Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use

Abstract

The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favourable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. We present the first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort. With no prior high-resolution profiling on this population, characterized by high antibiotic consumption, this cohort contributes to understanding microbiome variation in European populations. We report microbiome features consistent with other European populations, including well-defined community configurations, and provide new insights into how these relate to within-phylum diversity. We observe an enrichment of Enterobacteriaceae, a pattern that may be shaped by population-level exposures, including antibiotic use. The analysis of antimicrobial resistance genes, contextualized with data from other cohorts and the European Centre for Disease Prevention and Control, showed an increased prevalence of genes linked to beta-lactams, macrolides, and quinolones--antibiotics commonly used in this population. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify a potential immune-priming role for Collinsella species and a link between the Prevotella enterotype and the cytokine production capacity. ImportanceThis first comprehensive study of the healthy gut microbiome in a Romanian cohort contributes to a baseline for the microbiome and resistome composition of this population. While universally accepted definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such data help contextualise future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes, and the concordance with commonly used antibiotics in the community reinforces the need to address antibiotic use in public health strategies. Although links between the gut microbiome and host immunity are not fully understood, our findings are consistent with a role for microbiome composition in immune-related traits. The association between the Prevotella enterotype and cytokine balance may provide a basis for further investigation of enterotype-specific immune characteristics.