Signals triggering prophage induction in the gut microbiota

Abstract

Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages are probably a major actor in the gut, as it is estimated that 80% of intestinal bacteria are lysogens, meaning that they are carrying prophages. In addition, prophage induction rates are higher in the gut than in vitro. However, studies on the signals leading to prophage induction have essentially focused on genotoxic agents with poor relevance for this environment. In this review, we sum up recent findings about signals able to trigger prophage induction in the gut. Three categories of signals are at play: those originating from interactions between intestinal microbes, those from the human or animal host physiology and those from external intakes. These recent results highlight the diversity of factors influencing prophage induction in the gut, and start to unveil ways by which microbiota composition may be modulated.

Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection

“…reuterii , fructose consumption and acetic acid release was suggested as the origin of the genotoxic stress inducing its prophages in the GIT [ 3 ]. Few RecA-independent pathways have also been described for prophage induction [ 15 – 19 ] and other sensors and pathways certainly await discovery.…”

“…In the mammalian gut, molecules activating the SOS response, might not only be produced by the host itself, but also by the microbiota [14]: for L. reuterii, fructose consumption and acetic acid release was suggested as the origin of the genotoxic stress inducing its prophages in the GIT [3]. Few RecA-independent pathways have also been described for prophage induction [15][16][17][18][19] and other sensors and pathways certainly await discovery.…”

Activity and diversity of prophages harbored by wheat phyllosphere bacteria

“…This widespread cross-plaquing supports and extends the proposed role of prophages in enabling warfare between bacterial strains 11 . Although almost unexplored in the phyllosphere, prophage induction is widely observed in gut bacteria 13 , with evidence suggesting they may play important roles in modulating their microbial community 59 . In the phyllosphere, depletion of phages in microbial communities were shown to alter bacterial composition 60 , although the role of prophages was not investigated.…”

“…Although most known prophages are SOS-inducible, this observation may be a self-fulfilling prophecy; as the most well-known induction pathway, it is also the most widely manipulated in the lab. Further study of alternative induction triggers [13][14][15] will be necessary to characterize the prophage repertoire of bacteria more fully.…”

“…Many possible triggers for prophage induction exist, including DNA damage 12 , specific metabolites 13 , bacterial toxins 14 , and phage-encoded communication systems 15 . Many prophages also exhibit so-called spontaneous induction, where lysogens produce detectable levels of free phage in regular bacterial cultures 16,17 , although there is evidence to suggest that most "spontaneous" induction is in response to triggers such as DNA damage observed in a subset of the bacterial community [18][19][20] .…”