Learning functional groups in complex microbiomes

ABSTRACT From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~ 4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology. Abstract Figure Graphical Abstract An integrated ML and experimental pipeline to discover functional groups and their dynamics in complex microbiomes and beyond. (a) First, our Soft Clustering Function Informed (SCiFI) algorithm identifies functional groups directly from species abundances data using neural networks. Crucially, the learned functional groups are informed by a chosen community function. (b) Descriptions of the system in terms of the original high-dimensional abundances of individual species are prohibitively complex (left). By contrast, a description in terms of the few functional groups identified by SCiFI leads to a simple structure-function map (right). (c) Next, the identified groups can be directly input as variables into predictive mathematical models for the dynamics of the community. (d) The last step of our pipeline relies on the identified groups comprising only a small number of species. This sparsity enables targeted experiments that interrogate isolated species (e.g. with whole-genome sequencing or phenotyping) shedding light on the mechanistic underpinnings of the structure-function map with potential applications beyond microbiomes, from gene expression to neuronal activity.