The microbiome encompasses the complex microbial ecosystems associated with plants, animals, soils, and virtually every environment on Earth. Advances in DNA sequencing and metagenomics have revealed the extraordinary diversity and functional importance of these communities, driving a wave of companies seeking to harness or engineer microbiomes for beneficial purposes. In agriculture, the soil and plant-associated microbiome influences nutrient availability, disease resistance, stress tolerance, and crop yield, representing a vast untapped resource for sustainable intensification.
Agricultural microbiome companies have attracted significant investment. Pivot Bio engineers nitrogen-fixing bacteria for cereal crops, while Indigo Agriculture identifies and deploys beneficial plant-associated microbes as seed treatments. Biome Makers uses DNA sequencing to characterize soil microbiomes and provide actionable recommendations for farmers. Ginkgo Bioworks entered the agricultural microbiome space through its acquisition of Joyn Bio's technology assets, applying its biofoundry platform to engineer crop-associated microorganisms with enhanced beneficial functions.
In human health, microbiome engineering is emerging as a therapeutic approach. Companies like Synlogic engineered bacteria with synthetic gene circuits for therapeutic applications in the gut, while Seres Therapeutics developed a microbiome-based therapy (VOWST) approved for preventing recurrence of Clostridioides difficile infection. The integration of synthetic biology tools with microbiome science is enabling increasingly precise manipulation of microbial communities, from rational design of engineered probiotics to community-level engineering approaches that reshape the composition and function of complex microbial ecosystems.