Functional Genomic Analysis of Taxonomic and Typing Loci for Pathogenic Bacteria Based on Orthologous Genes

Approaches based on gene sequences of pathogenic microbes have become increasingly popular to distinguish infectious diseases. According to the Library of Pathogen Infecting in Human which is established by the Ministry of Health of China, our research covered 103 species of bacterial pathogens in China. In general, we have grouped orthologous genes for each taxonomic rank, and picked out the genes which are fitted for the identification and typing of pathogenic bacteria. In total, we aligned and analyzed 836415 genes of 275 pathogenic bacteria strains with whole genome sequenced, and obtained specific orthologous gene groups for phylum, class, order, family and genus respectively, by using bioinformatic and genomic methods. These orthologous genes were then annotated by similarity search against COG database. Further analyses on the differences of functions of consered genes of each taxonomic rank showed that a total of 19563 gene groups are fitted for the identification and typing in hierarchical taxonomic ranks (2891 for phylum, 1016 for class, 3601 for order, 10130 for family and 1925 for genus). It is also showed that the functions of these gene groups are different in each taxonomic rank, as well as in gram positive/negative bacteria. These findings will help us to design primers and microarrays for fast detection of pathogen bacteria in China. Meanwhile, it is also the first time to combine the whole genome sequences of bacteria and the taxonomy of pathogenic bacteria in China, which can provide a new and effective method to select candidate genes/loci for the pathogen detection. These results may also shed light on the research of bacteria metagenomics.