Correlation analysis of multi-omics techniques suggest that betaine intervention could cause significant correlations between certain gut microbiota (e.g., Lactobacillus, Ruminococcus), certain lipid species (e.g., DHA-TG, DHA-PE), genes and pathways involving glycerophospholipid synthesis and lipid metabolism, and gastrointestinal hormones (e.g., CCK, PYY), which may be specific biomarkers of betaine to reduce HFD-induced obesity. Here, PYY is linked to obesity due to melanocortin 4 receptor deficiency.