High-throughput sequencing for the study of bacterial pathogen biology.
Bottom Line: A revolution in sequencing technologies in recent years has led to dramatically increased throughput and reduced cost of bacterial genome sequencing.For example, the capacity to sequence large numbers of bacterial isolates is enabling high resolution phylogenetic analyses of bacterial populations leading to greatly enhanced understanding of the emergence, adaptation, and transmission of pathogenic clones.In this concise review we provide selected examples of how high throughput sequencing is being applied to understand the biology of bacterial pathogens, and discuss future technological advances likely to have a profound impact on the field.
Affiliation: The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom.Show MeSH
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Mentions: Differences in the composition of resident bacterial populations between healthy and disease states are increasingly being described, and deep sequencing meta-genomic methods can capture greater diversity from the microbiota in comparison to traditional methods relying on PCR amplification and Sanger sequencing . For example, decreased microbial diversity in CF patients in comparison to healthy controls is associated with more severe inflammation  and distinct shifts in metabolic pathways have been identified . Additionally, the effects of antimicrobial therapies on the gut microbiota have been investigated revealing increased phage mobilization [28,29], and profound shifts in composition that persist after the cessation of therapy  (Figure 1).
Affiliation: The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom.