http://arstechnica.com/science/2016/01/its-time-to-rethink-how-we-identify-disease-causing-microbes/
A recent scientific opinion piece advocates for revising the 130-year old Koch’s postulates which laid the foundation for germ theory and our understanding and ability to investigate, understand, control and prevent microbial disease, which at the time was the leading cause of human death. We have made substantial progress in infectious disease with the advent of antibiotics and improved sanitation and hygiene. However, the opinion piece referenced here suggests that our understanding of pathogens is being upended by new DNA methods which are revealing a more nuanced understanding of pathogens. DNA methods allow us to characterize an entire microbial community whereas older culture-based methods are typically limited to a single organism or group of related organisms. As a result researchers have found that the presence of pathogens does not necessarily result in disease if there are beneficial microbes present that keep the pathogen in check. This obviously complicates Koch’s postulates which hold that exposing a person to a candidate pathogen which is under investigation must cause a disease.