Colonisation of the human gut begins around birth. The gut microbiome is subsequently shaped during the first years of life and reaches its mature state at the age of three, when its composition and diversity resemble the adult gut microbiome. Early gut microbiome development can influence health outcomes later in life. Multiple factors have been identified to influence early development of the gut microbiome, including gestational age, mode of delivery, feeding methods, genetics, maternal microbiota (gut & vaginal) and antibiotic usage. Here, we provide an overview of the recent advances in understanding the early development of the gut microbiome. We introduce Lifelines-NEXT, a prospective birth cohort in the Northern Netherlands consisting of ~1,500 pregnant mothers, their new-borns and partners. Extensive sample collection starts at 12 weeks of gestation until at least one year after birth. Various biomaterials like blood, faeces, placental biopsies and breast milk are collected at multiple time points. Data on environmental, social and medical factors are collected using questionnaires at 14 time points. Making use of this cohort, we aim to understand the impact of maternal and environmental factors, breast milk composition and infant gut virome on the development of the gut microbiome.