This study investigated the associations between fecal microbiota and vaccine response variability in pigs. 98 piglets were vaccinated against influenza A virus (IAV), and their immune response was measured via serum IAV-specific IgG and hemagglutination inhibition (HAI) assays. Pre-vaccination microbiota analysis revealed a correlation between richer microbiota and a stronger vaccine response. 23 operational taxonomic units (OTUs) showed differential abundance between high and low IgG producers. *Prevotella* and *Muribaculaceae* were linked to stronger responses, while *Helicobacter* and *Escherichia-Shigella* were associated with weaker responses. A set of 81 OTUs accurately predicted IgG and HAI levels at all time points, demonstrating early and late associations between pre-vaccination microbiota and immune response.
