Toward the use of genomics to study microevolutionary change in bacteria - PubMed (original) (raw)

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Toward the use of genomics to study microevolutionary change in bacteria

Daniel Falush. PLoS Genet. 2009 Oct.

Abstract

Bacteria evolve rapidly in response to the environment they encounter. Some environmental changes are experienced numerous times by bacteria from the same population, providing an opportunity to dissect the genetic basis of adaptive evolution. Here I discuss two examples in which the patterns of rapid change provide insight into medically important bacterial phenotypes, namely immune escape by Neisseria meningitidis and host specificity of Campylobacter jejuni. Genomic analysis of populations of bacteria from these species holds great promise but requires appropriate concepts and statistical tools.

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Conflict of interest statement

The author has declared that no competing interests exist.

Figures

Figure 1

Figure 1. Acquisition of new tbpB genes by subgroup III Neisseria meningitidis during epidemic spread.

Colours indicate the family of each tbpB allele, with red corresponding to family 4, green corresponding to family 1, and blue corresponding to family 3. The bars highlight the time frame, most common tbpB type, and geographical extent of each epidemic (in 1987, pilgrims from the Hajj pilgrimage briefly distributed the lineage worldwide). The circles correspond to variant genotypes. Small circles indicating that the variant allele was found in only one strain; large circles indicate it was found in between two and four strains.

Figure 2

Figure 2. A schematic illustration of the evolution of the C. jejuni ST-21 clonal complex in cattle and chickens.

The common ancestor of the complex occurred in chickens (red). During evolution, the lineage occasionally switched to a cattle host (indicated by a blue branch) and sometimes back to chicken. The bacteria acquired DNA by homologous recombination from other C. jejuni in the same host. Since recombination is assumed to occur from donors within the same host, the gene pool is determined by the genomic composition of the strains that colonize each host. The gene pools are illustrated for two separate loci (right and left facing arrows) in chickens and cattle. The gene pools contain alleles whose frequencies occur at much higher frequency in one host than another (shown in colour) and others that did not (shown in black). The former are informative about the host in which the recombination event occurred, while the latter are not. The recombination event labelled a introduces the left facing black arrow gene from the cattle gene pool and is phylogenetically informative because it defines a lineage that is largely restricted to cattle. The five recombination events labelled b are not phylogenetically informative, since they only affect a single strain in the sample. These events are nevertheless informative because they introduce alleles that are characteristic of the host species. The event labelled c is both phylogenetically informative and characteristic of host. The event labelled d is noninformative.

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