MicroBinfie Podcast, 84 Bioinformatics in the noughties with Mark Pallen - MicroBinfie Podcast
MicroBinfie Podcast

MicroBinfie Podcast, 84 Bioinformatics in the noughties with Mark Pallen

  • Jun 09, 2022

Mark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time from model organisms and fearsome pathogens.

He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Pallen describes the addictive exhilaration of using PSI-BLAST to find new sortases and sortase substrates across a range of new genomes—for him this was the bioinformatics equivalent of crack cocaine. He quotes the philosopher Alfred North Whitehead in saying that the goal of every scientist is to seek simplicity but distrust it. What Mark found was that in most organisms sortases were behaving quite differently from the rather simple scenario seen in Staphylococcus aureus. He made similar observations on the WXG100 proteins and type VII secretion, which he found in many new contexts quite different from the original context of ESAT-6 as an antigen in Mycobacterium tuberculosis. Mark makes clear that we still don’t really fully understand the role of ESAT-6 twenty years on. The focus of Pallen’s work then shifted to E. coli, where he described vestigial gene clusters for non-functional type III secretion systems in this model organism. He came to realize that E. coli K-12 was not handed to microbiologist by God as a model organism but was just another strain of E. coli and nothing special. Many of the earliest genomes to be sequenced came from worn-out lab strains. To counter this problem, Gordon Dougan at the Wellcome Trust Sanger Institute moved the focus to genome-sequencing freshly isolated minimally passaged isolates. With Brendan Wren, Pallen wrote a review article for nature, emphasizing the importance of adopting an eco-evo perspective when trying to interpret bacterial genomes. Around that time, Scott Beatson joined Pallen’s group. Mark managed to persuade Scott to work on type III secretion in E. coli rather than Pseudomonas aeruginosa. The result was the discovery of dozens of new type III secretion effectors, tying together bioinformatics and lab work to culminate in a PNAS paper.

