New platforms for the diagnosis and identification of fungal and bacteria pathogens

This chapter focuses on analytical strategies for identifying pathogens (such as fungi) in mixed microbial communities, the so-called microbiome, which includes bacteria, fungi (mostly yeasts) and viruses, via metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. Fungi are an essential functional component of terrestrial ecosystems as decomposers, mutualists and pathogens, and are one of the most diverse groups of the Eukarya. The study of the ecological factors that support the dynamics of fungal communities is a challenge because of this high taxonomic and ecological diversity. PCR-based molecular methods and sequencing of ribosomal DNA have been successful in identifying subsets of the abundance of this species and have provided insight into the ecological processes affecting the structure and diversity of fungal communities. Genetic variations were detected in a large number of samples representing a broad range of biological material and this helped understand genetic mechanisms of different diseases. Even though an increasing number of genomes has already been sequenced, the importance of technical developments in the field of DNA analysis is clear. Pathogen identification in infectious diseases relies mostly on routine cultures and biochemical testing by means of semi-automated platforms in the clinical laboratory. The shift toward widespread adoption of nucleic acid sequencing for the identification of microbial pathogens has been slowed down by the user-intensive, highly technical nature of Sanger DNA sequencing. Nevertheless, several studies published in the 1990s indicated that sequencing of 16S rRNA genes could be useful for pathogen discovery and identification. The number of DNA sequencing technologies is currently high, even though some techniques are more advantageous than others depending on the application, and, therefore, a general ranking of the technologies may be incorporated or misleading. The advent of new high-throughput DNA-sequencing technologies promises to redefine how fungi and fungal communities - as well as other groups of organisms - are studied in their natural environment.