Table 1_Pathogen detection and microbial community characterization in clinically symptomatic pigs from commercial farms.docx

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.</p>