Pathogen detection and microbial community characterization in clinically symptomatic pigs from commercial farms

Effective swine disease control requires continuous monitoring of major pathogens and a comprehensive understanding of microbial community dynamics under disease conditions. Here, we collected lung, oral fluid, and fecal samples from clinically symptomatic pigs on commercial farms in South Korea. Molecular diagnostics targeting major respiratory and enteric pathogens were performed to assess infection status, alongside 16S rRNA gene sequencing to simultaneously characterize respiratory and enteric microbiota. Most respiratory pathogens were detected at higher rates in oral fluid than in lung samples. Pasteurella multocida was the most frequently detected pathogen overall, while porcine reproductive and respiratory syndrome virus (PRRSV) showed the highest detection rate in lung samples. Among enteric pathogens, rotavirus showed the highest detection rate. Microbiome profiling revealed that lung samples had the lowest species diversity, while distinct microbial community structures were observed among lung, oral fluid, and fecal samples. Prevotellaceae-associated genera were dominant in fecal samples. The lung microbiota was characterized by dominance of a limited number of taxa, including Escherichia-Shigella and Actinobacillus, whereas oral fluid exhibited a more evenly distributed microbial composition enriched in Moraxella and Streptococcus. Differentially abundant taxa and contrasting predicted functional profiles were identified between Clostridium perfringens-positive and -negative groups, indicating a potential association between Clostridium perfringens presence and gut microbial community composition. This study integrates molecular diagnostics with microbiome profiling in clinically diseased pigs under field conditions. These findings provide field-based evidence to support microbiome-informed monitoring and interpretation of pathogen-associated changes in swine production systems.