Agriculture + Microbiome

A panel discussion on the intersection of the microbiome and agriculture from five leading agricultural microbiome companies.

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On August 8th the SF Microbiome Meetup hosted a discussion at Illumina Accelerator on the agricultural microbiome. The following are notes and highlights from the panel discussion.




  • Definition: Microbiome from the perspective of interaction with environment. This ranges from waste water treatment to plant seed coatings. The analysis of microbiome structure and resilience.

Needs identification

  • Unmet needs: A lot of unmet need for soil disease, low regulatory hurdles from the USDA. There is a lot of interest in food be it from a perspective of climate change to the impact of metal bromide.
  • Crop identification: working with clients (e.g., Monsanto) to understand their needs (e.g., corn insect pests). Let the market drive our science selection. Finding large market crops - corn, soybeans, wheat, sorghum -, and testing technologies for them. Another instance is starting with the farmers - listening to their concerns (e.g., fungal overgrowth).
  • Farmers: They do get it. It’s about taking the time to explain. Data is intuitive. As soon as they get it, they are excited. They walk the field everyday; they want to understand it. It helps to have people who have experience on team. Conversation is quite simple: how much does it cost and what do I get in return?
  • Animal agriculture: Animal agriculture is much less explored and underserved with regard to the microbiome.

Regulatory environment

  • Animal agriculture: Inhumane not to provide antibiotics when an animal is in need. The microbiome presents possible solutions before an antibiotic is required. Naturally occurring microbes can be used.
  • Management in the field: Can predict the microbial community response to something. First principle is “do no harm.” You can give supplements. Difficult to get microbe to persist, especially for a very stable microbial community. The issues are necessarily around worrying about unleashing the probiotic into the wild, but at this point more concerned about getting the probiotic to stay alive in the wild.

Research gaps

  • Central database: There is a lack of a central database to curate “baseline” microbes present in certain areas.
  • Community diversity: Soil communities are very diverse and difficult to compare – the large diversity makes it much more challenging.

Intellectual property

  • Mix and process: You can protect the use of microbes and the mix.  Bioconsortia has patent on the process.
  • Formulation: Formulation, e.g. shelf stabilization.

The future

  • Bioconsortia - Experimental system.  Taking to the field to understand what establishes a “good” microbiome.  We need a technique to track microbes and look for low abundant strains that might be important.
  • Trace Genomics - Two-way communication between farmers and scientists. Farmers have wealth of knowledge in farming practices and operation.
  • Boost Biomes - Key focus for them is about reducing food waste.  Lots of waste come from microbes.
  • Second Genome - applying their platform to understand “dark matter.”
  • Resilient Biotics - Build great first database for the respiratory illness in cow. Testing in vitro assay to predict. A lot to be explored there.

Special thanks to the panelists, Illumina Accelerator, and the SF Microbiome Meetup team! 

George Roche

Founder, Revital Biome

Working at the intersection of food, biotech, and entrepreneurship. Focused on everything microbiome.