Toward a more systematic understanding of bacterial virulence factors and establishing Koch postulates in silico

Human health is threatened by various infectious bacterial pathogens but is also supported by many commensal bacteria particularly in the intestinal tract. However, many of the bacterial pathogens and commensal bacteria are taxonomically indistinguishable, with pathogenic and commensal bacteria existing in the same genus and even species. A typical example is Escherichia coli, which is commonly found in the lower intestine of humans. But some serotypes can cause severe diseases. Virulence factors are assumed to explain the differences between pathogenic and commensal bacteria. When a bacterium harbored a specific virulence factor, e.g., Escherichia coli secreting Shiga toxin, it could turn commensal to pathogenic. However, with more factors revealed to be involved in the bacterial virulence, the boundary between pathogenic and commensal bacteria defined by virulence factors becomes obscure. Some virulence factors playing vital roles in bacterial infection are also found to be encoded in genomes of commensal bacteria. The conflicts between the definitions of infection experiments and the genomic distributions of virulence factors raise critical questions on the understanding of bacterial pathogenecity and virulence factors. In this issue of Virulence, Niu et al. recognized the contradiction and classified bacterial virulence factors into two groups. One group is formed by those virulence factors only found in pathogenic bacteria, called pathogen-specific Toward a more systematic understanding of bacterial virulence factors and establishing Koch postulates in silico