Microbiome diversity protects against pathogens by nutrient blocking
Résumé
The human gut microbiome plays an important role in resisting colonisation of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonisation of two major bacterial pathogens, both in vitro and in gnotobiotic mice. While single species alone had negligible effects, colonisation resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explain these ecological patterns via the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Further, we apply our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities.
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