In many infectious disease systems, a small fraction of hosts accounts for a disproportionate share of transmission, but the biological basis of this heterogeneity remains poorly resolved. In avian influenza, mallards show substantial variation in viral shedding, raising the possibility that only a subset of individuals contributes strongly to environmental contamination and onward spread. To examine whether host microbiome structure is associated with this variation, we experimentally infected wild, captive mallards with low-pathogenic avian influenza virus. We characterized cloacal microbiomes across control, low-shedding, and high-shedding birds using shotgun metagenomic sequencing combined with read-based taxonomic profiling and co-assembled metagenome-assembled genome (MAG) reconstruction. Although infected and uninfected birds were highly similar in species presence-absence, abundance-based analyses showed clear differences in shared taxa, particularly in high-shedding birds relative to controls. Differentially abundant taxa were dominated by taxa that belonged to groups that include host-associated opportunists, consistent with compositional imbalance rather than complete community restructuring. The phylum Pseudomonadota, especially the families Enterobacteriaceae and Moraxellaceae, is well represented. Together, these findings suggest that avian influenza infection is associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in species membership and that microbiome structure is associated with heterogeneity in shedding in a key wildlife reservoir.IMPORTANCEA small fraction of infected hosts often accounts for a disproportionate share of pathogen shedding, but the biological factors underlying this variation remain poorly understood. In experimentally infected mallards, a key wildlife reservoir for avian influenza A viruses, we found that high viral shedding was associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in microbial species membership. These results suggest that host-associated microbiome structure may be linked to shedding heterogeneity and could help explain why some individuals contribute more strongly to environmental contamination and onward transmission.