Production Phase Affects the Bioaerosol Microbial Composition and Functional Potential in Swine Confinement Buildings

Simple Summary In the present study, air samples from different types of swine confinement buildings (SCBs), which exclusively housed weaning piglets (WP), finishing pigs (FP), farrowing sows (FS), gestating sows (GS), and breeding boars (BB), respectively, were used to study the effects of the production phase on the taxonomical composition and functional potential of microbial communities in the SCBs bioaerosols (airborne particles that are biological in origin). Whole metagenome shotgun sequencing, which is the untargeted ('shotgun') sequencing of all microbial genomes ('metagenome') present in a sample, was adopted to profile the bioaerosol microbiome (full collection of genes of all the microbes in a community). The results showed that bioaerosol microbiome of BB shared a high similarity with GS, and WP bioaerosol microbiome was more similar to FP than other types of SCBs. The findings of this study suggested that the production phase of pigs contributes to the variations of SCBs bioaerosol microbiome. Bioaerosols from swine confinement buildings (SCBs) pose a challenge to public health, and microorganisms within the SCBs bioaerosols originate from swine feces, of which the microbial composition is associated with the production phase. The present study adopted the whole metagenome shotgun sequencing approach, to assess the effects of the production phase on the composition and functional potential of microbial populations in SCBs bioaerosols. Most annotated proteins were assigned into domain bacteria, within which the predominant phylum was Firmicutes. The taxonomical profiles of bioaerosols from different types of piggeries showed that buildings housing weaning piglets (WP) exhibited higher abundances of Bacteroidetes and Proteobacteria than buildings housing finishing pigs (FP), gestating sows (GS), farrowing sows (FS), and breeding boars (BB). Regarding the functional potential, the WP bioaerosol had more genes involved in the protein turnover and fewer genes involved in the carbohydrate metabolism than bioaerosols from other types of SCBs. Furthermore, production phase influenced the antibiotic resistance genes (ARGs) profile of the SCBs bioaerosols. Bioaerosol microbiome of BB, shared a high similarity with GS, and WP bioaerosol microbiome was more similar to FP than other types of SCBs. Our study suggests that the production phase plays a key role in the SCBs bioaerosol microbiome.