Who Inhabits Our Gut? Introducing the Human Gut Microbiota

Abstract

While all regions of our digestive tract are colonized by micro-organisms to some degree, the densities, composition and nature of the associated microbial communities change markedly as we travel down through the gut (Fig. 5.1). The mouth (oral cavity) is well colonised, particularly the surfaces of teeth and crevices between the tooth and gum. As semi-permanent features, teeth allow the development of microbial biofilms, in which different species attach to each other and to the tooth surface in a highly structured manner [1]. Microbial biofilms can develop elsewhere, for example on implanted catheters, but the rapid turnover of epithelial cells and digesta particles probably limits their formation further down the gut. Infections of teeth and gums can have a major impact on health not only through tooth decay, but also through their effects on the heart, brain and immune system. These problems are due to pathogenic oral bacteria such as Streptococcus mutans and the anaerobe Porphyromonas gingivalis, a member of the Bacteroidetes phylum. The protein-destroying enzyme gingipain, which is produced by P. gingivalis was recently proposed as a factor in the development of Alzheimer’s disease [2]. Rapid passage of gut contents after swallowing means that the healthy oesophagus shows very low numbers of micro-organisms, while the highly acidic stomach also deters most colonisers. Some specialist microorganisms do however manage to colonise the stomach wall, notably Helicobacter pylori [3].