Extension of PERMANOVA to Testing the Mediation Effect of the Microbiome

Abstract

AbstractBackgroundRecently, we have seen a growing volume of evidence linking the microbiome and human diseases or clinical outcomes, as well as evidence linking the microbiome and environmental exposures. Now comes the time to assess whether the microbiome mediated the effects of the exposures on the outcomes, which will enable researchers to develop interventions to modulate the outcomes by modifying the microbiome composition. Use of distance matrices is a popular approach to analyzing complex microbiome data that are high-dimensional, sparse, and compositional. However, the existing distance-based methods for mediation analysis of microbiome data, MedTest and MODIMA, only work well in limited scenarios.ResultsPERMANOVA is currently the most commonly used distance-based method for testing microbiome associations. Using the idea of inverse regression, here we extend PER-MANOVA to testing microbiome mediation effects by including both the exposure and the outcome as covariates and basing the test on the product of their F-statistics. This extension of PERMANOVA, which we call PERMANOVA-med, naturally inherits all the flexible features of PERMANOVA, e.g., allowing adjustment of confounders, accommodating continuous, binary, and multivariate exposure and outcome variables including survival outcomes, and providing an omnibus test that combines the results from analyzing multiple distance matrices. Our extensive simulations indicated that PERMANOVA-med always controlled the type I error and had compelling power over MedTest and MODIMA. Frequently, MedTest had diminished power and MODIMA had inflated type I error. Using real data on melanoma immunotherapy response, we demonstrated the wide applicability of PERMANOVA-med through 16 different mediation analyses, only 6 of which could be performed by MedTest and 4 by MODIMA.Availability and ImplementationPERMANOVA-med has been added to the existing function “permanovaFL” in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.