Data-driven prediction of colonization outcomes for complex microbial communities

Abstract

Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.

A systematic discussion and comparison of the construction methods of synthetic microbial community

“…While these tools have demonstrated efficacy in the biomedical domain, particularly in the discovery of new antibiotics, their application in the assembly of synthetic microbial community remains underexplored. Machine learning and AI are critical for forecasting the construction of microbiome-driven synthetic community, offering the promise of advancing the field to unprecedented level [ 62 , [111] , [112] , [113] ]. 3) Shifting from a microbial portfolio to a synbiotic portfolio, composed of core functional microorganisms (probiotics) and their beneficial host metabolites (prebiotics) [ 114 ], may enable synthetic microbial community to overcome fluctuations in seasonal environments and soil microbial communities.…”