Ecological Interactions of Bacteria in the Human Gut

Abstract

The colon or large intestine is one of the most important organs of the human body (Macfarlane and Cummings, 1991). Moreover, its inhabitants, the colon microbiota, are the key elements of the human digestive ecosystem. The vast complexity of the human large-intestinal microbiota has inspired researchers to consider it as an organ itself, located inside the colon and acquired postnatally (Bäckhed et al., 2005; Zocco et al., 2007). From a physiologist's point of view, this image of the colon microbiota is relevant: like an organ, it is composed of different cell lineages that communicate with both one another and the host; it consumes, stores, and redistributes energy; it mediates physiologically important chemical transformations; and it is able to maintain and repair itself through self-replication (Bäckhed et al., 2005). As a microbial organ, the human colon community does not only broaden the digestive abilities of the host (Gill et al., 2006), but also influences body processes far beyond digestion (Roberfroid, 2005b; Turnbaugh et al., 2007). From a microbiologist's point of view, the simplified perception of the microbial colon community as a functional entity narrows down colon ecosystem research toward a 'black box' approach, not only with respect to the identification of its inhabitants, but also concerning the numerous metabolic activities and interactions that take place in the large instestine (Pryde et al., 2002). As the exact composition of the colon microbiota remains at present largely unexplored, input/output-based studies might appear manageable tools to investigate a terrifying complexity. However, even though such studies would generate com-prehensive results, they inherently neglect the sometimes subtle fluctuations in composition and metabolic activity within the microbial colon community. Such changes – with a possible impact on the host's health – can only be monitored after thorough dissection of the colon microbiota and subsequent identification # Springer ScienceþBusiness Media, LLC 2009 of the dominant microbial clusters and their interactions (Flint et al., 2007). The latter will eventually lead toward a global, ecological understanding of the colon ecosystem. During the last few years, the implementation of culture-independent mo-lecular techniques in the field of gut research has revealed the presence of an unsuspected microbial diversity in the human colon (Eckburg et al., 2005; Frank et al., 2007; Li et al., 2008). Further exploration of this microbial wealth is a necessary step toward a better understanding of the relationship between the human host and its symbionts. However, defining a complex ecosystem, such as the human large intestine, does not end with the construction of a catalogue of its members, but also implies the determination of the habitat (ecological or envi-ronmental area inhabited) and niche (relational position within the ecosystem) of each (cluster of) inhabitant(s) and its functional role(s) (Ley et al., 2006). This functional characterization of large bacterial groups within the colon ecosystem is probably one of the greatest challenges for microbiologists in the years to come (Turnbaugh et al., 2007).