Projects | lesleyo

Gut microbiome - host interactions in health and disease

Humans are host to a variety of microbial residents, with the human gut harbouring the densest populations. There is growing awareness that these resident microbes have a significant impact on our health and wellbeing, therefore current research is focused on understanding the gut microenvironment, with the ultimate aim of being able to manipulate this complex community. Such strategies, however, require in-depth knowledge of the human gut and while efforts are already underway there remains a vast uncharted reservoir of biological “dark matter” waiting to be discovered in the form of human gut-specific bacteriophages (phages). Ongoing projects are taking a systems-level approach to the exploration of the tri-partite symbiosis between bacteriophage, bacteria and their human hosts in health and disease:

Phage-orientated dissection of whole community metagenomes

Bacteriophage represent an unexplored majority that is beginning to be recognised as a key facet of the human gut microbiome. High-throughput metagenomic studies are providing unprecedented glimpses into viral ecosystems, including the human gut, suggesting they are a potent force driving ecological functioning and evolutionary change. However, methods used to generate these datasets are targeted towards analysis of free-phage particles (virus-like particles) present at the time of sampling, which restricts access to the quiescent virome fraction and obscures host-range information. Whole-community metagenomes, which contain significant fractions of viral DNA (4-17%), represent a valuable resource for the analysis of phage communities and in tandem with VLP-derived datasets, have the potential to provide a more complete picture of the phage component of ecosystems. A genome-signature based approach has been developed for the phage-orienated dissection of conventional whole-community metagenomes. This method takes advantage of similarities in global nucleotide usage patterns, or the genome signature, arising between phage infecting the same or related host bacterial species. Application of this strategy has permitted the identification of a subset of gut-specific Bacteroidales-like phage sequences poorly represented in existing VLP-derived viral metagenomes. These phage sequences were shown to encode functions of direct relevance to human health, and provided new insights into the structure and composition of the human gut virome (Ogilvie et al., 2013, Nature Communications). Future work will now extend these analysis to incorporate other phylogenetic groups and investigate the usefuleness of the genome signature pipeline for the retrieval of other semi-conserved elements from whole community metagenomes.

Gut bugs, bacteriophage and colorectal cancer

Colorectal cancer (CRC) is the third most prevalent malignancy worldwide, leading to an estimated 609,000 deaths each year (WHO). Although it is known that CRC results from a complex interplay between host-derived genetic susceptibilities and environmental factors such as diet, the exactaetiology of the disease remains unknown, with epidemiological efforts failing to reveal concrete causal links and large scale dietary intervention studies failing to reduce disease risk. A growing body of recent work has started to implicate the indigenous gut microbial community as a significant factor in the pathogenesis of CRC, suggesting that resident microbes are mediating the effects of genetic and environmental factors leading to CRC. For the last couple of years i have been investigating the association between microbial bile acid modification in the human gut microbiome and acquisition of CRC. The capacity for bile acid metabolism in healthy individuals, and those with CRC and pre-cancerous polyps has been determined using a combination of functional and sequence-based metagenomics, metabolomics and qPCR , in tandem with bio-informatic analyses. To provide further mechanistic insight, cell and murine models of infection have been established to decipher the contribution of microbial bile salt hydrolase (BSH) to the activation of key host encoded genes involved in inflammation, inhibition of apoptosis, and acquisition of CRC. Ultimately, this work will take a major leap forward in clarifying the relationship between microbial bile acid metabolism and CRC, and aid elucidation of the underlying mechanisms of this disease. Results will be published soon!

While there is much interest in characterising the bacterial dysbiosis signature of CRC and exploring the bacterial oncogenic potential, data are severely lacking on the retinue of bacteriophage associated with the human gut microbiome, which are increasingly being recognised as an important facet of the gut ecosystem. Using a combination of microscopy, high-throughput sequencing and associated novel bioinformatics, this project aims to elucidate the potential role of phage in mediating CRC associated microbial dysbiosis. Collaborative work is also exploring the use of statistical techniques to identify potential associations between human genetic and microbial CRC signatures from tumour samples.

Exploring the diagnostic potential of human gut specific bacteriophage

Information regarding the ecology and composition of phage infecting predominant bacterial types within the gut are virtually absent. Previous work carried out by myself and colleagues has not only highlighted the paucity of information on this component of the gut microbiome but has also hinted at an intriguing association with the onset of human gut inflammatory diseases such as Crohn’s disease. Further understanding of the role of human gut-specific phage within healthy and diseased individuals is crucial to the successful harnessing of the full diagnostic and/or therapeutic potential of the human gut microbiome. Current work is seeking to determine the association between human gut-specific phages and the acquisition of inflammatory bowel disease. In doing so we will determine the usefulness of gut-specific phages as novel disease biomarkers through a blend of culture-dependent and molecular methods, in combination with novel high-resolution bioinformatic analyses, which will effectively shine a light on the gut microbiome.

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