4.8. Metagenomics—Metabolomics Data Integration
Metabolites are significantly different between control and HMO at V3 or V6, and bile acid ratios affected by HMO supplementation over time were selected (Interdomain correlation between KO and metabolite abundances: The analysis was based on all V3 and V6 samples from EE infants with available metagenomic and metabolomic information (Association between metabolites/KOs and HMO treatment: For the V3 and V6 visits separately, each of the 16 metabolites and 17 KOs was compared between HMO-treatment groups (control vs. test) with two-sided Mann–Whitney U tests and Cliff’s delta as effect size. Each comparison was based on all available samples from EE infants for the given visit (i.e., KO comparisons included samples without matching metabolomic information). The Benjamini–Hochberg procedure was used to control the false discovery rate at 10% for each visit individually.Association between metabolites/KOs and FCT clusters: For the V3 and V6 visits separately, each of the 16 metabolites and 17 KOs was tested for association with progressive FCT cluster distribution with Kendall correlation, where the FCT clusters were encoded as ordered factors, with FCT1 = 1, FCT2 = 2, and so on. Each comparison was based on all available samples from EE infants for the given visit (i.e., KO comparisons included samples without matching metabolomic information). The Benjamini–Hochberg procedure was used to control the false discovery rate at 10% for each visit individually.