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Microbial Genomics


The Microbiology and Infection unit benefits from world-class expertise in microbial genomics and access to state-of-the-art facilities in high-throughput sequencing and bioinformatics.

Research in this field is underpinned by common interests in understanding the ecology, evolution, epidemiology and pathogenicity of bacterial pathogens through cutting-edge applications of:

  • High-throughput sequencing
  • Genomics
  • Metagenomics
  • Transcriptomics
  • Bioinformatics

Our work ranges from the fundamental science of model organisms to translational research on human and animal pathogens.

Current research:

  • Genomic epidemiology of nosocomial pathogens, particularly Acinetobacter baumannii (funded by MRC)
  • The chicken gut microbiome: includes shotgun metagenomics and 16S rRNA studies (funded by BBSRC)
  • Evolution and population structure of pathogenic bacteria including Helicobacter pylori, Salmonella enterica, Escherichia coli and Yersinia pestis
  • Functional genomics of the Negativicutes
  • Palaeogenomics of tuberculosis
  • Sedimentary ancient DNA
  • Transcriptomics of Bacillus subtilis and other Gram-positive species
  • Interaction between pathogenic bacteria and their human and insect hosts


  • Medical Research Council – UK
  • Medical Research Council – Gambia
  • AB Vista


  • Metagenomic analysis of tuberculosis in a mummy. Chan JZ, Sergeant MJ, Lee OY, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ. N Engl J Med. 2013 Jul 18;369(3):289-90. Impact Factor 52
  • Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine. Loman NJ, Gladstone RA, Constantinidou C, Tocheva AS, Jefferies JM, Faust SN, O'Connor L, Chan J, Pallen MJ, Clarke SC. PLoS One. 2013 May 28;8(5):e64731.
  • Genomics and outbreak investigation: from sequence to consequence. Robinson ER, Walker TM, Pallen MJ. Genome Med. 2013 Apr 29;5(4):36.
  • A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ. JAMA. 2013 Apr 10;309(14). Impact Factor 30
  • Recent Acquisition of Helicobacter pylori by Baka Pygmies Sandra Nell, Daniel Eibach Valeria Montano, Ayas Maady, Armand Nkwescheu, Jose Siri, Wael F. Elamin, Daniel Falush, Bodo Linz, Mark Achtman, Yoshan Moodley, Sebastian Suerbaum PLoS Genet 2013 9(9): e1003775. Impact Factor 8.7

Associated academic staff:

  • Mark Achtman
  • Mohan Balasubramanian
  • Judith Klein
  • Mark Pallen
  • Meera Unnikrishnan

Related Links

Microbiology and Infection