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][1]. Their bacteriotropism underscores the study of phage ecology in the gut, where they sustain top-down control[2][2]–[4][3] and co-evolve[5][4] with gut bacterial communities. Traditionally, these were investigated empirically via in vitro experimental evolution[6][5]–[8][6] and more recently, in vivo models were adopted to account for gut niche effects[4][3],[9][7]. 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][8] – 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. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-4 [4]: #ref-5 [5]: #ref-6 [6]: #ref-8 [7]: #ref-9 [8]: #ref-10