Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes

Significance Studies of the microbial communities living in association with animals, with plants, and in the environment have revolutionized our understanding of microbial diversity, but the interactions between these microbes remain largely elusive. Here, we characterize pairwise interactions during infection between a human pathogen and 25 diverse microbes from both sympatric (same) and allopatric (different) environments. We demonstrate that allopatric microbes increase survival of the pathogen. Furthermore, we identify the large set of genes (33% of the genome) that are essential for pathogen survival during coinfection, including a core set that are also required in monoinfection and diverse accessory essential genes. This work advances our understanding of how coinfecting microbes modulate the genes required for survival in vivo.

Recent evidence suggests that the genes an organism needs to survive in an environment drastically differ when alone or in a community. However, it is not known if there are universal functions that enable microbes to persist in a community and if there are functions specific to interactions between microbes native to the same (sympatric) or different (allopatric) environments. Here, we ask how the essential functions of the oral pathogen Aggregatibacter actinomycetemcomitans change during pairwise coinfection in a murine abscess with each of 15 microbes commonly found in the oral cavity and 10 microbes that are not. A. actinomycetemcomitans was more abundant when coinfected with allopatric than with sympatric microbes, and this increased fitness correlated with expanded metabolic capacity of the coinfecting microbes. Using transposon sequencing, we discovered that 33% of the A. actinomycetemcomitans genome is required for coinfection fitness. Fifty-nine “core” genes were required across all coinfections and included genes necessary for aerobic respiration. The core genes were also all required in monoinfection, indicating the essentiality of these genes cannot be alleviated by a coinfecting microbe. Furthermore, coinfection with some microbes, predominately sympatric species, induced the requirement for over 100 new community-dependent essential genes. In contrast, in other coinfections, predominately with nonoral species, A. actinomycetemcomitans required 50 fewer genes than in monoinfection, demonstrating that some allopatric microbes can drastically alleviate gene essentialities. These results expand our understanding of how diverse microbes alter growth and gene essentiality within polymicrobial infections.