Microbiome Engineering
Food & Agriculture Challenge:

Reduce the environmental impacts of food production.

Develop alternative food sources (e.g., alternative meat, eggs, dairy, seafood) with a reduced environmental footprint that compete on taste, price, safety, and accessibility with their conventional counterparts.

Leverage microbiome-based approaches to improve the production efficiency and reduce the cost of ingredients (e.g., flavorings, fatty acids, enzymes) produced through industrial biotech for use in the alternative protein industry.

  • Technical Achievement: Identify plant-based or fermented food ingredients whose biosynthesis entails complex pathways and cannot reasonably be achieved with high efficiency within a single product host.
  • Technical Achievement: Engineer microbial communities that coexist in the appropriate ratios to synthesize ingredients requiring complex pathways with maximal efficiency, such that no community member represents a limiting step in biosynthesis.
  • Technical Achievement: Utilize microbiomes to create novel feedstocks, either for subsequent fermentation or for use in cell culture media for cultivated meat, from complex agricultural or industrial biotechnology residual biomass at low cost.

Engineer modular, diverse microbiomes to improve the functionality of plant-based proteins and reduce the environmental impact of processing for protein-enriched ingredients used in plant-based meat products.

  • Technical Achievement: Identify food-safe microbial strains that express enzymes with functionalizing capabilities for improving the properties of plant-based proteins (e.g., solubility, emulsification, gelling capacity, water- and fat-binding capacity).
  • Technical Achievement: Develop engineered microbial communities that can act simultaneously or sequentially to improve plant protein functionality (e.g., a population with high hydrolysis activity may first be needed to improve solubility, followed by takeover by a population with high crosslinking activity to recapture gelling capacity).
  • Technical Achievement: Develop microbial communities that are optimized to efficiently utilize plant-based substrates for fermentation processes that have historically been used on dairy or meat to endow foods like plant-based cheeses and salamis with complex flavors.

Develop new single-cell protein production platforms that offer optimized nutritional properties, decrease costs, and leverage nonconventional feedstocks (e.g., methanotrophic bacteria, photosynthetic cyanobacteria, green algae).

  • Technical Achievement: Conduct high-throughput screening of a wide array of microbial species to identify a suite of candidates that are suitable as novel protein sources (e.g., devoid of known toxins, low nucleic acid content, high digestibility and protein content, neutral or savory taste).
  • Technical Achievement: Develop stable microbiomes that exhibit balanced amino acid ratios, desirable flavor palettes, and the ability to leverage a diverse array of feedstocks including agricultural or industrial biotechnology sidestreams.
  • Technical Achievement: Utilize metabolic engineering to identify toxic or undesirable metabolites produced by some candidate strains, and screen the candidate library for strains that are able to metabolize those products as carbon sources to convert into usable biomass.
  • Technical Achievement: Engineer communities that are able to collectively combat contamination by undesirable strains (e.g., develop synthetic-lethal systems whereby two strains must coexist in equal ratios to keep each other alive and together synthesize competitor-targeted toxic metabolites when competitive strains disrupt this balance).

Engineer structured meat alternatives composed entirely or almost entirely of microbes.

  • Technical Achievement: Engineer microbiomes for partial conversion of lignocellulosic biomass into human-edible macromolecules (even as precursors for food production), such that the fibrosity of the starting material is maintained while improving palatability and digestibility.
  • Technical Achievement: Identify or engineer microbial communities that can collectively form sophisticated macro-scale structures (i.e., biofilms) that recapitulate the anisotropy of meat, with discrete fibers, structural alignment, and non-heterogeneous regions of soft and firm tissue.

Reduce the environmental impact of animal husbandry.

Reduce reliance on antibiotics for animal growth, weight gain, and health.

  • Technical Achievement: Engineer gut microbiome structure to be resilient to invasion by pathogenic bacteria.
  • Technical Achievement: Engineer microbiomes that grow in animal feed to detect and kill environmentally-occurring animal or human pathogens.
  • Technical Achievement: Control of rumen/hindgut (e.g., cattle, sheep, goats) microbiome structure to optimize volatile fatty acids production that sustains animal growth (VFAs promote growth).
  • Technical Achievement: Engineer microbiomes for increased livestock growth and weight gain without antibiotics (i.e., prebiotic introduction).

Engineer rumen/hindgut-fermenting animal (e.g., cattle, sheep, goat, cow) microbiomes so they release less carbon (e.g., methane).

  • Technical Achievement: Engineer methanotroph-containing microbiomes that stably colonize cattle and livestock after a single inoculation, to reduce methane production.
  • Technical Achievement: Engineer methanogens in rumen microbiomes to continue oxidizing methane into more environmentally friendly compounds (e.g., methanol).
  • Technical Achievement: Engineer microbiomes that secrete small molecules inhibitors to prevent methane production in ruminant guts.

Utilize microbiomes to pretreat animal feed to increase animal feed efficiency

  • Technical Achievement: Engineer microbiomes to synthesize animal nutrients (e.g., essential amino acids, micronutrients, vitamins) not naturally found in unprocessed feed.
  • Technical Achievement: Engineer microbiomes that maintain specific moisture content in hay, haylage, or silage to increase feed production efficiency.
  • Technical Achievement: Engineer microbiomes that rapidly generate and maintain anaerobic environments to prevent rot.

Reduce reliance on chemical fertilizers and pesticides.

Engineer phyllosphere microbiomes to produce pest repellents.

  • Technical Achievement: Design microbiomes that produce compounds that reduce insect herbivory.
  • Technical Achievement: Design microbiomes that inhibit the presence of salicylic acid-producing microbes, which increase insect herbivory.1Costarelli, A., Bianchet, C., Ederli, L., Salerno, G., Piersanti, S., Rebora, M., & Pasqualini, S. (2020). Salicylic acid induced by herbivore feeding antagonizes jasmonic acid mediated plant defenses against insect attack. Plant Signaling & Behavior, 15(1), 1704517. View Publication

Engineer food-safe, nitrogen-fixing microbiomes that decrease or eliminate the need for fertilizers and chemical supplements.

  • Technical Achievement: Develop spatially structured soil microbiomes that have anaerobic nitrogen-fixation fed or driven by aerobic, energy-rich processes, thereby reducing energy inputs and costs of fertilizer production.
  • Technical Achievement: Engineer microbiomes that expand the plant-host range of symbiotic nitrogen-fixing bacteria so they grow in association with more diverse crops (e.g., Rhizobia sp. with non-legume plants).
  • Technical Achievement: Engineer metabolic pathways in root microbiomes to increase nitrogen-fixing activity, especially for crops that do not have naturally occurring nitrogen-fixing microbiomes.
  • Technical Achievement: Engineer microbiomes to form epiphytic interactions with agricultural crops and fix nitrogen above ground.


  1. Costarelli, A., Bianchet, C., Ederli, L., Salerno, G., Piersanti, S., Rebora, M., & Pasqualini, S. (2020). Salicylic acid induced by herbivore feeding antagonizes jasmonic acid mediated plant defenses against insect attack. Plant Signaling & Behavior, 15(1), 1704517. https://doi.org/10.1080/15592324.2019.1704517
Last updated: October 1, 2020 Back