Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli

Anish Pandey, Maria Humbert, Myron Christodoulides, Alexandra Charlotte Jackson, Jade Passey, Robert La Ragione, David Hampson, David Cleary

Research output: Contribution to journalArticlepeer-review


The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira. Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.
Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalMicrobial Genomics
Issue number12
Publication statusPublished - 11 Nov 2020


  • bacterial evolution
  • microevolution
  • zoonosis
  • Homologous recombination
  • genomics


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