Bayesian compositional regression with flexible microbiome feature aggregation and selection

TL;DR

This paper introduces BRACElet, a Bayesian compositional regression method that uses a Dirichlet process to cluster microbiome features, improving variable selection and interpretation in high-dimensional, sparse, compositional data.

Contribution

The paper presents a novel Bayesian regression approach that adaptively clusters microbiome features to enhance variable selection and interpretability in compositional data analysis.

Findings

BRACElet outperforms existing methods in simulations

It effectively identifies functionally related taxa

Application reveals microbiome's impact on insulin resistance

Abstract

Ongoing advances in microbiome profiling have allowed unprecedented insights into the molecular activities of microbial communities. This has fueled a strong scientific interest in understanding the critical role the microbiome plays in governing human health, by identifying microbial features associated with clinical outcomes of interest. Several aspects of microbiome data limit the applicability of existing variable selection approaches. In particular, microbiome data are high-dimensional, extremely sparse, and compositional. Importantly, many of the observed features, although categorized as different taxa, may play related functional roles. To address these challenges, we propose a novel compositional regression approach that leverages the data-adaptive clustering and variable selection properties of the spiked Dirichlet process to identify taxa that exhibit similar functional roles. Our proposed method, Bayesian Regression with Agglomerated Compositional Effects using a dirichLET process (BRACElet), enables the identification of a sparse set of features with shared impacts on the outcome, facilitating dimension reduction and model interpretation. We demonstrate that BRACElet outperforms existing approaches for microbiome variable selection through simulation studies and an application elucidating the impact of oral microbiome composition on insulin resistance.