Dr. Eisen's research focuses on communities of microbes. His overarching research goal is to create a "Field Guide to Microbes" - such as exists for birds or trees. He is widely known as a leading authority on studies of microbes based on DNA sequencing, and is an author on more than 300 papers on this topic. His research focuses on the mechanisms underlying the origin of novelty (how new processes and functions originate). Most of his work involves the use of high-throughput DNA sequencing methods to characterize microbes and then use and development of computational methods to analyze this type of data. In particular, his computational work has focused on phylogenomics, the integration of evolutionary analysis with genome analysis.

Currently he is using sequencing and phylogenomic methods to study microbes directly in their natural habitats (i.e., without culturing). The main habitats he studies currently are microbiomes of plants, animals and the built environment. Prior to moving to UC Davis he was on the faculty of The Institute for Genomic Research (TIGR) in Rockville, Maryland. He earned his PhD in Biological Sciences from Stanford University, and his AB in Biology from Harvard College. Dr. Eisen is heavily involved in science communication and open science activities - see for example his Tree of Life Blog & Twitter feed, the micoroBEnet which he runs & a collaboration on "Innovating Communication in Scholarship".