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Lifelines NEXT is a birth cohort designed to study the effects of intrinsic and extrinsic determinants on health and disease in a four-generation design. It is embedded within the Lifelines cohort study, a prospective three-generation population-based cohort study recording the health and health-related aspects of 167,729 individuals living in Northern Netherlands. In Lifelines NEXT we include 1500 pregnant women intensively follow them, their partners and their children until at least 1 year after birth. This repository describes the codes for the microbiome associated projects within Lifelines NEXT including fecal (microbiome and virome), breastmilk microbiome, vaginal mcirobiome and oral microbiome. Here we also integrate mutpliple multi-omic layers including metabolomics, proteomics and extensive phenotypic data