Influence of pig farming on the human's nasal microbiota: The key role of the airborne microbial communities.

Kraemer, Julia G; Ramette, Alban; Aebi, Suzanne; Oppliger, Anne; Hilty, Markus (2018). Influence of pig farming on the human's nasal microbiota: The key role of the airborne microbial communities. Applied and environmental microbiology, 84(6) American Society for Microbiology 10.1128/AEM.02470-17

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It has been hypothesized that the environment can influence the composition of the nasal microbiota. However, the direct influence of pig farming on the anterior and posterior nasal microbiota is unknown. Using a cross-sectional design, pig farms (n=28) were visited in 2014-2015 and nasal swabs from 43 pig farmers and 56 pigs as well as 27 air samples taken in the vicinity of pig enclosure were collected. As controls, nasal swabs from 17 cow farmers and 26 non-animal exposed individuals were also included. Analyses of the microbiota were performed based on 16S rRNA amplicon sequencing and the DADA2 pipeline to define sequence variants (SVs). We found that pig farming is strongly associated with specific microbial signatures (including alpha- and beta-diversity), which are reflected in the microbiota of the human nose. Furthermore, the microbial communities were more similar within the same farm as compared to between the different farms, indicating a specific microbiota pattern for each pig farm. In total, there were 82 SVs that occurred significantly more abundantly in samples from pig farms than from cow farmers and non-exposed (i.e. the core pig farm microbiota). Of those, nine SVs were significantly associated with the posterior part of the humans' nose. The results strongly indicate that pig farming is associated with a distinct human nose microbiota. Finally, the community structures derived by the DADA2 pipeline showed an excellent agreement with the outputs of the mothur pipeline which was revealed by procrustes analyses.Importance The knowledge about the influence of animal keeping on the human microbiome is important. Previous research shows that pets are significantly affecting the microbial communities of humans. However, the effect of animal farming on the human microbiome is less clear although it is known that the air in farms, and in particular pig farms, is charged with high amounts of dust, bacteria and fungi. In this study we have simultaneously investigated the nasal microbiota of pigs, humans and the environment in pig farms. We reveal an enormous impact of pig farming on the human nasal microbiota which is far more pronounced as compared to cow farming. In addition, we have analyzed the airborne microbiota and found significant associations suggesting an animal-human transmission of the microbiota within pig farms. We also reveal that microbial patterns are farm-specific suggesting that the environment influences animals and humans in a similar manner.

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