Longitudinal assessment of the influence of lifestyle homogenization on the microbiome in a cohort of United States Air Force Cadets

Abstract Background: Humans spend much of their lives in the built environment, yet researchers are just starting to understand the underlying processes and consequences of the bidirectional exchange of microbial communities among occupants, as well as between occupants and their built environments. The ability to detect these exchanges is not trival, due to several confounding factors that govern the life and habits of the occupants including, for instance, diet as well as ethnic, geographic, and socioeconomic backgrounds, among others. Additionally, studies of the occupants and/or of the built environment need to consider the inherent temporal variability of the microbial communities. Here, we present a study of United States Air Force Academy (USAFA) Cadets (n = 34), in which we examined the bacterial microbiomes from: 1) skin and gut samples among roommate pairs, 2) four built environment samples from inside the pairs' dormitory rooms, and 3) four built environment samples from shared spaces in the dormitory. The Cadets were sampled longitudinally over one semester (5 months), starting after the summer break, when they moved into the dormitory with a roommate they had not lived with previously. Results: After quality filtering, the study contained 2,170 bacterial samples (21,866 unique sub-operational taxonomic units; sOTUs). The bacterial skin microbiome of cohabitating Cadets became more similar over time (ANOSIM, R = 0.231, panosim < 0.002). Linear convergence of skin microbial communities was also seen between the occupants and the dormitory surfaces that were considered individualized to a particular roommate (i.e., desk; ANOSIM R = 0.312, panosim < 0.05). In addition, microbial sharing between two Cadet roommate's skin and the common area (i.e. shared floor space between the two Cadet's beds) was evident (ANOSIM R = 0.406, panosim < 0.03). The gut-to-gut microbiome comparisons of cohabitating Cadets showed convergence overtime, the post-break gut profiles did not show significant change for roommates. Additionally, in squadrons with large shared places, the gut samples did show significant sharing of bacterial microbiomes with bathroom handle samples over the duration of time. Moreover, the gut bacterial microbiome was more predictive of occupant identity than the skin microbiome through random forest models. Conclusions: The shared ecosystem dynamics of this study enabled us to better understand how factors can influence the homogenization of bacterial microbiome of occupants and the built environment. These results show that cohabitation and indoor exposures associated with the built environment can significantly influence our microbiota directly. Whereas skin bacterial microbiome sharing was readily apparent, gut microbiome homogenization appeared to require longer periods of time; thereby suggesting that the latter is a more stable system.