Bacteriophage adaptation to a mammalian mucosa reveals a trans-domain evolutionary axis

The majority of viruses within the human gut are obligate bacterial viruses known as bacteriophages (phages) 1 . Their bacteriotropism underscores the study of phage ecology in the gut, where they sustain top-down control 2–4 and co-evolve 5 with gut bacterial communities. Traditionally, these were investigated empirically via in vitro experimental evolution 6–8 and more recently, in vivo models were adopted to account for gut niche effects 4,9 . Here, we probed beyond conventional phage-bacteria co-evolution to investigate the potential evolutionary interactions between phages and the mammalian “host”. To capture the role of the mammalian host, we recapitulated a life-like mammalian gut mucosa using in vitro lab-on-a-chip devices (to wit, the gut-on-a-chip) and showed that the mucosal environment supports stable phage-bacteria co-existence. Next, we experimentally evolved phage populations within the gut-on-a-chip devices and discovered that phages adapt by de novo mutations and genetic recombination. We found that a single mutation in the phage capsid protein Hoc – known to facilitate phage adherence to mucus 10 – caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan-binding phenotype provided the evolved mutant phage a competitive fitness advantage over their ancestral wildtype phage in the gut-on-a-chip mucosal environment. Collectively, our findings revealed that phages – in addition to their evolutionary relationship with bacteria – are also able to engage in evolution with the mammalian host.