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. 2018 Dec 20;49:123. doi: 10.1186/s13567-018-0617-8

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© The Author(s) 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Expansion of a single Clostridium OTU characterizes the microbiota of the ERE onset. Microbiota composition was analyzed in caecotrophs samples collected from rabbits that developed ERE (the day of ERE onset and after onset) and compared with healthy littermate controls (HLT). A PCoA obtained from the unweighted UniFrac values calculated between samples from rabbits with ERE collected the day of onset or after onset and samples from healthy rabbits at similar time points (days 9 and 11 after weaning). The microbiota of samples collected after ERE onset was significantly different from samples of healthy controls and from samples collected the day of ERE onset (AMOVA, p < 0.001). However, the overall microbiota composition the day of ERE onset did not differ from that one of healthy controls (AMOVA, p > 0.05). B Relative abundance of the genus Clostridium, the only change detected in ERE rabbits on the day of onset compared to healthy littermates (Wilcoxon two-sided test, p < 0.05, FDR < 0.1). The altered abundance of this genus in ERE rabbits was due to a single OTU (OTU172). **p < 0.01,***p < 0.001. The mean ± SEM for each group is shown. N = 7–10 per group and time point.