Additional file 2 of Integrative clustering by colonic volatile fatty acids reveals microbiota and host physiological variation in weaned piglets

Additional file 2: Fig. S1. Batch effect correction of 16S rRNA sequencing data from mid-colon digesta samples of weaned piglets. A total of 164 samples were sequenced in three independent batches: batch1 (lib487; n = 54), batch2 (lib589; n = 78), and batch3 (lib696; n = 32). The conditional quantile regression (ConQuR) method was applied to correct for batch effects. (a) Principal coordinate analysis (PCoA) plots based on Bray-Curtis distance showing community structure before and after correction with the ConQuR method. (b) The effectiveness of batch correction was assessed by comparing PERMANOVA R² values for the batch and key factors before and after correction. 1“Standard” refers to the default Bray-Curtis distance, “sqrt” to Bray-Curtis with sqrt.dist = TRUE, and “add” to the sequential model fitting option (add = TRUE). Batch correction substantially reduced the variance explained by the batch factor while retaining the biological variation attributable to the key factor.