Sampling Microbiota in the Human Gastrointestinal Tract

Angele P. M. Kerckhoffs, Melvin Samsom, and Gerard P. van Berge Henegouwen

Department of Gastroenterology, Utrecht University Medical Center, Utrecht, The Netherlands

Louis M. A. Akkermans and Vincent B. Nieuwenhuijs

Department of Surgery, Utrecht University Medical Center, Utrecht, The Netherlands Maarten R. Visser

Department of Microbiology, Utrecht University Medical Center, Utrecht, The Netherlands

INTRODUCTION General Introduction

Antonie van Leeuwenhoek (1632-1723) was the first to describe numerous microorganisms from the gastrointestinal tract, which he described as "animalcules," having designed the first glass lenses for the microscope that were powerful enough to observe bacteria. His curiosity brought him to investigate samples taken from his own mouth and other people who never brushed their teeth, and he compared these findings with people who brushed their teeth daily and used large amounts of alcohol. He even investigated his own fecal samples in a period of diarrhea, compared these findings with fecal samples of animals, and reported these observations to the Royal Society in London (1).

We now know that the mucosal surface of the human gastrointestinal tract is about 300 m2 and is colonized by 1013-1014 bacteria consisting of hundreds of different species. The prevalence of bacteria in different parts of the gastrointestinal tract depends on pH, peristalsis, oxidation-reduction potential within the tissue, bacterial adhesion, bacterial cooperation, mucin secretion containing immunoglobulins (Ig), nutrient availability, diet, and bacterial antagonism. The composition of the Gram-negative, Gram-positive, aerobic, and anaerobic microbiota has been extensively studied by culturing methods, and shown to change at the various sites of the gastrointestinal tract (Fig. 1).

The stomach and proximal small bowel normally contain relatively small numbers of bacteria because of peristalsis, and the antimicrobial effects of gastric acidity. An intact ileocecal valve is likely to be an important barrier to backflow of colonic bacteria into the

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