Understanding the link between the human gut microbiome and human health is one of the biggest scientific challenges in our decade. Because 90% of our cells are bacteria, and the microbial genome contains 200 times more genes than the human genome, the study of the human microbiome has the potential to impact many areas of our health. This PhD thesis is the first study to generate a large amount of experimental data on the DNA and RNA of the human gut microbiome. This was made possible by our development of a human gut microbiome array capable of profiling any human gut microbiome. Analysis of our results changes the way we link the gut microbiome with diseases. Our results indicate that inflammatory diseases will affect the ecological system of the human gut microbiome, reducing its diversity. Classification analysis of healthy and unhealthy individuals demonstrates that unhealthy individuals have lower diversity microbiomes with incomplete functional capacity. Diversity is an important measurement linking microbiome variance to diseases. Our results suggest that diseases are linked to the microbiome not by the presence of “bad” bacteria, but mostly by the loss of the “good” bacteria. Finally, we show that bacterial adaptations explain the shift observed in the human gut microbiome.