Learning beyond-pairwise interactions enables the bottom–up prediction of microbial community structure


Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e., the change of pairwise relationships in the community context, may lead to substantial deviation from reality. Herein, we have proposed a simple framework that incorporates higher-order interactions into a bottom–up prediction of the microbial community assembly and examined its accuracy using a seven-member synthetic bacterial community on a host plant, duckweed. Although the synthetic community exhibited emergent properties that cannot be predicted from pairwise coculturing results, our results demonstrated that incorporating information from three-member combinations allows the acceptable prediction of the community structure and actual interaction forces within it. This reflects that the occurrence of higher-order effects follows consistent patterns, which can be predicted even from trio combinations, the smallest unit of higher-order interactions. These results highlight the possibility of predicting, explaining, and understanding the microbial community structure from the bottom–up by learning interspecies interactions from simple beyond-pairwise combinations.
*This text is adapted from the following paper.

Paper Information


Proceedings of the National Academy of Sciences of the United States of America


Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure




Hidehiro Ishizawa, Yosuke Tashiro, Daisuke Inoue, Michihiko Ike, Hiroyuki Futamata


February 5, 2024


Hidehiro Ishizawa
Graduate School of Engineering
University of Hyogo


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