Inter-individual gene content variability of abundant bacterial species. For each species, the gene content differences between two individuals were calculated. Boxplots are colored according to phyla (red for Bacteroidetes and blue for Firmicutes), and species are sorted by decreasing mean. The inter-individual boxplot (green) shows pairwise comparisons of the same species between individuals. Biological replicates (purple) represent pairwise gene content comparisons of the same species in samples from the same individual at different time-points. Technical replicates represent gene content differences of Prevotella copri in four sequencing replicates of the same sample.