Under the collaboration, Janssen will make an upfront payment and fund research activities concerning the agreement in addition to potential payments on reaching certain research milestones.
The Johnson & Johnson Innovation Center and the Immunology Therapeutic Area within Janssen Research & Development, will fund the research.
Second Genome president and CEO Peter DiLaura said pharmaceutical R&D is now focusing on the role of the microbiome in health and disease.
"This collaboration with Janssen will identify mechanisms by which microbial populations in the gut have an impact in ulcerative colitis," DiLaura added.
Leveraging its microbiome modulation discovery platform, Second Genome will characterize the role of bacterial populations in ulcerative colitis.
In a separate announcement, Second Genome has completed third tranche of $11.5m Series A financing and expansion of board of directors and scientific advisors.