Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions.

Abstract

Motivation: Extensive research has uncovered the critical role of the human gut microbiome in various aspects of health, including metabolism, nutrition, physiology, and immune function. Fecal microbiota is often used as a proxy for understanding the gut microbiome, but it represents an aggregate view, overlooking spatial variations across different gastrointestinal (GI) locations. Emerging studies with spatial microbiome data collected from specific GI regions offer a unique opportunity to better understand the spatial composition of the stool microbiome.

Results: We introduce Micro-DeMix, a mixture beta-multinomial model that deconvolutes the fecal microbiome at the compositional level by integrating stool samples with spatial microbiome data. Micro-DeMix facilitates the comparison of microbial compositions across different GI regions within the stool microbiome through a hypothesis-testing framework. We demonstrate the effectiveness and efficiency of Micro-DeMix using multiple simulated data sets and the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project.

Availability and implementation: The R package is available at https://github.com/liuruoqian/MicroDemix.

Supplementary information: Supplementary data are available at Bioinformatics online.