Strain analysis
We used the same mapping described above. Reads were piled up to obtain per-position variant information for every detected species. Sub-species genetic dissimilarity was calculated as normalized pairwise distance, i.e. the number of positions that had no common alleles out of the number of comparable positions between two samples for each species. A comparison of a species between two samples was conducted if a minimum of 20K overlapping positions with at least three reads were available. Low dissimilarity values were clipped to 1/20K which is the method’s detection threshold. A microbial strain replacement was defined for each species as a case where the intra-person genetic dissimilarity between the pre- and post- intervention samples exceeds the lower 5% distribution of the inter-personal genetic dissimilarity of all the compared samples of a species. Correlations in the results section are between the quantity available for comparison and the percentage of strains replacements.