In order to understand the contribution of specific microbes to vaccine efficacy and immune response, we have developed discrete microbial consortia to manipulate vaccine responses in gnotobiotic mouse models. By reconstituting gnotobiotic mice with single microbes and microbial consortia prior to vaccinating mice, we can causally define the effects of microbes on mouse innate and adaptive immune responses.
Additionally we are interested in characterizing the in vitro dynamics of these consortia. We are comparing growth dynamics between single- and co-cultures, as well as microbial products and functions over time.
Using 16S and shotgun metagenomics sequencing of samples collected from vaccine clinical trial subjects before, during, and after vaccination, we are assessing the relationship between the microbiome and vaccine efficacy and immunogenicity. We are evaluating whether microbial community composition and function prior to vaccination contributes to clinical and immunological outcomes, as well as how the microbiome changes due to vaccination, in a number of HIV, TB, and malaria clinical trial cohorts.