Molecular Phylogenetics of Microbes

Abstract

Molecular phylogenetics or molecular systematic is the use of molecular structure to gain information on an organism’s evolutionary relationships which is expressed as a phylogenetic tree. The impact of molecular systematic on bacterial classification has been profound. In the year 1977, Woesian revolution occurred when Carl Woese, a chemist working on relative isolation compared 16S rRNA sequences to study the classification of microorganisms. This molecular approach revealed three (Archea, Bacteria, Eukarya), rather than five (Animalia, Plantae, Fungi, Monera, Protists) primary divisions of life to describe extraordinary levels of microbial diversity. Through cells different apparatus provides numerous information related to an organism but SSU rDNAs (genes coding for small subunit ribosomal RNA) offer a quality and quantity of information which make them one of the most useful macromolecular descriptors of microorganisms. However, 16S rRNA sequence analysis has been criticized as some of the cases of lateral gene transfer reported in those genes. To avoid this ambiguity along with the analysis of 16S rRNA gene, certain housekeeping genes like gapA, groEL, gyrA, ompA, pgi are also recommended. The targeted genes can be analyzed in various ways either by documenting the gel in which the amplified products run or by analyzing the sequences of the targeted genes of interests. This chapter will focus on various molecular techniques involving gel-based techniques, sequence-based techniques, analyzing Dendrogram, and Cladograms.