Bacteriophages are present in all bacterial communities and have profound impact on bacteria, by killing them or bringing new genes through lysogeny. Intestinal bacteria are lysogenized by prophages. Nonetheless, very few data exist concerning the impact of prophages on their hosts in intestinal environment (review, De Paepe et al., 2014).

By using mice mono-colonized with Escherichia coli, we show that the prophage lambda is costly to its host on the long run, due to a high rate of induction in response to DNA damage (De Paepe et al., 2016). Even higher prophages induction in key species of the gut microbiota could lead to a dysbiosis. In order to investigate this hypothesis, we studied the prophages of Faecalibacterium prausnitzii A2-165 and Roseburia intestinalis L1-82, two mutualistic dominant members of the human gut microbiota, since their abundance decreases in patients with chronic inflammatory diseases (IBD).

We predicted the presences of two prophages in the genome of R. intestinalis L1-82. Quantification of virions in the growth culture supernatant by qPCR showed that both prophages are highly active (10^8-10^9 genome/mL), reaching titers as high as bacteria (10^9 CFU/mL). Two prophages are also predicted for F. prausnitzii A2-165. However, virions were found for only one of them (10^6 genome/mL). All three active prophages are inducible by addition of H2O2 or mitomycin C.

In conclusion, R. intestinalis L1-82 and F. prausnitzii A2-165 harbor two and one active prophages, respectively, an observation compatible with the “molecular bomb hypothesis”. Work in progress consists in following the activity of these prophages in vivo, in mice colonized with a simplified microbiota, in particular during intestinal inflammation triggered by DSS.