Strain displacement in microbiomes via ecological competition

Microbes commonly live in diverse communities where changes in composition can be critical for health, industry and the environment. Yet, what enables one strain to competitively replace another in these complex conditions remains poorly understood. Here, we develop a general ecological model, which reveals general principles of strain displacement. Ecological invasion rests upon weak resource competition while displacement rests upon strong interference competition e.g. via bacteriocin production. We test these predictions by genetically-engineering Escherichia coli to manipulate both resource and interference competition. We then use our ecological principles to identify strains that out-compete multidrug-resistant clinical isolates via a combination of low resource, but high interference, competition. Experiments with diverse human gut symbionts reveal that displacement also relies on low resource competition with the broader community (low ‘nutrient blocking’). Our work establishes general rules for ecological success in microbiomes and suggests ways to perform targeted displacement of problematic bacteria.