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Conjugative plasmids represent major reservoirs for horizontal transmission of antibiotic resistance and virulence genes. Our knowledge about the ecology and persistence of these plasmids in the gut microbiota remains limited. The IncF plasmids are the most widespread in clinical samples and in healthy humans and the main aim of this work was to study their ecology and association with the developing gut microbiota. Using a longitudinal (2, 10, 30 and 90 days) cohort of full-term infants, we investigated the transmission and persistence of IncFIA and IncFIB plasmids. The prevalence of IncFIB plasmids was higher than IncFIA in the cohort, while IncFIA always co-occurred with IncFIB. However, the relative gene abundance of IncFIA was significantly higher than IncFIB for all time points, indicating that IncFIA may be a higher copy-number plasmid. Through linear discriminant analysis effect size and operational taxonomic unit-level associations, we observed major differences in the abundance of Enterobacteriaceae in samples positive and negative for IncFIB. This association was significant at 2, 10 and 30 days and showed an association with vaginal delivery. From shot-gun analyses, we assembled de novo multi-replicon shared (IncFIA/IncFIB) and integrated (IncFIA/IB) plasmids that were persistent through the dataset. Overall, the study demonstrates the nature of IncF plasmids in complex microbial communities.

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants