Abstract
Over the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems. Over the next 5 years, we need a merging of new omic technologies for exploratory studies with classical bacterial genetics, bacterial physiology, protein engineering, and biochemistry to further define the biochemical mechanisms of the gut microbiota. The future of the systems microbiology field will focus on targeted engineering and editing of the microbiome to alter function, which will be leveraged to prevent and/or treat human diseases. This perspective will focus on my contribution to the microbiome field, both past and present, and where I think research in the field is headed in the near future.