This is the first installment in a series on advancements in microbiome research and development. Our goal with this series is to inform readers about developments in this important and growing field and to highlight, where possible, Connecticut’s role in fostering this research. This first article will provide a brief overview of this technology area, featuring both prominent pharmaceutical companies and research labs. Future articles will discuss progress in commercializing this research, review new and relevant patents, and explore issues of law and policy in microbiome R&D.

Research into the microbiome seeks to characterize the microorganisms that live in and on different environments. Although these environments can be broadly terrestrial, extraterrestrial aquatic, and biological, we often use the term specifically to describe the bacteria living in and on different sites of the human body. The word “microbiome” refers either to the organisms themselves (also called “microbiota”) or their collective genomes. Within the human gut, the most bacteria-rich organ, these genes outnumber those in the human genome 100: 1, providing attractive candidates for pharmaceutical intervention. Inflammatory bowel disease (IBD), childhood-onset asthma, diabetes, obesity, cardiovascular disease, colorectal cancer, and antibiotic-associated diarrhea are some of the diseases that involve changes in the composition or loss of the function of the microbiome.

Microbiomics Companies

2015 is shaping up to be a banner year for microbiome-based drug development, or “microbiomics.” This year, Google Ventures President Bill Maris named microbiomics one of eight technologies with the potential to revolutionize life sciences, comparing its potential for impact to that of stem cells research, artificial intelligence, and gene editing. In late June, Seres Therapeutics became the first microbiomics company to go public, with a $134 million IPO. Table 1 provides more information about Seres and other leading companies in the microbiomics space.

Click here to view table.

Several local startups seek to enter this market. Mark Driscoll and Thomas Jarvie, formerly of 454 Life Sciences in Branford, have founded Shoreline Biome to develop diagnostics and therapeutics targeting the human microbiome. Azitra, the brainchild of Yale students in medicine and public health, is building a platform that combines microbiomics and synthetic biology for the treatment of skin disease.

Microbiome Research: Connecticut and Beyond

Connecticut boasts several outstanding leaders in microbiome research. George Weinstock, a Professor and Director for Microbial Genomics at The Jackson Laboratory for Genomic Medicine (JGM) in Farmington led the Human Microbiome Project, a five-year, $115 million initiative to characterize the microbiome and its contribution to disease. Recent hire Julia Oh is bringing her innovative work on the skin microbiome to the JGM as an Assistant Professor. Her arrival adds to a growing community of microbiome scientists in the state, including Andrew Goodman, an Associate Professor of microbial pathogenesis at Yale University whose work was recently honored by the Burroughs Wellcome Trust. Yale is also home to metagenomics pioneer Jo Handelsman (currently on leave as Associate Director for Science at the White House Office of Science and Technology Policy), immunobiologists Richard Flavell and Ruslan Medzhitov, and physician-scientist Martin Kriegel. At University of Connecticut (UConn), Joerg Graf and Xiaomei Cong are collaborating to investigate whether early life stress exposure, microbiome disruption, and psychological dysfunction are linked in preterm infants.

The studies of CT-based scientists complement the work of other outstanding researchers in this field. These include Jeffrey Gordon at Washington University in St. Louis (WashU), Martin Blaser at New York University (NYU), Wendy Garrett at Harvard University, Michael Fischbach at University of California San Francisco (UCSF), Lora Hooper at University of Texas Southwestern Medical Center (UT Southwestern), Sarkis Mazmanian at California Institute of Technology (Caltech), Justin Sonnenburg at Stanford University, Peter Turnbaugh at UCSF, and many others. Several of these scientists also hold key patents in microbiomics and some have also started or advise microbiome-based pharmaceutical companies. Table 2 reviews these key researchers and their contributions.

Click here to view table.


The microbiome represents a new frontier in health and disease. A number of microbiome-based therapies are now in the early stages of development. This recent flurry of commercialization would not be possible without basic research from labs both in CT and around the world. These trends will surely continue as R&D in this field progresses. Stay tuned for the next installment of this series, which will review the patent landscape in microbiome research, with a focus on applications and grants issued this year.