Subtle shifts in fecal microbiota diversity during early stages of Mycobacterium avium subsp. paratuberculosis pathogenesis in dairy cattle

Mycobacterium avium subsp. paratuberculosis (MAP) in cattle causes an intestinal infection that can induce persistent inflammation or tissue remodeling. Several studies have reported differences in microbial diversity between MAP-infected and non-infected ruminants. Still, most of these studies have focused on animals in advanced stages of the disease, whether subclinical or clinical. The present study aimed to describe fecal microbiota composition in dairy cattle during early stages of MAP-associated pathological processes, which remain poorly characterized. A cross-sectional study was conducted in a pasture-based dairy herd in southern Chile. Fecal samples from 25 clinically healthy multiparous cows, including MAP culture-positive and negative animals, were analyzed using 16S rRNA gene sequencing. MAP culture-positive animals showed significantly reduced alpha diversity and subtle but significant differences in community structure compared with MAP-negative animals, despite no major taxonomic differences at the phylum or genus level. These findings suggest that low-level MAP infection is associated with early alterations in fecal microbial ecology, supporting a potential role of microbiota disruption in the initial stages of MAP pathogenesis and highlight the need for longitudinal studies to clarify their role in disease progression.