Mark Pallen

Mark Pallen
Born	Mark John Pallen 1960 (age 63–64) Carshalton, England
Alma mater	Fitzwilliam College, Cambridge, London Hospital Medical College, Imperial College
Scientific career
Fields	Microbiology Metagenomics Evolution Bioinformatics Genomics Nomenclature Bacteriology
Institutions	London Hospital Medical College Royal Free Hospital St Bartholomew's Hospital Medical College Queen's University Belfast University of Birmingham University of Warwick Quadram Institute University of East Anglia University of Surrey
Doctoral advisor	Gordon Dougan
Doctoral students	Nick Loman
Website	quadram.ac.uk/people/mark-pallen

Mark J. Pallen is a research leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, he has been at the forefront of efforts to apply next-generation sequencing to problems in microbiology and ancient DNA research.

Education

Pallen was educated at Wallington High School.^[1] He completed an undergraduate degree in medical sciences at Fitzwilliam College, Cambridge and gained his medical qualification from the London Hospital Medical College.^[2][3] During the early 1990s, he gained an MD while working at St Bartholomew's Hospital Medical College.^[4] In the mid-1990s, he worked for a PhD ^[5] under the supervision of Gordon Dougan at Imperial College. During this time, he captained the winning team from Imperial College in the TV quiz show University Challenge,^[6] while also writing a series of articles for the British Medical Journal, introducing the medical profession to the Internet.^[7]

Microbial genomics, metagenomics and bioinformatics

In 2011, Pallen led a crowdsourced 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.^[8] Around the same time, he 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.^[9] He has also shown that whole-genome sequencing can be used to track the spread of resistant bacteria ^[10] and to study the emergence of antimicrobial resistance .^[11]

Through analyses of fecal samples from the 2011 German E. coli O104:H4 outbreak and sputum samples from The Gambia, Pallen showed that metagenomics can be used as a culture-independent approach to the diagnosis of bacterial infection.^[12][13] He has pioneered the use of metagenomics to open up new avenues in ancient DNA research, recovering 200-year-old Mycobacterium tuberculosis genomes from human remains and a medieval Brucella genome sequence.^[14][15] With Vince Gaffney and Robin Allaby, he has applied shotgun metagenomics to sedimentary ancient DNA samples, showing the presence of wheat in the British Isles 2000 years earlier than expected.^[16] Pallen has also used metagenomics to investigate the chicken gut microbiome, the gut microbiome of patients on the intensive care unit and the microbes that inhabit ticks.^[17][18][19]

From 2014 to 2020, Pallen was Principal Investigator on the £8 million MRC-funded cloud-computing project the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) and now serves as director of the successor project CLIMB-BIG-DATA.^{[20][21][22][23]} In 2020, the CLIMB project received the HPCWire Readers’ Best High Performance Computing Collaboration Award for supporting analysis and publication of coronavirus genome sequences during the COVID-19 pandemic.^[24]

Microbial nomenclature

Pallen's studies on the chicken gut microbiome led him to propose over 800 new names for bacterial taxa found in this setting.^[17] Pallen then developed a system for automating the creation of taxonomic names for bacteria, which resulted in the publication of over a million new names available for use by the microbiology research community to name new bacterial genera.^[25][26] Subsequently, in an opinion piece in the journal New Microbes and New Infections ^[27] and an invited talk for Bergey's International Society for Microbial Systematics,^[28] Pallen outlined his ideas for making bacterial nomenclature more accessible. In 2022, Pallen published over 65,000 names for previously unnamed bacterial and archaeal taxa in the Genome Taxonomy Database, using Python scripts to create user-friendly arbitrary names that comply with the phonotactics and grammar of Latin.^[29]

Pallen has also been active in viral nomenclature, starting with the creation of over 400 species epithets for the bacterial positive-sense single-stranded viruses in the family Leviviridae. ^[30] In March 2021, Pallen suggested in an Opinion article in New Scientist that an alternative should be found to the use of geographical names for variants of SARS-CoV-2, raiding the classical world for options.^[31] In early 2021, Pallen participated in a WHO working group, priming adoption of a scheme for naming variants of SARS-CoV-2 after letters in the Greek alphabet.^[32]

In recognition of Pallen's efforts in automating creation of names for microbes, in 2022 the name Palleniella was created for a new bacterial genus previously within the genus Prevotella. ^[33][34][35]

Public understanding of science

Pallen is the author of a popular science book, The Rough Guide to Evolution.^[36] In the wake of the 2005 Kitzmiller v. Dover Area School District trial, he wrote a review with Nick Matzke, outlining the evidence that the bacterial flagellum is an evolved rather than designed entity.^[37] He 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, Pallen appeared in an episode of Melvin Bragg's In our Time radio programme.^[38]

In 2018, Pallen published a book on the 1978 smallpox outbreak in the United Kingdom, The Last Days of Smallpox: Tragedy in Birmingham,^[39] which includes a mixture of popular science and a historical narrative of the outbreak and subsequent court case. Pallen has served alongside Alice Roberts on the advisory board of the Milner Centre for Evolution at the University of Bath^[40]

