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Additional file 2. Signs and gross lesions identified in ERE rabbits. In order to confirm ERE development, a necropsy was performed in all rabbits by a veterinarian specialist in anatomical pathology (co-author Jorge Martínez). Gross lesions compatible with ERE, such as distension of the stomach and intestine, caecum filled with gas, liquid or impacted with solid/dry content, and presence of abundant quantities of mucus in the colon were observed in all rabbits that developed a sharp decrease in food confirming the development of ERE. P = presence of a particular sign/gross lesion. aRabbits are sorted in the same order as ERE rabbits shown in Additional file 3. Healthy rabbits are not shown since they did not develop any of the signs/gross lesions.

Additional file 5. Equivalent bacterial genera abundance in healthy and ERE rabbits before onset. Microbiota composition before ERE onset was analyzed in caecotrophs samples collected from rabbits weaned at 30 days of age. Samples from rabbits with ERE, collected the day of the disease onset or after disease initiation, are not included in the analysis. Since most rabbits initiated ERE on day 9 or after, only the day of weaning (day 0) and days 1, 3, 5 and 7 after weaning are shown. Each panel shows the relative abundance, at different days after weaning of a bacterial genus that was found to be significantly different in rabbits that had developed ERE (Figure 1C). Horizontal lines represent the mean for each group. N = 8–11 per group and time point. No significant differences between healthy (HLT) and ERE rabbits were detected in any taxonomic level or OTU, at any time-point, before ERE onset (Wilcoxon two-sided test, FDR > 0.1).

Additional file 9. The majority of the changes detected after the initiation of ERE are not due to a decrease in food intake. Relative abundance of the genus Anaerovorax or the genus Clostridium in samples collected from 6 weeks old healthy rabbits that were forced to consume an amount of food similar to that of ERE rabbits during 48 h (food restricted) as compared to healthy age-match controls receiving food ad libitum. A caecotroph sample was collected from each rabbit and its microbiota composition was analyzed. From all changes detected in ERE rabbits, only an increase in the genus Anaerovorax was found to occur after food restriction, similarly to what was observed in ERE rabbits after the disease onset (Wilcoxon two-sided test, FDR

Additional file 1. Changes in food consumption in ERE and healthy rabbits. Fold change in food consumption (grams of food consumed by a particular rabbit during 24 h divided by grams of food consumed by that rabbit during previous 24 h). Fold changes in food consumption from healthy rabbits during the first 2 weeks post-weaning (blue dots), ERE rabbits before disease onset (green dots) or ERE rabbits the day of ERE onset (pink dots) are shown. The mean for each group ± SEM is also shown. The day of ERE onset is considered as the day in which a fold change lower than 0.5 was detected. All ERE rabbits developed other ERE compatible signs following the drop in food consumption (see “Materials and methods”, Additional file 2). A fold change of 0.5 was used since a few healthy rabbits diminished food intake, but to a lower extent, on specific days, without developing any sign consistent with ERE. Two sided T-test, ****p

Additional file 7. Statistically significant differences between rabbits with ERE (after disease onset) and age-matched healthy littermate controls. The microbiota composition of samples collected after ERE onset showed significant differences in abundances of hundreds of bacterial groups compared to the microbiota composition of healthy littermate controls (Wilcoxon test, p