Evaluating supervised and unsupervised background noise correction in human gut microbiome data

Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud

Abstract: Author summary The human gut microbiome is known to play a major role in health and is associated with many diseases including colorectal cancer, obesity, and diabetes. The prediction of host phenotypes and identification of biomarkers of disease is essential for harnessing the therapeutic potential of the microbiome. However, many metagenomic datasets are affected by technical variables that introduce unwanted variation that can confound the ability to predict phenotypes and identify biomarkers. Currently, supervised methods originally designed for gene expression and RNA-seq data are commonly applied to microbiome data for correction of background noise, but they are limited in that they cannot correct for unmeasured sources of variation. Unsupervised approaches address this issue, but current methods are limited because they are ill-equipped to deal with the unique aspects of microbiome data, which is compositional, highly skewed, and sparse. We perform a comparative analysis of the ability of different denoising transformations in combination with supervised correction methods as well as an unsupervised principal component correction approach and find that all correction approaches reduce false positives for biomarker discovery. In the task of predicting phenotypes, different approaches have varying success where the unsupervised correction can improve prediction when technical variables contribute to the majority of variance in the data. As new and larger metagenomic datasets become increasingly available, background noise correction will become essential for generating reproducible microbiome analyses.