Selective bibliography

  • Konings, F, Perkins, MD, Kuhn, JH, Pallen, MJ, Alm, EJ, Archer, BN, Barakat, A, Bedford, T, Bhiman, JN, Caly, L, Carter, LL, Cullinane, A, de Oliveira, T, Druce, J, El Masry, I, Evans, R, Gao, GF, Gorbalenya, AE, Hamblion, E, Herring, BL, Hodcroft, E, Holmes, EC, Kakkar, M, Khare, S, Koopmans, MPG, Korber, B, Leite, J, MacCannell, D, Marklewitz, M, Maurer-Stroh, S, Rico, JAM, Munster, VJ, Neher, R, Munnink, BO, Pavlin, BI, Peiris, M, Poon, L, Pybus, O, Rambaut, A, Resende, P, Subissi, L, Thiel, V, Tong, S, van der Werf, S, von Gottberg, A, Ziebuhr, J, Van Kerkhove, MD (2021) SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse Nature Microbiology 6 (7) 821 823
  • Pallen, MJ, Alikhan, NF (2021) Naming the Unnamed: Over 45,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database Preprints https://doi.org/10.20944/preprints2021110557v1
  • Pallen MJ (2021) Bacterial nomenclature in the era of genomics New Microbes New Infect 44 100942 https://doi.org/10.1016/jnmni2021100942
  • Pallen, MJ, Telatin, A, Oren, A (2021) The Next Million Names for Archaea and Bacteria Trends in Microbiology 29 (4) 289 298 https://doi.org/10.1016/jtim202010009
  • Gilroy, R, Ravi, A, Getino, M, Pursley, I, Horton, DL, Alikhan, N-F, Baker, D, Gharbi, K, Hall, N, Watson, M, Adriaenssens, EM, Foster-Nyarko, E, Jarju, S, Secka, A, Antonio, M, Oren, A, Chaudhuri, RR, Ragione, RL, Hildebrand, F, Pallen, MJ (2021) Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture PeerJ 9 e10941 https://doi.org/10.7717/peerj10941
  • Ravi, A, Halstead, FD, Bamford, A, Casey, A, Thomson, NM, Van Schaik, W, Snelson, C, Goulden, R, Foster-Nyarko, E, Savva, GM, Whitehouse, T, Pallen, MJ, Oppenheim, BA (2019) Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients Microbial Genomics 5 (9) 293 https://doi.org/10.1099/mgen0000293
  • Connor, TR, Loman, NJ, Thompson, S, Smith, A, Southgate, J, Poplawski, R, Bull, MJ, Richardson, E, Ismail, M, Thompson, SE, Kitchen, C, Guest, M, Bakke, M, Sheppard, SK, Pallen, MJ (2016) CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community Microbial genomics 2 (9) e000086 https://doi.org/10.1099/mgen0000086
  • Loman NJ, Pallen MJ (2015) Twenty years of bacterial genome sequencing. Nat Rev Microbiol 13:787–794. https://doi.org/10.1038/nrmicro3565
  • Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M*, Gaffney V, Allaby RG (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science 347:998–1001. https://doi.org/10.1126/science.1261278
  • Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ (2015) Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat
  • Halachev MR, Chan JZ, Constantinidou CI, Cumley N, Bradley C, Smith-Banks M, Oppenheim B, Pallen MJ (2014) Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Med 6:70. https://doi.org/10.1186/s13073-014-0070-x
  • Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ (2014) Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One 9:e91941. https://doi.org/10.1371/journal.pone.0091941
  • Pallen MJ (2014) Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology 141:1856–1862. https://doi.org/10.1017/S0031182014000134 Citations: 103
  • Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ (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. https://doi.org/10.7717/peerj.585
  • Chan JZ, Sergeant MJ, Lee OY, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ (2013) Metagenomic analysis of tuberculosis in a mummy. N Engl J Med 369(3):289–290. https://doi.org/10.1056/NEJMc1302295
  • Robinson ER, Walker TM, Pallen MJ (2013) Genomics and outbreak investigation: from sequence to consequence. Genome Med 5:36. https://doi.org/10.1186/gm440
  • Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309:1502–1510. https://doi.org/10.1001/jama.2013.3231
  • Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439. https://doi.org/10.1038/nbt.2198
  • Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599–606. https://doi.org/10.1038/nrmicro2850
  • Chan JZ, Pallen MJ, Oppenheim B, Constantinidou C (2012) Genome sequencing in clinical microbiology. Nat Biotechnol 30:1068–1071. https://doi.org/10.1038/nbt.2410
  • Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ (2012) Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12:302. https://doi.org/10.1186/1471-2180-12-302
  • Mol Microbiol 79:468–483. https://doi.org/10.1111/j.1365-2958.2010.07460.x
  • Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ*, Wang J, Aepfelbacher M, Yang R (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365:718–724. https://doi.org/10.1056/NEJMoa1107643
  • Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, Pallen MJ (2010) High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect 75:37–41. https://doi.org/10.1016/j.jhin.2010.01.012
  • Pallen MJ (2010) High-throughput sequencing as a tool in the discovery, diagnosis and epidemiology of nosocomial pathogens. Journal of Hospital Infection 76:S1. https://doi.org/10.1016/S0195-6701(10)00376-2
  • Pallen MJ, Loman NJ, Penn CW (2010) High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol 13:625–631. https://doi.org/10.1016/j.mib.2010.08.003
  • Pallen MJ, Nelson KE, Preston GM (2007) Bacterial Pathogenomics (ASM Press, Washington, DC, [Edited Book]
  • Pallen MJ (2007) Introduction to Pathogenomics in Bacterial Pathogenomics, eds Pallen
  • Tobe T, Beatson SA, Taniguchi H, Abe H, Bailey CM, Fivian A, Younis R, Matthews S, Marches O, Frankel G, Hayashi T, Pallen MJ (2006) An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci U S A 103:14941–14946. https://doi.org/10.1073/pnas.0604891103
  • Pallen MJ, Beatson SA, Bailey CM (2005) Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FEMS Microbiol Rev 29:201–229. https://doi.org/10.1016/j.femsre.2005.01.001
  • Pallen MJ, Beatson SA, Bailey CM (2005) Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion. BMC Microbiol 5:9. https://doi.org/10.1186/1471-2180-5-9
  • Pallen MJ, Penn CW, Chaudhuri RR (2005) Bacterial flagellar diversity in the post-genomic era. Trends in Microbiology 13:143–149. https://doi.org/10.1016/j.tim.2005.02.008
