Lifestyle associates with unique resistome and microbiome signatures in children

TL;DR

This study shows that lifestyle and environment influence the gut microbiome and antibiotic resistance in children, with farm and anthroposophic lifestyles leading to unique microbial and resistance profiles.

Contribution

The study reveals how lifestyle factors shape the gut resistome and microbiome in children, highlighting the role of the farm environment and breastfeeding.

Findings

Farm children had unique bacterial species and ARGs linked to their environment.

Age, breastfeeding duration, and obesity significantly influenced resistance load.

The study highlights the need for further research on rare microbes and ARGs in relation to the environment.

Abstract

Antibiotic resistance is a global health crisis that is not solely explained by antibiotics usage. However, environmental and lifestyle contributions to antimicrobial resistance (AMR) in children are not well understood, especially compared to adults. 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 (Prevention of Allergy Risk factors for Sensitization In children related to Farming and Anthroposophic Lifestyle) 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, independently of lifestyle. Despite limited statistical power, our findings suggest that lifestyle and environment both shape the microbiome and resistome of children.

This study corroborates the possible influence of the farm environment on the gut microbiome and resistome, revealing a highly individualized repertoire of low-abundance microbes and ARGs in farm children. Additionally, associations of age, obesity and the duration of exclusive breastfeeding with ARG load were found in a currently understudied age range. Overall, this study raises the need for further research on rare species and ARGs as well as their transmission dynamics in relation to the environment.

The online version contains supplementary material available at 10.1186/s12866-025-04665-2.

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