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Professor Mark Pallen


Vice-Chancellor's Fellow

Academic and research departments

School of Veterinary Medicine.

My publications

Publications

Rachel Gilroy, Joy Leng, Anuradha Ravi, Evelien Adriaenssens, Aharon Oren, Dave Baker, Roberto M. La Ragione, Christopher Proudman, Mark J. Pallen (2022)Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity, In: PeerJ – the Journal of Life & Environmental Sciences10e13084 PeerJ

Background The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. Results We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes. Conclusions Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

Anuradha Ravi, Fenella D Halstead, Amy Bamford, Anna Casey, Nicholas M. Thomson, Willem van Schaik, Catherine Snelson, Robert Goulden, Ebenezer Foster-Nyarko, George M. Savva, Tony Whitehouse, Mark J. Pallen, Beryl A. Oppenheim (2019)Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients, In: Microbial Genomics5(9)pp. 1-12 Microbiology Society

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of