Effects of Experimental Infection with Lagovirus europaeus GI.1 and GI.2 on the Fecal Microbiota of Rabbits: New Insights into Virus–Host Microbiota Associations

Lagovirus europaeus GI.1 (RHDV) and GI.2 (RHDV2), the causative agents of rabbit hemorrhagic disease (RHD), are highly virulent pathogens of the European rabbit; however, their impact on the host fecal microbiota remains poorly understood. Previous field studies have suggested an association between the fecal microbiota and RHDV2 epidemiology in wild rabbits, highlighting the need for studies under controlled experimental conditions. To address this knowledge gap, we investigated the effects of experimental infection with L. europaeus GI.1 and GI.2 on the fecal microbiota of rabbits. Eighteen rabbits were assigned to three groups: an uninfected control group and two groups experimentally infected with L. europaeus GI.1 or GI.2 (n = 6 per group). Fecal microbiota composition was characterized by high-throughput sequencing of the V3–V4 region of the 16S rRNA gene using the HiSeq 2500 platform (Illumina). Rabbits infected with either genotype developed clinical signs consistent with RHD. No significant differences in alpha and beta diversity were observed. However, selective taxonomic shifts were detected, particularly in the GI.2 group, in which the relative abundance of Firmicutes was significantly higher and that of Bacteroidota significantly lower than in the control group. The abundance of Muribaculaceae was lower in both infected groups, whereas Sporosarcina reached its highest abundance in the GI.2 group. Correlation analysis revealed associations between selected bacterial taxa and clinical parameters. Muribaculaceae abundance was positively correlated with survival time and negatively correlated with lethargy and diarrhea, whereas Sporosarcina showed the opposite pattern, with positive correlations with lethargy and diarrhea and a negative correlation with survival time. Our findings indicate that experimental infection with L. europaeus GI.1 and GI.2 was not associated with a global restructuring of the fecal microbiota but rather with selective changes in the abundance of specific bacterial taxa, some of which were associated with viral genotype and the clinical course of infection. To our knowledge, this is the first controlled experimental study to directly compare the effects of L. europaeus GI.1 and GI.2 infection on the rabbit fecal microbiota. This study extends previous field observations by providing experimental evidence and offers new insights into the associations between L. europaeus infection and the host fecal microbiota during RHD.