Fig. 5: Intrastrain genetic variations driven by immune interactions and genome recombination between cellular microbial symbionts and their viruses.

a Mutation proportion and degree at restriction recognition sites in genomes of prokaryotic host-linked viruses in the metagenomes of microbial cell fractions of individuals CC1-CC4. Mutated proportion is calculated by dividing the number of mutated loci by the number of all recognition loci found in the viruses. The mutation degree is calculated by summing up the proportion of mutated bases in all recognition sites found in viruses. Gray boxes show viruses with recognition sites having average mapped bases of less than 100, which are excluded from the analysis. b Read coverage of bacterial contigs containing CRISPR arrays in the metagenomes of microbial cell fractions of individuals CC1-CC4. The array regions are shown with a shaded background. Sequencing depth is the number of bases mapped to each site. c The Spearman correlation (two-sided test) between intrastrain nucleotide diversity of viruses and their bacterial/archaeal hosts in their entire genomes in the metagenomes of microbial cell fractions of individuals CC1-CC4. d The Spearman correlation (two-sided test) between nucleotide diversity of viruses and their bacterial/archaeal hosts in their recombination regions in the metagenomes of microbial cell fractions of individuals CC1-CC4. A sequence identity threshold of 95% is used in the mapping step of inStrain to ensure read coverage. e Genomic map of the transposable virus V957 infecting the bacterium M10 Rhizobiaceae and M11238 Alphaproteobacteria. f Genome recombination regions (shaded sections) between V63657 and M6 Arenicellales, V36967 and M6398 Opitutales, and V4473 and M8024 Alphaproteobacteria. Source data are provided as a Source Data file.