LAUSR

Simple Summary Mycoplasma hyopneumoniae is a bacterium that causes pneumonia in pigs and can facilitate the establishment of other respiratory diseases. The microbiota, which comprises the microorganisms found in a specific environment (in this case, the respiratory tract), can be altered by the presence of several pathogens. Therefore, knowing how M. hyopneumoniae can affect the microbiota of the lower respiratory tract and nasal turbinates in experimentally infected pigs is important to understand the interaction between microorganisms that could lead to the development of disease. Thus, we investigated the bacterial composition of the lungs and noses of infected and non-infected pigs. The results showed that the lungs of infected pigs were mostly colonized (growth and multiplication of a microorganism) by M. hyopneumoniae, and there were not many other species in the lungs. In contrast, in the non-infected pigs, a more diverse lower respiratory microbiota was observed, meaning that there were more species of bacteria in the non-infected pigs than in the infected ones. No differences were observed between the nose microbiota in infected and non-infected pigs. In conclusion, this pathogen can alter the number of bacterial species in the lungs, which could result in more respiratory problems in swine production. Abstract Mycoplasma (M.) hyopneumoniae, the etiological agent of swine enzootic pneumonia, has been reported to increase the susceptibility to secondary infections and modulate the respiratory microbiota in infected pigs. However, no studies have assessed the influence of M. hyopneumoniae on the respiratory microbiota diversity under experimental conditions. Therefore, this study evaluated the impact of M. hyopneumoniae infection on the respiratory microbiota of experimentally infected swine over time. To accomplish this, 12 weaned pigs from a M. hyopneumoniae-free farm were divided into two groups: M. hyopneumoniae strain 232 infected (n = 8) and non-infected (n = 4). The first group received 10 mL of Friis medium containing 107 CCU/mL of M. hyopneumoniae while the control group received 10 mL of sterile Friis medium. Inoculation of both groups was performed intratracheally when the animals were 35 days old (d0). At 28 days post-inoculation (dpi) and 56 dpi, 4 infected animals plus 2 controls were humanely euthanized, and biopsy samples of nasal turbinates (NT) and bronchus-alveolar lavage fluid (BALF) samples were collected. The DNA was extracted from the individual samples, and each group had the samples pooled and submitted to next-generation sequencing. Taxonomic analysis, alpha and beta diversity indexes, weighted unifrac, and unweighted unifrac distances were calculated. A high relative frequency (99%) of M. hyopneumoniae in BALF samples from infected animals was observed with no significant variation between time points. The infection did not seem to alter the diversity and evenness of bacterial communities in NT, thus, M. hyopneumoniae relative frequency was low in NT pools from infected animals (28 dpi—0.83%; 56 dpi—0.89%). PCoA diagrams showed that BALF samples from infected pigs were grouped and far from the control samples, whereas NT from infected animals were not separated from the control. Under the present coditions, M. hyopneumoniae infection influenced the lower respiratory microbiota, which could contribute to the increased susceptibility of infected animals to respiratory infections.