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Most human gut phages are prophages (1) that integrate their genome into the host chromosome to be replicated under unfavorable conditions. This integration is facilitated by specific integrases. Prophages can provide hosts with advantages such as antibiotic resistance (2, 3), but they also carry the risk of reverting to the lytic cycle. Over time, prophages can accumulate mutations that impair their mobility (4), while some genes are acquired by the host (5). Additionally, prophages can promote horizontal gene transfer through transduction (6)
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(5) Bobay et al. 2014 Proc Natl…