Bottleneck/Challenge: Need data from diverse ecosystems, environments to build predictive models.
Potential Solution: Generate and include data from many environments so that models can integrate information with respect to the community, including major functions and surrounding ecosystem.
Bottleneck/Challenge: Ability to selectively remove species from a biome.
Potential Solution: Targeted anti-microbials.
Bottleneck/Challenge: Need to be able to undertake modeling and comparative pathway analysis to determine most robust, prioritized, and resilient systems.
Potential Solution: Controlled laboratory experiments or observational studies where microbiome function is determined as a function of community composition and environment.
Potential Solution: Machine learning approaches to determine whether there are patterns between microbiomes of interest (with respect to both form and function); follow-up with strategies designed to improve mechanistic understanding, as needed.
Biome/consortia modifications include: 1) adding functions such as the ability to sense the environment and coordinate responses for defined outcomes (pathogen defense, substrate transformation, and biosensing), and 2) manipulating composition of host-associated communities to address dysbiosis or add new functions.
Bottleneck/Challenge: Need controlled invasion of non-native organism with desired properties or the ability to reintroduce a host-associated organism after engineering.
Potential Solution: In situ gene editing to add function to a community with minimal disruption.
Bottleneck/Challenge: Ability to selectively add and remove community members, including engineered cells, and have them persist in a community for a desired length of time and at a desired population density.
Potential Solution: Kill switches (to remove organisms), auxotrophy/complementation and shared metabolisms (to retain organisms).
Bottleneck/Challenge: Need an integrated understanding of microbial community ecology and function; ability to predict how adding a new member with desired functions will affect community health and stability.
Potential Solution: Focus on developing organisms that can integrate into host consortia and deliver the required functions; recent evidence suggests that function is more important that what organism is carrying it out.