Leveraging metagenomes from the Finnish HELMi birth cohort, a large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 proviral sequences longer than 10kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed in Coriobacteriaceae, Eggerthellaceae, Veillonellaceae and Burkholderiaceae, while a very high prevalence of lysogen MAGs was observed for Oscillospiraceae, Enterococcaceae, Enterobacteriaceae. Interestingly for several bacterial families such as Bifidobacteriaceae and Bacteroidaceae, the prevalence of proviruses in MAGs was higher in early infant time point (3 weeks and 3 months) than in later sampling points (6 and 12 months) and in adults. The proviral sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. This repository contains the fasta files for the MAGs collection and the proviral sequences retrieved in this study.