Extended Data Fig. 7: Antagonistic interactions are depleted in samples, individuals, and families.

(a) Antagonism frequencies (AF) between co-resident lineages in samples appears depleted relative to the frequency across all S. epidermidis lineages (red). When lineages were present in a sample but were absent from our screen, we calculated the range of AF that would be expected based on the average rate of antagonism between any two isolates. Error bars depict the upper bound of the AF range in a given sample. This is likely an overestimate of the range, since on-person antagonism frequencies are lower than population-wide antagonism frequency. (b) We took the mean AF across samples of the same participant (subject), and still found that mean within sample AF appeared to be depleted relative to the expected AF. Reproduced from Fig. 3a. (c-f) Since t-tests are invalid for non-independent samples, we performed permutation testing by simulating scenarios that retained the structure in the interaction matrix and the composition of samples (for example uneven lineage distribution). For each simulation, we shuffled lineage labels in the relative abundance matrix and the p-value represents the fraction of simulations with less on-person antagonism than observed (black arrow indicates observed value of ΔAF). (c) The rows of the composition matrix were shuffled once across all lineages in our collection. This simulation tests for depletion of antagonism while maintaining the same degree of lineage sharing seen between individuals in the same family. Reproduced from Fig. 3c. (d) The rows of the composition matrix were shuffled, AF values were calculated for samples of the first participant, then rows were shuffled again before each new subject. These simulations broke the relatedness between individuals in the same family, while retaining similarity between samples from the same participant, thereby testing depletion of antagonism under the assumption that lineages are acquired from the environment independent of family. (e) To test for depletion of antagonism under the assumption that one can only acquire strains from a family member, shuffling was only performed on submatrices composed only of lineages on a family were shuffled, by row, as in C. (f) As in F, but without maintenance of lineage sharing between family members; submatrices shuffled but by once per participant. Note that less shuffled conditions (e,f) will definitionally have higher p-values because of fewer possible permutations. Under all tested assumptions, antagonism is depleted among strains present on the same person at the same time. Significance P-values are derived from two-sided permutation tests with shuffled lineage labels (Methods), without multiple hypothesis correction.