Batch effects between healthy controls from different studies can be reduced by ComBat and percentile-normalization.

<p>Non-metric multidimensional scaling (NMDS) plot showing the distribution of healthy controls from three colorectal cancer studies in ordination space (Bray-Curtis distances of relative abundance OTU-level data). Despite standardized bioinformatic processing, healthy patients differed significantly in their gut microbiomes across studies (PERMANOVA p < 0.001; batch accounts for 6.342% of the total variance). Studies were still significantly different after applying ComBat, an established batch-correction method (PERMANOVA p < 0.01). However, percentile-normalization did a better job of stabilizing the variance across studies and removed any apparent batch effect (PERMANOVA p > 0.5).