Copper-induced microbiota shifts and its effect on pig-gut colonisation by sil and sopE encoding Salmonella

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We will test the hypothesis that copper (Cu)-induced gut microbiota changes in the pig provides a niche exploited by S. Typhimurium ST34 in a sil and sopE gene-dependent mechanism.

The effect on gut bacterial communities of supplementation of pig feed with therapeutic concentrations of Cu will be determined in 120 pigs on a working farm. Piglets will be weaned on a high protein diet supplemented with either 10ppm (nutritional) or 150ppm (therapeutic) Cu and the microbiota defined by metataxonomic analysis using shotgun metagenome sequencing. Computational analysis will be used to identify species and strains that differ in the two feed groups. The role of the sil and sopE genes in colonisation of the pig gut will be determined using an in vitro gut model and experimental infections of pigs. ST34 strains in which sil or sopE or both are deleted will be constructed and assessed for their ability to grow in the presence of in vitro microbiota cultures established from faecal samples collected from pigs on Cu nutritional or Cu therapeutic diets. The same ST34 strains will be tested by experimental infection of pigs from each diet.

Together, these experiments will reveal whether the sil and sopE genes increase colonisation of the pig gut and whether this is dependent on microbiota changes associated with a diet with therapeutic concentrations of copper. Gut microbiota whose composition is altered in response to therapeutic concentrations of copper will be isolated from faecal samples of pigs, and potential direct or indirect agonistic and antagonistic properties assessed by co-culture in vitro or with organic phase extracts of spent media.

In a follow-on study, and through an ongoing collaboration with the Baumler lab (UC Davis), we will test the hypothesis that specific microbiota isolates affect colonisation of Salmonella in the murine model of infection using precision microbiota editing methodology.