Quantitative assessment of the human gut microbiome using multitag pyrosequencing.

Recent advances in molecular techniques have now made it possible to interrogate the human microbiome in depth to better understand the interactions with the host organism and its role in diseases. We now report the utility of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to survey samples and a proprietary Multitagged Pyrosequencing (MTPS) methodology to interrogate the gut microbiome in healthy and disease states. We present an overview of our studies demonstrating the application of these molecular-biology techniques to an example disease state such as Inflammatory Bowel Disease (IBD). The findings show that there is a core mucosal bacterial microbiome (i.e., a mucosal biofilm) that is distinct from the luminal microbiome in health, and that the mucosal microbiome appears to be dysbiotic in IBD. We propose that the mucosal microbiome forms a synergistic and stable interaction with the host immune system, while the lumen microbiome varies based on diet or other environmental factors. We define this composite ecosystem of the human microbiome and human host as the Human Metabiome.