Indoor environmental conditions correlate with the microbial landscape of food production facilities across space and time.

The microbial communities inhabiting food production environments are distinguished from those of other built environments in their capacity to influence food quality and safety, impacting consumer health. However, the degree to which indoor environmental conditions influence the composition of the bacterial and fungal communities throughout food production facilities remains insufficiently explored. In this study of five commercial food production facilities, we employed remote wireless sensors paired with marker-gene amplicon sequencing (bacterial 16S rRNA genes and fungal internal transcribed spacer sequences) of processing equipment and non-processing built environment surfaces (N = 2329) to profile spatial and longitudinal changes in bacterial and fungal communities, and their association with indoor climate. Indoor sensor data only explained a small proportion of overall variance in microbiota composition, suggesting that other latent and stochastic factors predominate. Nevertheless, we identify multiple associations between indoor environmental conditions and microbial community structure, including CO2 levels with overall microbial diversity in creameries, and higher temperature and relative humidity with lower bacterial diversity in wineries, demonstrating the possible role of the indoor environment in shaping microbial communities on food processing and non-processing surfaces. This highlights indoor climate as a modifiable factor for manipulating microbial surface communities to enhance food quality and safety.