By James GallagherPresenter, The Second Genome, BBC Radio 4
Antibiotics and vaccines have been the weapons unleashed against the likes of smallpox, Mycobacterium tuberculosis or MRSA.
That's been a good thing and has saved large numbers of lives.
But some researchers are concerned that our assault on the bad guys has done untold damage to our "good bacteria".
Prof Ley told me: "We have over the past 50 years done a terrific job of eliminating infectious disease.
"But we have seen an enormous and terrifying increase in autoimmune disease and in allergy.
"Where work on the microbiome comes in is seeing how changes in the microbiome, that happened as a result of the success we've had fighting pathogens, have now contributed to a whole new set of diseases that we have to deal with."
The microbiome is also being linked to diseases including inflammatory bowel disease, Parkinson's, whether cancer drugs work and even depression and autism.
Obesity is another example. Family history and lifestyle choices clearly play a role, but what about your gut microbes?