Fig. 4

Identification of inducible prophages in murine gut model microbiota. (a) Mean OPR counts (upper panel) and ΔPtoH ratio shown as mean l₂fc (lower panel) of each gene in mitomycin C-induced versus control Akkermansia muciniphila YL44 revealed two inducible prophages. For both prophages, a two-sided tent-like shape is observed when plotting l₂fcs of ΔPtoH ratio for each gene against the corresponding genome position. (b) Same analysis as in (a) for Blautia coccoides YL58 revealed one inducible prophage. The elevated mean OPR counts in control cultures (purple bars) suggest that spontaneous induction of this prophage occurred also under control conditions. (c-e) For E. coli HS cultures two regions with significant l₂fcs (orange dots) were observed. Grey areas highlight the regions shown in detail in panels d and e. Mean OPR counts were increased after induction (red) in the first (d), but not in the second region (e). The first and last gene with a significant l₂fc are homologous to IS3 family transposases, suggesting that the second region may represent a linear mobile genetic element. (f) Enriched A. muciniphila YL44 virion DNA was sequenced to verify mature virion production upon induction, as indicated by a clear increase in OPR counts and read coverage in the prophage region. (g) Genes at the attR site of YL44 phage 1 and at the attL site of YL44 phage 2 showed a higher read coverage (brown circles; coverage > 50X) than other host genes (blue circles, coverage < 50X), suggesting that these phages may mediate lateral transduction. Statistical significance of l₂fc between induced (n=3) and control (n=3) cultures was tested as described in the legend of Fig. 3. Genes with a significant fold change are shown as orange data points; non-significant ones are shown in grey