Investigating the role of Enterocloster clostridioformis bacteriophages in gut microbiome dysbiosis associated with metabolic disease states.

The gut microbiome – the collective term for bacteria, viruses, fungi and protozoa in the intestine – plays a critical role in health and disease and represents a potential untapped reservoir for novel therapeutic approaches to treating certain human conditions. Disruption of the normal microbiome balance (‘dysbiosis’) can have significant effects on the affected host, with numerous studies showing relationships between the presence of specific gut bacteria and certain diseases, including Type 2 diabetes (T2D) and obesity. Since almost 1 in 20 people in Scotland were diagnosed with T2D in 2018, and over 1 in 4 of all adults aged 16-64 were categorised as obese, there is an urgent need to understand the relationship between dysbiosis and disease, and the mechanisms underpinning its development.
Enterocloster clostridioformis is a commensal bacterium found at low or undetectable levels in the healthy gut but is significantly increased (up to 14 times higher) in the microbiomes of those with T2D and obesity. The underlying reasons for this are unclear. We have isolated a hyper adapted strain of E. clostridioformis (LM41) from a mouse model of dysbiosis that reproduces the outgrowth characteristics observed in human dysbiosis, and can comprise up to 60% of all intestinal bacteria. The mechanisms enabling this are unknown, however genome sequencing has revealed its genome is ~40% larger than other sequenced E. clostridioformis, suggesting acquisition of advantageous traits that may contribute to its fitness in this niche. Among this DNA are 15 prophages, comprising almost 10% of the total LM41 genome; an unusually high proportion for this species. Prophages are bacteriophages (viruses that exclusively infect bacteria) that insert into their bacterial host’s DNA. Here they remain dormant until an environmental trigger causes them to emerge from the bacterial DNA and begin to reproduce, producing many hundreds of viral particles per bacterium. These particles burst out of the bacterium, killing it, and infect new bacteria. Spontaneous activation of prophages can also occur in subsets of bacteriophage-carrying populations in the absence of environmental triggers, releasing bacteriophages into the local environment where they may infect and kill rival bacteria, and providing a competitive advantage to the original bacterial population from which they were released. Importantly, bacteriophages also mediate bacterial DNA exchange between cells, passing new and advantageous traits (e.g. antimicrobial resistance, toxins, or metabolic capabilities) between related strains and to different species, potentially permitting greater metabolic flexibility that could facilitate better growth in competitive environments.
This project will use molecular and classic culture approaches to determine the functionality of LM41 prophages and assess whether they have inhibitory activity against other Enterocloster and related Clostridial species that could explain LM41’s niche dominance. The preliminary data generated will support future major grant and/or fellowship applications to determine the role of E. clostridioformis bacteriophages in facilitating interspecies competition in gut infection models, as well as whether these elements participate in the exchange of DNA between E. clostridioformis and other species, with the eventual aim of developing novel therapeutic approaches that impede or ameliorate the processes underlying dysbiosis development.