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Professor Mark Pallen


Vice-Chancellor's Fellow; Consultant Medical Microbiologist

Academic and research departments

School of Veterinary Medicine.

Publications

Rachel Gilroy, Anuradha Ravi, Maria Getino, Isabella Pursley, Daniel L. Horton, Nabil-Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martin Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand, Mark J. Pallen (2021)Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture, In: PeerJ (San Francisco, CA)9e10941 Peerj Inc

Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Matthew Crossfield, Rachel Gilroy, Anuradha Ravi, David Baker, Roberto M La Ragione, Mark J Pallen (2022)Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces, In: Microbiology resource announcements11(1)e0114221

We report the recovery of metagenome-assembled genomes (MAGs) from fecal samples collected in 2018 from five healthy adult female pigs in southeast England. The resulting nonredundant catalog of 192 MAGs encompasses 102 metagenomic species, 41 of them novel, spanning 10 bacterial and 2 archaeal phyla.

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