Collaborations are a critical way we leverage our microbiome platform and data science to advance understanding of and potential treatments for human diseases. We engage in strategic relationships focused in drug discovery, biomarkers and scientific research studies with industry leading biotechnology and pharmaceutical companies and academic institutions. We are continuously exploring strategic relationships related to our approach to microbiome science in our core disease focus areas, including oncology and gastro-intestinal diseases where microbiome science is most advanced. We are also interested in exploring opportunities related to metabolism and neurology. If you are interested in partnering with us, please reach out to us at

Gilead Sciences

Gilead Sciences, Inc. and Second Genome entered into a four-year strategic collaboration to identify biomarkers associated with clinical responses in up to five of Gilead’s pipeline compounds in inflammation, fibrosis and other diseases, and to identify potential new targets and drug candidates for the treatment of inflammatory bowel disease (IBD). Second Genome utilizes its proprietary platform and comprehensive data sets to identify novel biomarkers associated with clinical response to Gilead’s investigational medicines.


Bayer (formerly Monsanto Company) and Second Genome have been working under a research agreement to accelerate the discovery of new microbiome-based solutions to help farmers better manage environmental challenges on their farms. The collaboration has leveraged Bayer’s extensive genomic databases with Second Genome’s expertise in analyzing microbial function through big data metagenomics, protein discovery, machine learning and predictive analytics. Second Genome applied its novel bioinformatics platform to predict and analyze the efficacy of beneficial proteins from the microbiome for agricultural use.

Arena Pharmaceuticals

Arena Pharmaceuticals and Second Genome entered into a strategic collaboration to identify biomarkers associated with clinical response for Arena’s lead program in gastroenterology, etrasimod. The partnership utilizes Second Genome’s proprietary sg-4sight discovery engine to identify microbiome biomarkers associated with clinical benefit or adverse effects observed within data from Arena’s CULTIVATE clinical trial. Arena’s CULTIVATE trial is a Phase 2/3 clinical trial evaluating the efficacy and safety of etrasimod, a next-generation, once-daily, oral, highly selective sphingosine 1-phosphate (S1P) receptor modulator, in patients with moderately-to-severely active Crohn’s disease. This work will help inform patient stratification and optimize potential treatments for patients in the future.

Other Key Partnerships

Second Genome has held various other collaborations spanning applications of its microbiome platform and data science, types of collaborations and length. Collaborations of note have included an alliance with the Alimentary Pharmabiotic Centre (APC) Microbiome Institute at University College Cork (UCC), Ireland, to advance the development of therapies that prevent and treat IBD, and a multi-year collaboration with Stanford University School of Medicine, “Microbiome, Metabolites and the Mind (M3),” through a Fast-Track 1R44 Small Business Innovation Research (SBIR) grant to study the relationship between the human microbiome and autism spectrum disorders (ASDs) as a model to be generalized to other central nervous system diseases, with Second Genome to develop a commercial platform to discover and validate key microbial bioactives that have a potential therapeutic impact on ASDs.