Influence of S . Enteritidis on the estimated number of OTUs. Chickens were infected with S. Enteritidis at 3-day intervals and sacrificed 3 days later (red lines) with appropriate non-infected control chickens (blue lines). No reproducible effect of S. Enteritidis infection on total OTU numbers was recorded. Panel A, experiment 1. Panel B, experiment 2 in which luminal microbiota diamonds and squares) and mucus-associated microbiota (triangles and circles) were characterized independently. Data are presented as averages from 3 chickens sacrificed at each time point ± standard deviation. In days 7, 10 and 13 in Panel A, and day 10 in Panel B, the two samples are slightly shifted to avoid overlaying standard deviations one over another.