The biogeography of polymicrobial infection

Abstract

Bacteria usually cause human infections as multispecies communities. These communities often spatially organize into surface-attached structures known as biofilms. Within biofilms, bacteria interact by exchanging metabolites and competing for nutrients, such as carbon and iron sources. These interactions can result in synergy, or enhanced bacterial persistence. Despite its clinical relevance, we lack approaches for understanding synergy. One of the most prevalent polymicrobial infections is periodontitis, or severe gum inflammation. This condition leads to tooth loss, and the associated bacteria also cause life-threatening abscesses. The most abundant bacteria in the oral cavity are streptococci. Streptococci release high amounts of lactate and peroxide as waste. Previously we showed that Streptococcus gordonii (Sg) enhances the persistence of the periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa) in murine abscesses. Aa prefers lactate as a carbon source, and cross-feeding by Aa on lactate made by Sg is critical for synergy in abscesses. Unclear from these studies was how Aa simultaneously tolerates peroxide, an antimicrobial, in the abscess. Furthermore, Aa can only catabolize lactate if oxygen is available, but abscesses are generally considered anaerobic. Through 3D spatial analysis of abscesses, I showed that Aa senses peroxide to localize to a 4-13 μm distance from Sg, where it can presumably cross-feed on lactate but avoid peroxide. I then applied high-throughput genomic approaches to study Aa synergy with Sg. Through transposon mutant fitness profiling (Tn-seq) on Aa in abscesses, I showed that Sg enhances oxygen availability, shifting Aa from a low- to high-energy metabolism where it can cross-feed on lactate. Through RNA-seq and chromatin immunoprecipitation followed by sequencing (ChIP-seq) on the Aa Ferric uptake regulator (Fur), I showed that in mono-abscesses Aa can access iron, an essential nutrient often sequestered by the host, but in co-culture abscesses Sg reduces iron availability. Furthermore, I showed that in human oral infections, the shift to disease also reduces Aa iron availability. Together, these studies reveal novel interactions that underlie synergy in model and human polymicrobial infections.