Extended Data Fig. 5: Prophage induction in the early-life virome.

a, Comparison of the extent of sequence alignment of induced VLP sequences from bacterial strains compared with VLP sequences from stool samples. Contigs were generated from mitomycin-C-induced VLPs from purified bacterial strains from stool (n = 33 phage contigs from 16 bacterial isolates), then VLP reads from faeces were aligned to these contigs and quantified. ‘Within infants’ indicates matching stool VLPs to induced VLPs from purified bacteria for samples all from the same infant. ‘Between infants’ indicates alignment of stool VLPs versus induced VLPs from different infants. The horizontal lines in box plots represent the third quartile, median and first quartile. The dots represent the outliers. Samples were compared using a two-sided Wilcoxon rank-sum test. b, Correlation between the proportion of each bacterium in the infant gut community and the proportion of prophages from that bacterial species in the infant’s gut virome. This plot is based on VLP sequences of phages produced by spontaneous induction (n = 42 phage contigs from 20 bacterial isolates). This is different from Fig. 2d, which is based on VLP sequences of phages produced after induction with mitomycin C. The black dashed line shows the linear regression line and the grey-shaded region shows the 95% confidence interval for the slope. The correlation was tested using a two-sided Spearman’s rank-order correlation (R represents Spearman’s ρ).