| Summary: | <p>The mammalian gut is home to hundreds of species of microbes, collectively known as the gut microbiome. A key benefit conferred by the gut microbiome is protection against pathogens, known as colonisation resistance. The importance of colonisation resistance by the microbiome has been recognised for decades. A range of potential mechanisms underlying the protection against pathogens have been identified, including direct competition between the resident microbiota and pathogens. But when I started my research for this thesis, understanding how they work was restricted to specific communities and contexts and we lacked the ability to understand why one microbial community is protective while another is not. In this thesis I take an ecological approach to the human microbiota to seek general rules of colonisation resistance and discover two key ecological principles and the mechanism that underlies them.</p>
<p>I begin with an <em>in vitro</em> screen of 100 human gut strains to assess their individual ability to resist the growth of a critically antimicrobial-resistant model pathogen, <em>Klebsiella pneumoniae</em>. This screen shows that single species have negligible effects on pathogen growth. Next, I combine the best-ranked species from the screen and find that, together, colonisation resistance ability is greatly increased. To explore this community effect further, I randomly assemble gut communities of varying diversity and composition. Testing these communities against <em>K. pneumoniae</em> reveals that, in general, more diverse communities provide better colonisation resistance against the pathogen. A closer look at the data shows it is the communities that are both diverse and contain the competitor species <em>Escherichia coli</em> that have the greatest ability to suppress <em>K. pneumoniae</em> growth. Along with dropout experiments, where diverse communities are constructed without <em>E. coli</em>, it is deduced that species richness and community composition are both important for colonisation resistance. Diverse communities that do not contain <em>E. coli</em> are much less effective at resisting pathogen growth than those that do. The first general ecological principle of colonisation resistant communities is, therefore, the presence of a key competitor species closely related to the pathogen, such as <em>E. coli</em>. However, <em>E. coli</em> also needs to be part of a community of other gut species in order to exert strong suppression on <em>K. pneumoniae</em> growth. It follows that the second general principle of colonisation resistance is having an ecologically diverse community. To find out if these results apply in a more spatially complex host environment, I test the communities using a gnotobiotic mouse model. <em>In vivo</em>, I discover that I am able to reproduce the <em>in vitro</em> results.</p>
<p>Next, I turn to identifying the mechanism that underlies these two ecological principles. Comparing the nutrient use profiles of the communities and <em>K. pneumoniae</em> shows that the higher the nutrient use overlap is between a community and the pathogen, the greater the ability of the community to resist pathogen growth. This ability of a microbial community to resist pathogen growth by using the available nutrients is termed nutrient blocking. Supplementing the communities with a nutrient unique to <em>K. pneumoniae</em> removes suppression of pathogen growth, supporting the finding that nutrient blocking is the basis for colonisation resistance in these communities. Moreover, it is shown that predictions based on nutrient use or protein family overlap between gut communities and another pathogen, a clinical isolate of <em>E. coli</em>, can be made and experimentally validated. The ability to predict which combinations of gut bacteria will best suppress pathogen growth suggests a way to rationally design pathogen-protective communities ahead of time. I discuss the implications of my work for the current goal to engineer gut communities to prevent and treat infectious disease as a much-needed alternative to antibiotics.</p>
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