Understanding and predicting why some animals respond better to vaccination than others is a main concern to strengthen vaccination efficiency. Our aim was to study whether the gut microbiota before vaccination presents composition patterns associated with individual variabilities of vaccine responses in pigs. Ninety-eight Large White piglets were vaccinated against the influenza A virus (IAV) at weaning at 28 days of age (D28) with a booster three weeks later. Stools were collected before the vaccination at D28, and were further processed to perform 16SRNA gene sequencing (Illumina MiSeq) and assess microbial taxonomic composition. The piglets’ humoral response was evaluated by ELISA of seric IAV-specific IgGs and by hemagglutination inhibition assays (HAI) at D49, D56, D63, and D146 to identify extreme animals with either high or low responses to vaccination. Piglets with a richer microbiota had higher levels of HAI at D63 (p<0.05) and had a tendency towards more IAV-specific IgGs. Extreme high and low responders for IAV-specific IgGs at D63 had also a dissimilar microbiota (p<0.01) and displayed differentially abundant operational taxonomic units (OTUs); bacteria from the Paludibacteraceae family and Prevotella genera were more abundant in high responders, while bacteria from Helicobacter and Escherichia-Shigella genera were more abundant in low responders (FDR<0.05). Thus, our results show that the faecal microbiota before vaccination could be further investigated to identify biomarkers predictive of vaccine response levels and analyse the underlying biology.