Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometries

The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, while P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in microfluidic microchambers that mimic the spatial characteristics of alveoli. In these microenvironments, slowly growing C. albicans is able to leverage fast eccentric hyphal growth to conquer boundary spaces, where it establishes itself excluding the other pathogens. We show that the emerging spatial patterning is robust to changes in the virulence of the community, enabling coexistence and potentially determining infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure is a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.