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Excited to share our preprint on Directed evolution of microbial communities!! https://www.biorxiv.org/content/10.1101/2020.07.24.214775v2.full.pdf+html
No work can describe how much I enjoyed working with co-first @Oxfordvila and @asanchez_lab!!
No work can describe how much I enjoyed working with co-first @Oxfordvila and @asanchez_lab!!
Great thanks to Sanchez lab members Juan, @sylvieestrela @mrebolleda @MaddieOBender It has been a wonderful experience with you all to push this out! Also many thanks to PBoC and Microbial EBB students/coauthors who have helped shaped the early stage of this project!!
How do we engineer the functions of microbial communities toward our interest? We seek to address this question from a top-down approach, aka artificial microbiome selection. 1/11
By selecting a set of microbial communities with varied functions that are heritable, in principle we can select for those with high desired function (like breeding a strain of dog with traits that humans like). How do we design a selection protocol? 2/11
In the early stage of project, we got the students in PBoC course at Woods Hole to design the selection protocols and test it using community-simulator ( https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230430). As the protocol scale getting bigger, we need a way to manage the protocols in high throughput. 3/11
So we developed a python package Ecoprospector (based on community-simulator) that allows us to probe any arbitrary set of parameters of selection protocols. 4/11
Inspired by using directed evolution of biomolecules to navigate fitness landscape, we considered directed evolution of microbial communities as navigating in an "ecological structure-function landscape" that maps the community composition to its function. 5/11
Directed evolution of microbial communities is basically searching for stable high-functioning communities in steps: 1) stabilize 2) select and replicate the best community 3) keep one copy intact and perturb the rest. Repeat from step1. 6/11
How to perturb a community? You can either remove or add species, single one or in bulk. In all cases we successfully improve the Fmax (the best of 96 communities in a selection line), relative to no-selection control. 7/11
Bottleneck works by eliminating deleterious species whereas migration brings in new species beneficial to community function. If both combined, we hypothesize that such method can do better than either one alone. 8/11
And indeed, a protocol that iteratively implementing directed evolution of two perturbations combined results in a highly performing community. 9/11
Moreover, this Directed Evolved community is also highly resistant to external invasion, a trait that is not intentionally selected for. As recurrent migration is part of the iterative protocol, DE community is naturally robust to such perturbation. 10/11
In sum, directed evolution of microbial communities can act as a guided way to navigate the ecological structure-function landscape, in search of highly performing and ecological resistant communities. 11/11
