Phylogenetic Diversity of Microbial Pathogens

Culture methods remain significantly inadequate in duplicating the physiological needs of microorganisms and, in particular, environmental microorganisms. With the advent of sequence-based (molecular) phylogeny has come the ability to detect and analyze the compositions of microbial communities without reliance on in vitro microbial cultivation. Pathogenic microorganisms often elicit host tissue pathology and clinical manifestations as they propagate in privileged anatomic sites. Comparative rRNA analysis depends upon selection of an appropriate group of homologous sequences, rigorous sequence alignment with preservation of conserved secondary structures, and use of appropriate phylogenetic inference methods. Several features make ss rRNA molecules useful and reliable evolutionary clocks. First, they are ubiquitous among living cells, and they do not seem to be transferred horizontally among mixed populations. Second, the function of the molecule is essential, and as a result, its secondary and tertiary structures are highly conserved. Third, these molecules are large enough to contain sufficient information content for comparisons among diverse organisms. The phylogeny of the Whipple's disease bacillus reveals a second theme that may be common to previously uncultivated microbial pathogens. On the basis of a culture-independent analysis of bacterial diversity within soil, it is not surprising that previously unidentified human microbial pathogens would be found in this environment.