Lifestyle associates with unique resistome and microbiome signatures in children

Antibiotic resistance is a global health crisis that is not solely explained by antibiotics consumption. However, environmental and lifestyle contributions to antimicrobial resistance (AMR) in humans and especially children are not fully understood. As the gut functions as a reservoir for antibiotic resistance genes (ARGs), the aim of this study was to better understand the influence of lifestyle on the gut microbiome and resistome using shotgun-metagenomic sequencing data of Swedish children from the PARSIFAL study. Farm children exhibited high proportions of unique bacterial species and differentially abundant ARGs linked to the farm environment, and similar differences were found in anthroposophic children. Age, breastfeeding duration, and obesity significantly influenced the overall resistance load, independent of lifestyle. Despite limited statistical power, our findings suggest that lifestyle and environment both shape the microbiome and resistome. This study highlights the need for further research on species and ARG transmission from the environment to humans.