The gut microbiota, probiotics and infectious disease

The human gastrointestinal (GI) tract represents a vast microbial ecosystem with a high degree of complexity and inter-individual diversity. The large intestine contains an estimated 10¹¹-10¹² bacteria per gram of contents and it is thought that total bacterial cells outnumber human cells by at least an order of magnitude (O'Sullivan 2005; O'Hara and Shanahan 2006). These bacteria comprise between 1,000 and 1,150 different species including 160 species which are common between individuals and may provide core functions that are essential for the health of the host (Qin et al. 2010). In this context the human individual has been proposed as a 'superorganism' in which the individual co-exists with their unique microbiota (Wilson and Sober 1989; Zilber-Rosenberg and Rosenberg 2008). The gut microbiota therefore comprise a 'virtual organ' that carries out significant metabolic, digestive and immunoregulatory roles that benefit the host (O'Sullivan 2005; O'Hara and Shanahan 2006).