References

1. "Distinguished Alumni - Wallington County Grammar School". www.wcgs-sutton.co.uk.
2. "Good reads from Fitz". www.fitz.cam.ac.uk. 17 April 2020.
3. Society, Microbiology. "Fleming Showcase speaker profile: Professor Mark Pallen". microbiologysociety.org.
4. Pallen, Mark John (1993). Detection and characterisation of diphtheria toxin genes and insertion sequences by PCR and other molecular techniques. MD thesis, St Bartholomew's Hospital Medical College, 1993 (Ph.D).
5. Pallen, Mark John (1998). An investigation into the links between stationary phase and virulence in Salmonella enterica entercial serovar typhimurium. PhD thesis, Imperial College London, 1998 (Ph.D).
6. "University Challenge winners – May 1996".
7. Mark Pallen (1995). "Guide to the Internet: Introducing the Internet". British Medical Journal. 311 (7017): 1422–4. doi:10.1136/bmj.311.7017.1422. PMC 2544383. PMID 8520280.
8. Rohde; et al. (2011). "Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4" (PDF). N Engl J Med. 365 (8): 718–24. doi:10.1056/NEJMoa1107643. PMID 21793736.
9. Loman; et al. (2012). "Performance comparison of benchtop high-throughput sequencing platforms". Nature Biotechnology. 30 (5): 434–9. doi:10.1038/nbt.2198. PMID 22522955. S2CID 5300923.
10. Halachev; et al. (2014). "Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England". Genome Medicine. 6 (11): 70. doi:10.1186/s13073-014-0070-x. PMC 4237759. PMID 25414729.
11. Hornsey; et al. (2011). "Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy". J Antimicrob Chemother. 66 (7): 1499–503. doi:10.1093/jac/dkr168. PMID 21565804.
12. Loman; et al. (2013). "A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4". JAMA. 309 (14): 1502–10. doi:10.1001/jama.2013.3231. PMID 23571589.
13. Doughty; et al. (2014). "Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer". PeerJ. 2: e585. doi:10.7717/peerj.585. PMC 4179564. PMID 25279265.
14. Kay; et al. (2015). "Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe". Nature Communications. 6: 6717. Bibcode:2015NatCo...6.6717K. doi:10.1038/ncomms7717. PMC 4396363. PMID 25848958.
15. Kay; et al. (2015). "Recovery of a medieval Brucella melitensis genome using shotgun metagenomics". MBio. 5 (4): e01337-14. doi:10.1128/mBio.01337-14. PMC 4161259. PMID 25028426.
16. Smith; et al. (2015). "Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago". Science. 347 (6225): 998–1001. Bibcode:2015Sci...347..998S. doi:10.1126/science.1261278. hdl:10454/9405. PMID 25722413. S2CID 1167101.
17. Gilroy; et al. (2021). "Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture". PeerJ. 9: e10941. doi:10.7717/peerj.10941. PMC 8035907. PMID 33868800.
18. Ravi; et al. (2019). "Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients". Microbial Genomics. 5 (9). doi:10.1099/mgen.0.000293. PMC 6807385. PMID 31526447.
19. Ravi; et al. (2019). "Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus". PLoS Negl Trop Dis. 13 (1): e0006805. doi:10.1371/journal.pntd.0006805. PMC 6347332. PMID 30640905.
20. "Cloud Infrastructure for Microbial Bioinformatics".
21. "The MRC Consortium for Medical Microbial Bioinformatics".
22. "CLIMB-BIG-DATA: A Cloud Infrastructure for Big-Data Microbial Bioinformatics".
23. Connor; et al. (2016). "CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community". Microbial Genomics. 2 (9): e000086. doi:10.1099/mgen.0.000086. PMC 5537631. PMID 28785418.
24. "CLIMB Receives Honours in 2020 HPCwire Readers' and Editors' Choice Awards". 16 November 2020.
25. Pallen; et al. (2020). "The Next Million Names for Archaea and Bacteria". Trends Microbiol. 29 (4): 289–298. doi:10.1016/j.tim.2020.10.009. PMID 33288384.
26. "Researchers Propose Automating the Naming of Novel Microbes".
27. Pallen (2021). "Bacterial nomenclature in the era of genomics". New Microbes and New Infections. 44: 100942. doi:10.1016/j.nmni.2021.100942. PMC 8479249. PMID 34621526.
28. "BISMiS Live - 2022 Inaugural Session with Mark Pallen". YouTube. 20 February 2022.
29. Pallen; et al. (2022). "Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database" (PDF). International Journal of Systematic and Evolutionary Microbiology. 72 (9): 005482. doi:10.1099/ijsem.0.005482. PMID 36125864.
30. "Code assigned: 2020.095 B".
31. "Coronavirus variant names are too confusing. There is a better way".
32. Konings; et al. (2022). "SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse". Nature Microbiology. 6 (7): 821–823. doi:10.1038/s41564-021-00932-w. hdl:1887/3214303. PMID 34108654.
33. Hitch; et al. (2022). "A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter". Systematic and Applied Microbiology. 45 (6): 126354. Bibcode:2022SyApM..4526354H. doi:10.1016/j.syapm.2022.126354. PMID 36067550.
34. "NCBI Taxonomy Palleniella".
35. "LPSN genus Palleniella".
36. Mark Pallen (2009). The Rough Guide to Evolution. Rough Guides Limited. ISBN 978-1858289465.
37. Mark J. Pallen and Nicholas J. Matzke (2006). "From The Origin of Species to the origin of bacterial flagella" (PDF). Nature Reviews Microbiology. 4 (10): 784–790. doi:10.1038/nrmicro1493. PMID 16953248. S2CID 24057949.
38. "BBC Radio 4 - In Our Time, The Origins of Infectious Disease". BBC.
39. Mark Pallen (2018). The Last Days of Smallpox: Tragedy in Birmingham. Independently Published. ISBN 978-1980455226.
40. "Milner Centre for Evolution Advisory Board". www.bath.ac.uk.