From Genome Sequence to Taxonomy - A Skeptic’s View

The relative ease of sequencing bacterial genomes has resulted in thousands of sequenced bacterial genomes available in the public databases. This same technology now allows for using the entire genome sequence as an identifier for an organism. There are many methods available which attempt to use genome sequences to classify bacteria, and the method of choice, as always, depends on
the question asked and the particular need. For example, 16S rRNA can define a bacterial species, and relate species, genera, and higher orders into groups consistent with their known biological properties. However, distinguishing between strains of the same species requires additional information. The advantage of having the whole-genome sequence is that roughly a 1,000 times as much information is available, and this information can be used for rapid classification of strains, based on DNA sequence. This chapter reviews many commonly used methods and also describes potential pitfalls if used inappropriately, as well as which questions are best addressed by particular methods. After a brief introduction to the classical methods of taxonomy, a description of the bacterial genomes currently available is given, and then whole-genome-based methods are explored using three different data sets.