Prof. Mark Pallen

Group Leader

Contact via email

Bacterial Genomics and Metagenomics

I am a Group Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, I have been at the forefront of efforts to apply high-throughput sequencing to problems in microbiology and ancient DNA research. I started academic life as a medical microbiologist, with training in medicine (BA from Cambridge MBBS, MD from London) and laboratory research (PhD in Gordon Dougan’s lab at Imperial College, during which I captained the winning team in University Challenge). I am director of the MRC Doctoral Training Programme Microbes, Microbiomes and Bioinformatics.

I have a track record of over fifteen years of research council funding for a research programme that spans bioinformatics and bench-based research. My research interests have included bacterial protein secretion and gene regulation, particularly in E. coli; the evolution of domains, proteins and bacterial flagella; and microbial pathogenomics.

In 2011, I wrote-up a crowd-sourced analysis of the genome of the outbreak strain from the 2011 German E. coli O104:H4 outbreak, which had been genome-sequenced on the Ion Torrent platform by the BGI. Around the same time, I also led a project in which an isolate from the 2011 German E. coli O104:H4 outbreak was genome-sequenced on three new benchtop sequencing platforms, benchmarking these new platforms.

In recent years, I have turned my attention to the genomic epidemiology of bacterial pathogens of humans and animals (e.g. multi-drug resistant Acinetobacter baumannii, MDR-TB in Africa, Staphylococcus aureus in monkeys and Brachyspira in pigs) and to pioneering new applications of metagenomics, including the characterisation of complex microbial communities (particularly gut microbiomes), the detection of pathogens in historical samples (includes recovery of medieval Brucella and leprosy genomes) and sedimentary ancient DNA studies (shedding light on the Neolithic transition).

Through analyses of faecal samples from the 2011 German E. coli O104:H4 outbreak and sputum samples from the Gambia, I have shown that metagenomics can be used as a culture-independent approach to the diagnosis of bacterial infection. With collaborators in Palestine, I have been using metagenomics approaches to detect pathogens in ticks. Since joining the Quadram Institute, I have developed an interest in the development of smart probiotics using synthetic biology approaches and consolidated my interests in the gut microbiomes of food animals and of critically ill patients.

I am Principal Investigator on the £8.4m MRC-funded Cloud Infrastructure in Microbial Bioinformatics (CLIMB) project, a cross-institutional collaboration to develop and deploy a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK.

I have made important contributions to public understanding of science. I am the author of The Rough Guide to Evolution, a popular and wide-ranging introduction to Charles Darwin, the theory of evolution and their ramifications in science and society, which has earned numerous five-star reviews. With Nick Matzke, I have written a review article, outlining the evidence that the bacterial flagellum is an evolved rather than designed entity. I commissioned and peer-reviewed Baba Brinkman’s Rap Guide to Evolution and was responsible for recruiting Alice Roberts to the role of Professor of Public Engagement in Science at the University of Birmingham. In June 2011, I appeared in an episode of Melvin Bragg’s In our Time radio programme. I have written a book entitled The Last Days of Smallpox, covering the 1978 Birmingham smallpox incident and its aftermath.

In recent years, I have taught on microbiology and human genome evolution: my recent lectures and research talks are available on my YouTube channel.

Key Publications

Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline, Millard, Andrew D., Quick, Joshua, Szikossy, Ildiko, Pap, Ildiko, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D., Pallen, Mark J. (2015). Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nature Communications, Volume 6, pp. 1-9

Smith, Oliver, Momber, G., Bates, R., Garwood, P., Fitch, S., Pallen, Mark J. (joint last author) Gaffney, V., Allaby, Robin G (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science, Volume 347 (Number 6225), pp. 998-1001

Halachev, Mihail R., Chan, Jacqueline, Constantinidou, Chrystala, Cumley, Nicola, Bradley, Craig, Smith-Banks, Matthew, Oppenheim, Beryl, Pallen, Mark J.(2014) Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Medicine, Volume 6 (Number 11), pp. 1-13

Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Rohde, Holger, Chan, Jacqueline, Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey, Betley, Jason R., Aepfelbacher, Martin, Pallen, Mark J. (2013) A culture independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-Toxigenic Escherichia coli O104:H4. JAMA: The Journal of the American Medical Association, Volume 309 (Number 14), pp. 1502-1510,

Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J., Constantinidou, Chrystala, Gharbia, Saheer E., Wain, John, Pallen, Mark J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, Volume 30 (Number 5), pp. 434-439 (cited >700 times)

Ereqat S, Alikhan N-F, Al-Jawabreh A, Matthews M, Al-Jawabreh A, de Oliveira Martins L, Al-Kaila M, Page A, Pallen M, Nasereddin . (2024)

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine


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Pallen M, Gilroy R, Kumar B, Adam M. (2023)

An initial genomic blueprint of the healthy human oesophageal microbiome

Access Microbiology

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Pallen . (2023)

Request for an Opinion on the standing and retention of Firmicutes as a phylum name

International journal of systematic and evolutionary microbiology, 73, ijsem.0.005933

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Pallen MJ, Rodriguez-R LM, Alikhan N. (2022)

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.

International journal of systematic and evolutionary microbiology

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Merhi G, Trotter AJ, de Oliveira Martins L, Koweyes J, Le Viet T, Abou Naja, Al Buaini, Prosolek SJ, Alikhan NF, Lott M, Tohmeh T, Badran B, Jupp OJ, Gardner S, Felgate MW, Makin KA, Wilkinson JM, Stanley R, Sesay AK, Webber MA, Davidson RK, Ghosn N, Pallen M, Hasan H, Page AJ, Tokajian . (2022)

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021.

Microbial genomics

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Thomson NICHOLAS, Gilroy RACHEL, Getino MARIA, Foster-nyarko EBENEZER, Van Vliet ARNOUD, La Ragione ROBERTO, Pallen MAR. (2022)

Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens

PeerJ, PeerJ 10:e12935

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