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Bacteria-phage-antibiotic interactions in variable environments: a community ecology perspective

Periodic Reporting for period 1 - COEXIST (Bacteria-phage-antibiotic interactions in variable environments: a community ecology perspective)

Reporting period: 2018-07-01 to 2020-06-30

There is increasing awareness that diversity in microbial communities likely plays a critical role in multiple biological processes, from regulating human health to sustaining ecosystem services. Along with advances in molecular technologies, this realisation has seen a rapid growth in efforts to catalogue microbial life, and yet we still have a surprisingly poor understanding of the mechanisms maintaining microbial diversity. The overarching goal of the project was to investigate whether recent theoretical advances in understanding coexistence in non-equilibrium systems can provide insights into microbial diversity exposed to antimicrobials that naturally vary in concentration in space and time. From an applied perspective, understanding the dynamics of bacterial systems is fundamental to the management of infectious diseases. Antimicrobial resistance arising from adaptive evolution in bacterial populations has emerged as one of the single greatest threats to public health in Europe and worldwide. As part of efforts to combat antimicrobial resistance, there is growing awareness that we need to look beyond one-to-one host pathogen relationships and consider the full web of interactions in which pathogenic species are embedded.
During my Marie Sklodowska-Curie Actions fellowship I developed a theoretical framework for partitioning costs of antimicrobial resistance into changes in competitive ability and changes in niche overlap (relative to sensitive strains and other community members), and the effects of antibiotic-resource covariation on the evolution of resistance. I also carried out experimental work verifying theoretical predictions that costs of resistance do indeed affect both competitive ability and niche overlap, which emphasizes the importance of adopting a community-wide perspective on understanding the evolution of resistance. In addition, I carried out a separate experiment investigating the effects of broad versus narrow spectrum antibiotics on competitive release in human gut communities. I found that the strength of competitive suppression was more strongly associated with the identity of the donor community than it was the spectrum of the antibiotic. This result suggests variation in the degree of antibiotic-mediated competitive release is highly contingent on gut microbiome composition.
The work conducted during the fellowship has expanded our ecological understanding of the ecology of antibiotic resistance. This is in line with European policy objectives, and specifically the EU’s action plan on antimicrobial resistance.
Bacterial relative abundance across faecal donors and antibiotic treatments