  • Ideses D, Gophna U, Paitan Y, Chaudhuri RR, Pallen MJ, Ron EZ (2005) A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis. J Bacteriol 187:8164–8171. https://doi.org/10.1128/JB.187.23.8164-8171.2005
  • Ren CP, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM, Pallen MJ (2004) The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriol 186:3547–3560. https://doi.org/10.1128/JB.186.11.3547-3560.2004
  • Zhang L, Chaudhuri RR, Constantinidou C, Hobman JL, Patel MD, Jones AC, Sarti D, Roe AJ, Vlisidou I, Shaw RK, Falciani F, Stevens MP, Gally DL, Knutton S, Frankel G, Penn CW, Pallen MJ (2004) Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7. Infect Immun 72:7282–7293. https://doi.org/10.1128/IAI.72.12.7282-7293.2004
  • Chaudhuri RR, Khan AM, Pallen MJ (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res 32:D296–9. https://doi.org/10.1093/nar/gkh031
  • Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J (2003) The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res 31:6516–6523. https://doi.org/10.1093/nar/gkg874
  • Pallen MJ, Francis MS, Futterer K (2003) Tetratricopeptide-like repeats in type-III-secretion chaperones and regulators. FEMS Microbiol Lett 223:53–60. https://doi.org/10.1016/S0378-1097(03)00344-6
  • Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA, Dover LG, Norbertczak HT, Besra GS, Quail MA, Harris DE, von Herbay A, Goble A, Rutter S, Squares R, Squares S, Barrell BG, Parkhill J, Relman DA (2003) Sequencing and analysis of the genome of the Whipple’s disease bacterium Tropheryma whipplei. Lancet 361:637–644. https://doi.org/10.1016/S0140-6736(03)12597-4
  • Roche FM, Massey R, Peacock SJ, Day NP, Visai L, Speziale P, Lam A, Pallen M, Foster TJ (2003) Characterization of novel LPXTG-containing proteins of Staphylococcus aureus identified from genome sequences. Microbiology 149:643–654. https://doi.org/10.1099/mic.0.25996-0
  • Pallen MJ (2002) The ESAT-6/WXG100 superfamily – and a new Gram-positive secretion system? Trends in Microbiology 10:209–212. https://doi.org/10.1016/S0966-842X(02)02345-4
  • Spiers A, Lamb HK, Cocklin S, Wheeler KA, Budworth J, Dodds AL, Pallen MJ, Maskell DJ, Charles IG, Hawkins AR (2002) PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide. J Biol Chem 277:39443–39449. https://doi.org/10.1074/jbc.M202790200
  • Pallen M (2002) From sequence to consequence: In silico hypothesis generation and testing. Methods in Microbiology 33:27–48. https://doi.org/10.1016/S0580-9517(02)33003-4
  • Pallen M, Chaudhuri R, Khan A (2002) Bacterial FHA domains: neglected players in the phospho-threonine signalling game? Trends in Microbiology 10:556–563. https://doi.org/10.1016/S0966-842X(02)02476-9
  • Pallen MJ, Lam AC, Loman N (2001) Tricorn-like proteases in bacteria. Trends in Microbiology 9:518–521. https://doi.org/10.1016/S0966-842X(01)02199-0
  • Pallen MJ, Lam AC, Antonio M, Dunbar K (2001) An embarrassment of sortases - a richness of substrates? Trends in Microbiology 9:97–102. https://doi.org/10.1016/S0966-842X(01)01956-4
  • Pallen MJ, Lam AC, Loman NJ, McBride A (2001) An abundance of bacterial ADP-ribosyltransferases–implications for the origin of exotoxins and their human homologues. Trends in Microbiology 9:302–7; discussion 308. https://doi.org/10.1016/S0966-842X(01)02074-1
  • Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S, Jagels K, Karlyshev AV, Moule S, Pallen MJ, Penn CW, Quail MA, Rajandream MA, Rutherford KM, van Vliet AH, Whitehead S, Barrell BG (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665–668. https://doi.org/10.1038/35001088
  • Ponting CP, Pallen MJ (1999) beta-propeller repeats and a PDZ domain in the tricorn protease: predicted self-compartmentalisation and C-terminal polypeptide-binding strategies of substrate selection. FEMS Microbiol Lett 179:447–451.
  • Ponting CP, Pallen MJ (1999) A beta-propeller domain within TolB. Mol Microbiol 31:739–740. https://doi.org/10.1046/j.1365-2958.1999.01168.x
  • Pallen MJ, Ponting CP (1997) PDZ domains in bacterial proteins. Mol Microbiol 26(2):411–413. https://doi.org/10.1046/j.1365-2958.1997.5591911.x
  • Pallen MJ (1996) Medicine and the Internet: dreams, nightmares and reality. Br J Hosp Med 56:506–509.
  • Pallen M, Kiley R (1996) Medical Information on the Internet. British Medical Journal 313:1411. https://doi.org/10.1136/bmj.313.7069.1411a
  • Mullany P, Pallen M, Wilks M, Stephen JR, Tabaqchali S (1996) A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile. Gene 174:145–150. https://doi.org/10.1016/0378-1119(96)00511-2
  • Pallen MJ (1995) Medicine and the internet: dreams, nightmares and reality. British journal of hospital medicine 56:506–509.
  • Pallen M (1995) Guide to the Internet: Introducing the Internet. British Medical Journal 311:1422–1424. https://doi.org/10.1136/bmj.311.7017.1422
  • Pallen M (1995) Guide to the Internet: Electronic mail. British Medical Journal 311:1487–1490. https://doi.org/10.1136/bmj.311.7018.1487
  • Pallen M (1995) Guide to the Internet. The world wide web. British Medical Journal 311:1552–1556. https://doi.org/10.1136/bmj.311.7019.1552
  • Pallen M (1995) Guide to the Internet. Logging in, fetching files, reading news. British Medical Journal 311:1626–1630. https://doi.org/10.1136/bmj.311.7020.1626
  • Pallen MJ, Hay AJ, Puckey LH, Efstratiou A (1994) Polymerase chain reaction for screening clinical isolates of corynebacteria for the production of diphtheria toxin. J Clin Pathol 47:353–356. https://doi.org/10.1136/jcp.47.4.353
  • Mullany P, Clayton CL, Pallen MJ, Slone R, al-Saleh A, Tabaqchali S (1994) Genes encoding homologues of three consecutive enzymes in the butyrate/butanol-producing pathway of Clostridium acetobutylicum are clustered on the Clostridium difficile chromosome. FEMS Microbiol Lett 124:61–67. https://doi.org/10.1111/j.1574-6968.1994.tb07262.x
  • Clayton CL, Pallen MJ, Kleanthous H, Wren BW, Tabaqchali S (1990) Nucleotide sequence of two genes from Helicobacter pylori encoding for urease subunits. Nucleic Acids Res 18:362. https://doi.org/10.1093/nar/18.2.362