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Microbiome researchers in the Department of Life Sciences

Find out more about the people currently working in microbiome research and their areas of study.


Neil Brown

Our food, and particularly animal feed, is increasingly contaminated with harmful fungal toxins, costing billions, and threatening our health and food security. I am focused on finding solutions to this problem. One aspect of my research aims to understand fungal interactions with the microbiome in farming environments. Competing microbes isolated from these environments produce natural antifungal compounds and detoxifying enzymes, which could be exploited in developing alternative strategies to protect, or detoxify, infected cereal crops, to deliver safer food and feed for farmed animals.

Volkan Cevik

We study how fungal and oomycete plant pathogens manipulate host cellular processes and evade plant immunity to impose susceptibility. We are also interested in determining how rhizosphere and phyllosphere microbiomes impact the diseases caused by such plant pathogens and, in turn, how these pathogens shape microbial community structure through their secreted proteins.

Ed Feil

We use genomics data on multiple human and animal pathogens to address basic questions in population biology and evolution, and more public health-facing challenges regarding epidemiology and antimicrobial resistance (AMR). In recent years we have focused on non-clinical (‘One Health’) settings. We analysed metagenomic data from wastewater and the broader urban water cycle to investigate the anthropogenic impact of the abundance of AMR. We have also characterised the microbiome of lumpfish (Cyclopterus lumpus), now being farmed as a ‘cleaner fish’ to help mitigate the spread of lice on farmed salmon. This study aimed to minimize pathogen transmission and maintain the health of both lumpfish and salmon. We are currently contributing to a project investigating the impact of exercise on human gut microbial communities. We're also interested in microbial community dynamics, and in particular, deploying statistical approaches to large-scale ‘omics' data to identify antagonistic interactions between pathogenic bacteria and fungi.

Daniel Henk

Fungi are critical, yet often ignored, components in diverse microbial communities that live alongside, connected to, and inside both plants and animals. Often these fungi fill multiple roles within systems acting as both specialists and generalists. Our work focuses on fungal interactions in microbial communities and how those interactions modify the stability and functioning of the communities in healthy and diseased contexts, both in the short term of a growth chamber or single host and over the longer term of evolution and diversification. While all of our work is focused on fungi, we try to span a wide array of systems from microbes inside of plant seeds and covering their leaves to those in animal guts and covering their skin. We aim to translate what we learn from these communities into applications for health, sustainable industries, and education. We use a variety of methods including a combination of ecological study, phylogenomics, population genomics, metabolic models, experimental evolution, and chemical analysis to pick apart fungal components of community responses to perturbation and the trajectories of evolutionary change in fungal genomes themselves in response to biotic and abiotic changes.

Vicky Hunt

We are interested in intestinal parasites such as the soil-transmitted helminth, Strongyloides spp., which infects over 600 million people worldwide. We use both shotgun metagenomics (long and short read) and PCR-based methods to investigate intestinal flora and fauna of humans and other animals. This aspect of our research focuses on:

  • Dysbiosis in the gastrointestinal system associated with helminth parasite infection, and
  • How methods to characterise the microbiome can be developed as a diagnostic for gastrointestinal parasites and to detect co-infections in the intestine.

These studies embrace both experimental wet-lab research and computational analysis, using established laboratory study systems, as well as human and wildlife samples.

Zamin Iqbal

Our expertise lies in genomic analysis of genetic variation of bacteria and their mobile elements, in particular using graph genomes. The lab is interested in tracking and modelling the evolution of plasmids, vertically and horizontally. A long-term interest is the diversity of plasmids, the nature of their cargo, and differences in mutation/rearrangement rates in microbiomes from pristine to polluted environments, to clinical and then to the human gut. We are very interested in ideas and collaborations relating to technological solutions to associate plasmids with their hosts in the microbiome.

Brian Jones

The overall theme of work in my laboratory is to understand the role of bacteria in health and disease. Within this broad theme, we have a particular focus on aspects of the human gut microbiome and polymicrobial communities that develop during medical device-associated infections. Recent and ongoing work in these areas includes projects aimed at providing a fundamental understanding of how distinct routes of antibiotic delivery impact the gut microbiome and contribute to the development of antibiotic resistance in this ecosystem. Our work with colleagues at the United Kingdom Health Security Agency examines the evolution of antimicrobial resistance within microbiomes associated with infection or the wider healthcare environment. This includes developing in vitro models of polymicrobial infections in the catheterised urinary tract, which are being used to understand the response of these microbiomes to biocide exposure, and the consequences of bacterial adaptation to commonly used antiseptics and disinfectants.

Stephanie Lo

The respiratory microbiome represents a complex ecosystem of microorganisms that reside within the respiratory tract, influencing human health and disease states. Our research focuses on understanding the intricate interactions among these microbial communities (microbe-microbe interactions); and between the microbiome and the host (microbe-host interactions). Understanding these interactions provides critical insights into the mechanisms of respiratory health; the pathogenesis of diseases; and potentially informs novel vaccine design and therapeutic strategies.

Charareh Pourzand

Chronic exposure of skin to sunlight has been shown to enrich the skin microbiome with UVB-resistant bacterial families, producing photoprotective metabolites against sun damage. A current interest in our laboratory is to evaluate the radiation-specific effects of the oxidising components of sunlight - notably UVA, visible and near-infrared - on the skin microbiome, using reconstructed human epidermal models colonised with human microbiota. Identifying radiation-specific metabolomic fingerprints of sun-exposed skin can clarify the interactions between the skin and its microbiota. This will provide novel metabolites as skin photo-protectants for longer wavelengths of sunlight, for which this research is currently internationally leading.

Tamas Szekely

The association between an animal and its gut microbiota is a particularly complex symbiosis in which microbes regulate a multitude of processes associated with host health and fitness, such as nutrition uptake and pathogen defence. The microbiomes of wild animals are understudied, and the possible associations between microbiome, immune system and fitness need to be better understood. Our team is working on 4 related topics:

  • We quantify the microbiome diversity of shorebirds (plovers, sandpipers and allies) in several field sites in Africa, Asia and Europe, and seek to understand the association between individual birds’ microbiomes and their fitness.
  • The gut bacteria can crosstalk with the response from the adaptive immune system in the host. We hypothesize that MHC variation, alongside other host and environmental factors, is associated with individual gut microbiota variation.
  • We previously demonstrated that male and female shorebirds have different mortality patterns, and we are now comparing the microbiome of males and females. Specifically, we are testing whether sex-different microbiomes predict sex-different mortalities.
  • Finally, we are investigating the microbiomes of endangered shorebirds and comparing them to the microbiomes of non-endangered species.

Tiffany Taylor

An overarching aim of our research is to understand the predictability of evolution across scales. Firstly, at the level of the gene regulatory network, we investigate why certain genes are more accessible to evolution for co-option during rewiring than others. At the molecular level, we explore features of the DNA that bias evolutionary outcomes. We aim to understand how these features work together to drive adaptive outcomes across different environments and genetic backgrounds, with potential applications in synthetic biology. We also explore the role of multiple bacterial defence systems, such as CRISPR-Cas, in driving bacteria-phage interactions. Our research investigates the evolutionary and ecological drivers of defence system acquisition, maintenance, and regulation across different strains and environments. Future ambitions include developing strategies to build ecological complexity into our approaches, to deepen our comprehension of evolutionary processes across both community and molecular scales within relevant microbiome communities.

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