MOSAIC: A Pipeline for MicrobiOme Studies Analytical Integration and Correction

Large-scale and consortium microbiome studies have enabled identification of reliable population-level biomedical signals, wherein integration is essential to eliminate unwanted variations between batches or studies and retain biological signals. Many strategies, each with distinct advantages and limitations, have been adapted or developed for microbiome data. The optimal strategy for a given study needs to be determined on a data-specific, case-by-case basis. Here, we develop the first-of-its-kind MicrobiOme Studies Analytical Integration and Correction (MOSAIC) pipeline to enable a convenient, fair, and comprehensive comparison of integration strategies. It includes modules for pre-processing, integration, and evaluation of artifact removal and signal preservation, using metrics relevant to common microbiome analyses, including alpha and beta diversities, disease prediction, and differential abundance analysis. We applied MOSAIC to extensive real-world and simulated data and found that though no single strategy excels in all aspects, yet certain strategies, the ComBat and ConQuR families, perform better overall.