Fig. 5

A 16S rRNA gene sequence-based taxonomic distribution of bacteria by days since the nest sampled first housed a chick and individual nest litter faecal samples at the species level. Bars on the aggregated graph (left) are in the same order as the sample-level profile groups from left to right. Individual samples are ordered within groups chronologically and alphabetically. Taxa with mean relative 16S rRNA gene sequence abundance < 0.5% are grouped as ‘Other species’. B Observed richness and C Inverse Simpson (plotted on a log10 scale) alpha-diversity indices for litter samples grouped by days since the first chick was introduced to the nest. The y-axes for corresponding bar- and box-plots are identical. Significant Dunn’s test pairwise comparisons with Benjamini–Hochberg adjustment between groups in the box-plots are denoted by asterisks (*p < 0.05, **p < 0.01, ***p < 0.001). Box-plot details are as described for Fig. 3