Application of next-generation sequencing for genetic and phenotypic studies of bacteria

Abstract

One of the fundamental tasks for studying a bacterium is its accurate classification and identification. A large amount of the required data is provided by whole genome sequencing (WGS). WGS reveals the sequences of small subunit ribosomal RNA genes, the similarity of which provides the basis for species classification. It also allows the calculation of average nucleotide identity, used for the same purpose. At the subspecies level, WGS provides information on both single nucleotide variants and structural variants, which can be used in several ways for genotyping. As a predominantly haploid organism, a bacterial species is usually classified genetically with a premise that a genotype descends from a common ancestor and expectedly shares a number of phenotypes as well. The genotypes, therefore, serve as units for studying the correlation to the phenotypes, which would provide a better understanding of the species. The genotypes can also serve as units for studying correlation with host genetics. Nevertheless, the plasticity of the bacterial genome, especially due to horizontal gene transfer and homologous recombination, complicates the tasks. The use of WGS for bacterial classification, therefore, requires careful analysis to avoid various pitfalls. The results would provide a major advancement in the understanding of bacterial pathogenesis and lead to better control and prevention of bacterial infectious diseases.