Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation

When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat’s microbiome in the long term if they overcome the habitat’s biotic resilience toward immigration. This process should become more difficult with increasing biodiversity, as exploitable niches are reduced when more diverse competitors are present. Consequently, microbial diversity could provide a natural barrier toward antimicrobial resistance by reducing the persistence time of immigrating ARB and ARGs. To test this hypothesis, a pan-European sampling campaign was performed across rewilded environments of low anthropogenic impact. In soils, higher diversity, evenness, and richness were significantly negatively correlated with the relative abundance of more than 85% of ARGs. Furthermore, the number of detected ARGs per sample was inversely correlated with diversity. However, no such effects were present in more dynamic riverbeds. Hence, microbiome diversity can serve as a barrier toward antimicrobial resistance dissemination in static, structured environments, where long-term, diversity-based resilience against immigration can evolve.

Uli Klümper, Giulia Gionchetta, Elisa Cataó, Xavier Bellanger, Irina Diehlacher, Alan Xavier Elena, Peijun Fang, Sonia Galazka, Agata Goryluk-Salomonowicz, David Kleis, Uchechi Okoroafor, Elena Raud, Mateusz Szadziul, Edina Szekeres, Adela Teban-Man, Cristian Coman, Norbert Kreuzinger, Magdalena Popowska, Julia Virehilig, Fiona Walsh, Markus Woegerbauer, Helmut Bürgmann, Christophe Merlin, Thomas Ulrich Berendonk