Occupational and environmental livestock exposures are associated with alterations in the upper respiratory tract microbiome

Abstract

Livestock farm emissions have been linked to respiratory health, potentially mediated through alterations in the respiratory microbiota. We investigated the associations between occupational and environmental livestock farm exposures and changes in the upper respiratory tract (URT) microbiome. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from goat farmers (91 NP and 96 OP samples) and rural residents (956 NP and 954 OP samples), and microbial community composition was characterised using 16S rRNA gene amplicon sequencing. First, we compared the respiratory microbiome of goat farmers and residents to assess the effects of occupational exposure. Next, we evaluated how varying levels of environmental livestock exposure influenced the microbiome of rural residents. Goat farmers exhibited higher NP microbial diversity but lower OP diversity compared to the residents. NP samples from farmers had higher relative abundances of the genera Sphingomonas, Pseudomonas and Jeotgalicoccus, and lower abundances of Corynebacterium, Lawsonella and Nocardioides. In the OP of goat farmers, Rothia was the most significantly increased genus. Residential exposure levels - assessed through livestock density (pigs, cattle, poultry, and goats) and modelled livestock-related microbial emissions - were not associated with overall microbiome diversity or composition. However, increasing livestock exposure was associated with subtle taxonomic shifts, particularly in the NP. Our findings highlight the pronounced influence of occupational exposure on the URT microbiome and the more subtle effects of environmental exposure, both of which may have implications for respiratory health.