Chapter 2 Microbes , Metabolites and Health

High throughput DNA sequencing has revolutionised the analysis of complex communities of microorganisms (microbiota). In humans, this paradigm shift, allowing analysis of the membership of microbial communities without the need to culture individual organisms, has spawned an avalanche of research and a number of important collaborative programs characterising not only the catalogue of species comprising the microbiota associated with different ecological niches in the body in states of both health and disease (Group et al. 2009) but also their genetic potential (Qin et al. 2010). Nowhere in the human body are the microbes more numerous or the microbiota more complex than in the colon of the gastrointestinal tract (Savage 1977). With its trillions of bacteria, comprising over one thousand individual microbial species present in varying abundances, the microbiota of the human gut and the genes they carry (collectively the microbiome) provides the host with a vast metabolic potential over and above that afforded by the 20,000–25,000 protein coding genes of the human genome. The composition of the human colonic microbiota is remarkably diverse between individuals with each person’s microbiota being unique (Qin et al. 2010; Yatsunenko et al. 2012). Despite this diversity at the taxonomic level, when analysed for functional potential by whole genome analysis at the gene level, conservation of bacterial genes between individuals was high suggesting that