The human body contains an estimated thirty trillion microbial cells, with the large intestine harbouring the most densely populated microbial ecosystem with 10¹³-10¹⁴ estimated microbial cells per gram of faecal matter. It is well established that our gut microbial flora is largely responsible for our overall health. Gut microbes have coevolved symbiotic relationships with our bodies, imparting specific functions associated with; nutrient metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Conversely, a faulty or dysbiotic gut microbiome can contribute to a range of gut disorders such as hyper inflammation, metabolic diseases, cancers and even mental illness. Hence, several studies have been conducted in order to define a “health human gut microbiome”.

Lately, the multitude of ways that bacteriophages influence their microbial hosts is becoming evident. Within the human gut, temperate appears to be the preferred phage lifecycle. Temperate phages integrate their genome within a host bacterium’s genome as a prophage. Although temperate phages are not actively replicating in this lifecycle, the prophage is propagated and spread to daughter cells every time its bacterial host replicates. Prophages can encode a vast genomic repertoire which can provide novel functions, infer genomic plasticity and increase survival of their bacterial hosts. Prophages can be induced out of the temperate lifecycle back into the lytic lifecycle, lysing their bacterial host and releasing infectious phages back into the surrounding environment.

Accordingly, the idea of a “healthy gut phageome” has arisen. Yet the vast majority of phages within our gut remains unidentified; only a scratch on the surface has been made. At the Barr Lab, we are interested in the identification and characterisation of these gut prophages. We aim to decode some of the gut phageome in order to answer questions regarding human gut health.

My name is Sofia Dahlman, I’m a PhD student in the Barr lab where my main goal is to decipher the human gut phageome and its impact on human health. To this end, I will use extensive bioinformatic techniques in order to identify potential prophages within the genomes of a large number of human clinical gut bacterial isolates. I will then use wet lab techniques and anaerobic biology to culture the bacterial hosts and induce their resident prophages. Using these phage-host systems I will investigate prophage biology with relation to gut health. This will enable a greater understanding of the hidden genomic reservoir of our gut microbiome.