Analysis of diversity and function of the human small intestinal microbiota

The gastrointestinal (GI) tract is the main site where the conversion and absorption of food components takes place in humans. As the small intestine is the first site of interaction between the microbiota and ingested food, knowledge about the microbial composition as well as functionality is essential for a complete understanding of the symbiotic interactions and to the potential modulation of metabolically important groups. Subjects carrying an ileostomy were chosen as model system and ileostomy effluent samples were collected over time. The diversity as well as activity of the inhabiting microbiota was analysed in ileostomy effluent samples of five healthy individuals, collected in the morning and afternoon over a period of 28 days. This revealed that the diversity of the ileostomy effluent microbiota was different from that in the faeces, mainly concerning the lower complexity and stability over time. In terms of composition the relative abundance of species belonging to the genera Streptococcus and Veillonella was higher, whereas a lower relative abundance of species related to the Ruminococcus obeum, R. gnavus and Bacteroides plebeius-like organisms was observed in ileostomy effluent samples. Marked differences in microbiota composition between the five subjects with an ileostomy were found, indicative for a highly personal ileal microbiota profile. Differences in microbiota composition profiles were observed over time, even visible within one day, although the overall fluctuations were around a relatively large stable core group, consisting of species belonging to three streptococci-related groups (S. bovis, S. intermedius and S. smitis), Clostridium cluster I, Enterococcus, Veillonella and Oxalobacter formigenes. Overall, the data presented in this thesis indicated that the genus Streptococcus is not only numerically abundant, but also predominates randomly generated metabolic activity profiles of the microbial ecosystem of the ileostomy effluent microbiota. Predominant functions exerted were related to metabolism, especially carbohydrate metabolism and transport. The fast transit of the ileal contents appears to generate an environment in which the capacity to rapidly metabolise the available carbohydrates is an important selective advantage.