Understanding resistome response in a native microbiome using amplicon sequencing

Antimicrobial resistance (AMR) poses a substantial threat to human and environmental health. To understand evolution of AMR within native microbiomes, we used the lung lichen (Lobaria pulmonaria L.) as a model for a defined, native microbiome. Exposure to different types of antimicrobials (colistin, tetracycline, alkylpyrazine, glyphosate) and doses induced general and specific shifts in the microbiome. Bacterial abundances were not affected but we observed changes in the community structure, .g., members of Chthoniobacterales were substituted by fast-growing, more resistant Pseudomonadales. A general functional response, which comprised activation of intrinsic resistance mechanisms (mainly multidrug efflux pumps, ABC transporters) and reduction of bacterial metabolic activity (energy production and conversion, carbohydrate and inorganic ion transport and metabolism), has been deciphered by a holistic multi-omics approach. Together, this can accelerate resistance development as a long-term adaption. Interestingly, non-mobile antibiotic resistance genes (ARGs) showed higher transcriptional response than abundant mobile ARGs. Analyses of metagenome-assembled genomes (MAGs) including Chthoniobacter, Methylobacterium, Granulicella, and Sphingomonas, revealed specific strategies supporting the general mechanisms. Moreover, each antimicrobial resulted in distinct responses, e.g., glyphosate treatment enriched bacterial r-strategists and activated corresponding ARGs. Altogether, the lichen symbiosis showed an extraordinarily high resilience towards antimicrobials driven by rare microbiota and complex functional interplays. The underlying mechanisms of AMR evolution, which include a balanced trade-off for the efficient response and survival after antimicrobial exposure, can be translated to other microbiomes and used to develop AMR management strategies for health issues.