Interactions between Mycoplasma hyopneumoniae strains and the resident lung microbiota in swine

Enzootic pneumonia (EP) in swine, caused by Mycoplasma hyopneumoniae (M. hyopneumoniae), is a chronic respiratory disease that leads to significant economic losses in pig production. Infection with M. hyopneumoniae can induce pulmonary dysbiosis; however, the impact of different strains with varying degrees of virulence on the composition of a healthy microbiota remains incompletely understood. This study investigated alterations in the lung microbiome of pigs experimentally infected with two distinct strains of M. hyopneumoniae (UFV1 and UFV2) using 16S rRNA gene-based metataxonomic analyses and bioinformatics approaches. Pigs were divided into three experimental groups: Control (uninfected), UFV1 (infected with strain UFV1), and UFV2 (infected with strain UFV2). Bronchoalveolar lavage fluid were collected for DNA extraction and sequencing. Alpha diversity was significantly lower in the infected groups compared to the Control. Beta diversity analysis revealed significant differences in microbiota composition among the groups, with a clear separation between the Control group and the infected groups. Mycoplasma was the most abundant genus in both UFV1 and UFV2 groups, whereas the Control group exhibited greater genus-level diversity, including Stenotrophomonas, Comamonas, and Pseudomonas. Linear discriminant analysis (LDA) confirmed the enrichment of Mycoplasma in the infected groups and identified additional differentially abundant genera. Predictive modeling based on microbiota composition demonstrated high accuracy in classifying the groups, with Varibaculum, Pseudomonas, and Actinobacillus emerging as key genera for prediction. The UFV1 and UFV2 strains exhibited distinct lung microbiota profiles, suggesting different infection dynamics and interactions with the resident microbiota. This study provides new insights into the impact of diverse M. hyopneumoniae strains on the porcine lung microbiome, with implications for the development of preventive and control strategies for EP.