Genetic Barcoding of Bacteria and its Microbiology and Biotechnology Applications
Oleg N. Reva, Wai Y. Chan, Oliver K. I. Bezuidt, Svitlana V. Lapa, Larisa A. Safronova, Lilija V. Avdeeva and Rainer Borriss
from: Bioinformatics and Data Analysis in Microbiology (Edited by: Özlem Taştan Bishop). Caister Academic Press, U.K. (2014)
A wide variety of genetic data about organisms of interest has become available with the advancement to next generation sequencing (NGS). For many potential new users, to process this huge amount of genetic data released by NGS and to utilise this information to resolve practical questions remains a challenge. Genetic barcoding of microorganisms is the first obvious area where NGS has met the requirements of applied microbiology. In general, barcoding in microbiology is a comparative genome approach to differentiate between species or strains that are hard to distinguish by traditional methods. In this chapter, we introduce the conceptual background of bacterial barcoding and present several basic bioinformatics tools and approaches to provide solutions to NGS data handling. While working with a putative industrial strain or potentially hazardous pathogen, the following questions arise: (i) is this strain unique and if so, what makes it unique genetically or practically speaking; (ii) how can it be detected in the environment; (iii) are there any genetic markers for its extraordinary activity? The possibility of barcoding of whole bacterial communities is considered and both the benefits and limitations of the traditional 16S rRNA based barcoding and multi-locus sequence typing are discussed read more ...