Imperial College London


Faculty of MedicineSchool of Public Health

Senior Lecturer in Bacterial Genomics



+44 (0)20 7594 3820n.croucher




UG5Norfolk PlaceSt Mary's Campus






BibTex format

author = {Marttinen, P and Croucher, NJ and Gutmann, MU and Corander, J and Hanage, WP},
doi = {10.1099/mgen.0.000038},
journal = {Microb Genom},
title = {Recombination produces coherent bacterial species clusters in both core and accessory genomes.},
url = {},
volume = {1},
year = {2015}

RIS format (EndNote, RefMan)

AB - BACKGROUND: Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined. RESULTS: We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates. CONCLUSIONS: The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.
AU - Marttinen,P
AU - Croucher,NJ
AU - Gutmann,MU
AU - Corander,J
AU - Hanage,WP
DO - 10.1099/mgen.0.000038
PY - 2015///
SN - 2057-5858
TI - Recombination produces coherent bacterial species clusters in both core and accessory genomes.
T2 - Microb Genom
UR -
UR -
UR -
VL - 1
ER -