Bacteriophages evolve enhanced persistence to a mucosal surface

Abstract

The majority of viruses within the gut are obligate bacterial viruses known as bacteriophages (phages). Their bacteriotropism underscores the study of phage ecology in the gut, where they modulate and coevolve with gut bacterial communities. Traditionally, these ecological and evolutionary questions were investigated empirically via in vitro experimental evolution and, more recently, in vivo models were adopted to account for physiologically relevant conditions of the gut. Here, we probed beyond conventional phage–bacteria coevolution to investigate potential tripartite evolutionary interactions between phages, their bacterial hosts, and the mammalian gut mucosa. To capture the role of the mammalian gut, we recapitulated a life-like gut mucosal layer 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 coexistence. Next, we experimentally coevolved lytic phage populations within the gut-on-a-chip devices alongside their bacterial hosts. We found that while phages adapt to the mucosal environment via de novo mutations, genetic recombination was the key evolutionary force in driving mutational fitness. A single mutation in the phage capsid protein Hoc—known to facilitate phage adherence to mucus—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 its ancestral wild-type phage in the gut-on-a-chip mucosal environment. Collectively, our findings revealed that phages—in addition to their evolutionary relationship with bacteria—are able to evolve in response to a mammalian-derived mucosal environment.

Involvement of Pf-like phages in resistance to phage infection in clinical isolates of P. aeruginosa from cystic fibrosis patients

“…The mucus in the lungs of CF patients is hyper-concentrated and has a unique structure that favours bacterial colonization and, as also occurs in gut mucosa, the phages bind to the mucus. The mucus creates spatial refuges that favour the coexistence between phages and bacteria, which can explain the coevolution of both (32)(33)(34).…”

Pulmonary bacteriophage and cystic fibrosis airway mucus: friends or foes?

“…However, very limited studies have reported the phage-mucus interactions in the airway and the potential impacts of phage efficacy on respiratory bacterial infection. Recent evidence suggests that phages can bind to aspects of normal mucus that improve their bactericidal activity ( 11 ). However, little is known about how the CF mucus impacts phage functionality ( Figure 2 ).…”

“…This binding increased the retention of T4 in the environment, allowing more interaction between phage and E. coli and serving as a critical regulator for phage-mediated bacterial lysis ( 132 ). Other work in non-respiratory research has shown that phages adhering to mucin have enhanced virulence toward bacteria ( 11 , 133 ), empowering the chances of phage encountering bacterial hosts and providing additional mucosal immunity protection. Almeida et al ( 133 ) demonstrated using a natural infection system that tailed phages with Ig-like domains in the phage capsids preferentially bind to mucin-containing agar.…”

“…The resultant mucus flakes create a microenvironment favorable for bacterial colonization ( 17 , 19 ). The mucus layer is an essential entity facilitating phage diffusion across the mucosal surface, and recent evidence in the gut suggests that they can bind to parts of mucus, improving their bactericidal activity ( 11 ). Knowing that mucus and its structure in CF are distinctly unique, little is known about how this would impact phage functionality.…”

Targeted Viromes and Total Metagenomes Capture Distinct Components of Bee Gut Phage Communities

“…For example, the comparatively high-density bacterial communities associated with the human gut 19,20 , mucosal layer of corals 21 , and other host environments is suggested to favor integrase encoding temperate phage, as opposed to obligately lytic phage [22][23][24] . Phage targeting bacteria adhered to gut mucosa have also been shown to evolve the ability to adhere to and persist in the animal mucosa where their target bacteria reside 25 . Given the fundamental differences in the ecology of free-living and hostassociated phage communities 22 , it remains unclear whether sampling methods developed for free-living communities are also appropriate for other habitat types.…”