human body (eukaryotic and prokaryotic) are anaerobic bacteria growing in the colon (Savage, 1977). Bacteria comprise 40–45% of fecal material on a dry weight basis (Stephen and Cummings, 1980), which equates to about 18 grams of bacterial dry matter, or a total bacterial mass in the colon of about 90 grams (Macfarlane and Cummings, 1991).

The large bowel is the main area of permanent microbial colonization of the human gastrointestinal tract, and several hundred bacterial strains and species have been isolated from this complex ecosystem, where viable counts in feces typically reach 10¹¹–10¹² per gram (Finegold 1983, Moore 1974), with anaerobic bacteria predominating (Finegold 1974, Hentges 1993, Holdeman 1976, Moore 1974). Microbial cell population densities increase progressively from the cecum to the distal large intestine (Fig. 1). Bacterial colonization of the gut is affected by a wide variety of host, microbiological, environmental and dietary factors, as indicated in Table I.

Until recently, our knowledge of bacterial diversity in the large intestine was derived by using classical viable counting techniques; however, the advent of molecular methods of analysis has led to renewed interest in the structure and composition of the gut ecosystem.