Pathogen detection and gut microbiota analysis in subcutaneous abscesses in goats

Subcutaneous abscesses in goats result in carcass condemnation, reduced milk and wool production, growth retardation, and increased mortality, thereby causing substantial economic losses in goat production systems. This study investigated the major pathogens associated with subcutaneous abscesses in goats and characterized alterations in the gut microbiota of infected animals. A cross-sectional survey of 554 Saanen goats from a single farm revealed an overall incidence of clinical abscesses of 13.0% (72/554). The incidence in male goats was 39.6% (21/53), which was markedly higher than that observed in female goats (10.2%; 51/501). Subcutaneous abscesses were predominantly distributed on the cheeks, neck, shoulders, and abdomen. Bacterial isolation and culture of abscess samples revealed Corynebacterium pseudotuberculosis as the predominant pathogen (68.1%), followed by Trueperella pyogenes (18.1%), Staphylococcus aureus (16.7%), and Escherichia coli (9.7%). Single-pathogen infections accounted for 93.1% of the cases, whereas mixed infections involving two or three pathogens accounted for 5.6% and 1.4%, respectively. Furthermore, faecal microbiota sequencing revealed distinct differences in the gut microbiota between healthy and diseased goats. Diseased goats had lower microbial diversity, altered flora structure, fewer beneficial Lactobacillus strains and more opportunistic pathogens such as Escherichia-Shigella . Co-occurrence network analysis indicated substantial alterations in the dominant bacterial genera in diseased goats, with a shift in interspecies relationships from predominantly positive to negative correlations. In summary, these results provide new insights into the precise prevention and control of this disease and potential microbiome-based intervention strategies.