Effect of Eimeria spp. and Staphylococcus aureus challenge on cecal microbiome in broilers

Staphylococcus aureus, associated with Bacterial Chondronecrosis and Osteomyelitis (BCO), is a leading cause of lameness in modern-day broilers, often seen with concomitant gut health aberrations such as coccidiosis. This study aims to uncover changes in cecal microbiome which hasn't been characterized well in broilers challenged with S. aureus and Eimeria spp. Day-old male Cobb broilers were randomly allocated to eight treatments with five replicates each receiving various doses (2 × 10⁵ or 2 × 10⁸ CFU/mL) and timings (Day 0 and/or 18) of S. aureus. A mixed challenge of E. acervulina (62,500 Oocysts), E. maxima (12,500 Oocysts), and E. tenella (12,500 Oocysts) were administered orally on day 14 to all treatments except non challenged control (T1). Cecal contents were collected on days 20 and 26 from each bird per replicate for microbial analysis and 16s rRNA gene sequencing. On days 20 and 26, significant changes among the treatments were found in alpha diversity (Shannon Index and Faith's phylogenetic diversity) and beta diversity (unweighted and weighted UniFrac). Higher and /or repeated exposure of S. aureus induced greater microbial shifts which can be seen from taxonomic composition at the phylum and family levels where Actinobacteria, Microbacteraceae, and elevated Leuconostocaceae. On day 26, high dose treatments revealed higher Bacteroidetes with decreased firmicutes besides shift in their ratios. Furthermore, functional pathway analysis unveils alterations in lipid metabolism, osteoclast differentiation, MAPK signaling, Fc gamma R mediated phagocytosis which are directly or indirectly linked with bone health. The above changes were spotlighted among the co-challenged high dose S.aureus treatments indicating the link for BCO pathogenesis. This study demonstrates that co-challenge with Eimeria and S.aureus alters cecal microbiome in a dose and time dependent way, leading to possible predisposition of BCO in broilers. This marks the need of exploring microbiome targeted mitigation strategies alleviating the prevailing skeletal problems in poultry.