Fig. 6: Example of co-transmission of a temperate phage and its bacterial host: a temperate phage of Bifidobacterium bifidum.

a Phylogenetic trees of a temperate phage (L34922_LS1) and its predicted host (Bifidobacterium bifidum SGB17256). Colours indicate the mother-infant pairs (family) affiliation, and shapes indicate infant or mother sample. Symbol borders show whether the strain was reconstructed from a total metagenome/MGS metavirome (light grey) or VLP metavirome (black). b Presence patterns of L34922_LS1 and B. bifidum in the samples of the mother-infant pair (FAM0234) where the transmission of L34922_LS1 was detected. X-axis indicates timepoints, Y-axis shows the mother or infant sample. Shape indicates total metagenome (square), VLP metavirome (triangle) or MGS metavirome (rotated triangle). Colour of the shape indicates the presence (red) or absence (white) of the virus or bacterial strain in the sample, and the missing samples are coloured in grey. c Synteny plot of L34922_LS1 genome sequence mapping to the fragment of the B. bifidum genome fragment. X-axis indicates the genome coordinates (in kilobases). Lines connecting the L34922_LS1 and B. bifidum genome fragment indicate the prophage insertion region. d Genome organisation of L34922_LS1. X-axis depicts the genome coordinates in kilobases. A polygon represents every predicted protein, and its orientation indicates the location of the predicted protein at the positive (right-orientation) or negative (left-orientation) strands. Colours indicate the source of protein annotation: Pfam (blue), VOG (orange). Proteins with no functional annotations are shown in white. Orange and blue polygons without text indicate hypothetical proteins with unknown function. e Depth of the B. bifidum genome fragment coverage by sequencing reads from total metagenomes that were positive for B. bifidum, and (f) VLP metaviromes that were positive for L34922_LS1. Each transparent grey line corresponds to a sample and represents mean depth in a 1,001-nt sliding window. X-axis depicts the genome coordinate in kilobases. Coloured lines represent samples from the mother-infant pair (FAM0234), and colours show timepoints. Dashed lines indicate the prophage insertion region. Source data are provided as a Source Data file.