Taro: Tree-Aggregated Factor Regression for Microbiome Data Integration

Authors

Aditya K Mishra
Iqbal Mahmud
Philip L Lorenzi
Robert R Jenq
Jennifer A Wargo
Nadim J Ajami
Christine B Peterson

Publication Date

6-3-2024

Journal

Bioinformatics

Abstract

MOTIVATION: Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns.

RESULTS: We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the taxonomic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances.

AVAILABILITY AND IMPLEMENTATION: The R package TARO implementing the proposed methods is available online at https://github.com/amishra-stats/taro-package.

Keywords

Humans, Microbiota, Software, Metabolomics, Colorectal Neoplasms, Gastrointestinal Microbiome, Algorithms

Comments

Supplementary Materials

PMID: 38788190