Maternal microbiota in relation to mortality, culling, and offspring survival in rabbits

Mortality and culling in rabbits, particularly among breeding does and their offspring, present significant challenges by reducing longevity, productivity, and profitability. This study investigates whether fecal microbiota composition varies depending on whether the female will experience death, culling, or remain healthy and how it correlates with the proximity of the event. Additionally, it examines whether disruptions in the maternal microbiota, transferred naturally to offspring, is associated with their survival. To do so, does were categorized based on their fate: death (D, deceased naturally during productive lifespan), culled for reproductive reasons (CR), or healthy controls (C). Soft fecal samples were collected for V3-V4 16S rRNA sequencing to assess microbial diversity and composition. The results revealed that does approaching death or reproductive culling exhibited lower microbial richness, particularly near the event, with significantly higher values observed in the control group compared to the CR and D groups. Classification models using metataxonomic ASVs data accurately classified fate outcomes, with an Area Under the Curve (AUC) of 0.99 when samples were collected close to the event (∼50 d). The deceased group had the highest recall rates (0.80-0.99), suggesting that their microbiota profiles are the most distinct, potentially because of dysbiosis. However, performance decreased as time to the event increased. Concerning offspring survival, first, we found that maternal fate significantly impacted kit survival, with offspring from deceased does showing a 9% lower survival rate at weaning and those from reproductive culls showing a 5% reduction. Additionally, maternal microbiota composition has accounted for a significant portion of the variability in kit survival. Different taxa were found to influence both maternal fate and kit survival, such as Clostridia UCG-014, Ruminococcus, Christensenellaceae R-7 group, and uncultured Eubacteriaceae. These findings highlight the potential of microbiota-based biomarkers for predicting mortality and reproductive culling risks in rabbits, improving management practices, and enhancing offspring survival. Furthermore, the results emphasize the critical link between maternal health, microbiota composition, and offspring survival, underscoring the importance of maintaining maternal microbiota stability for improving both welfare and productivity.