Chapter 3 : Genomic Fluidity of the Human Gastric Pathogen Helicobacter pylori

Schema showing the origins of genetic heterogeneity among bacteria and its implications. The genetic diversity among microbial pathogens is possibly due to the acquisition or loss of DNA. Mechanisms such as mutation, transformation, recombination, transposition, transduction, and horizontal gene transfer, and genetic elements such as genomic or pathogenic islands, plasmids, etc., result in DNA rearrangements, inversions, duplications, deletions, and insertions that lead to alteration of gene expression and to loss or gain of gene function. These alterations in the genome are responsible for novel phenotypes, varied drug resistance, enhanced pathogenicity, and bacterial fitness in diverse environments.doi:10.1128/9781555817213.ch03f01

Orthologous genes of helicobacters (common gene pools): Every area in the Venn diagram represents a subset of the compared genomes and is labeled with the number of genes in the concerned subset. Helicobacter shares about 774 genes at the genome level, and H. pylori shares about 1,244 genes, indicating closer connections at species level with conserved functions of genes. The H. pylori core genome plateaus around ~1,244 genes with conserved functions, wherein horizontal gene transfer and positive selection are playing key roles in the adaptive evolution of this core genome.doi:10.1128/9781555817213.ch03f02

Dendrogram based on comparative metabolomics of Helicobacter (produced by using KEGG). Organisms which share a larger number of enzymes are clustered together. This highlights the commonality of biochemical transformation between their metabolic pathways.doi:10.1128/9781555817213.ch03f03

Acquisition of virulence, optimization of fitness, and geographically compartmentalized spread of H. pylori (sub)populations ( Ahmed et al., 2009 ). Horizontal gene transfer and genome plasticity probably contributed to the evolution of pathogenic variants from nonpathogenic colonizers. Modern H. pylori populations thus derived their gene pools from ancestral populations that arose on different continents and can be correlated with different migrations of human populations and other Neolithic events such as the arrival of agriculture. The beginning of agriculture and the domestication of farm animals (which seem to have occurred hand in hand but across multiple domestication events in a continent-specific manner) suggest a scenario, as depicted here, which can be linked to the acquisition of virulence by H. pylori. It can be hypothesized that early bacterial communities originating from crop plants, animals, or rodent pests, etc., very common in the vicinity of early human societies, may have served as donors of some of the virulence gene cassettes. Such genetic elements may have been acquired by H. pylori either bit by bit or en bloc, at some time, through horizontal gene transfer events. There is indirect evidence to this effect in the form of sequence and structural similarities of some of the H. pylori virulence genes to their homologues in plant pathogens and environmental bacteria. Also, we think that the extraneous virulence genes may have conferred some survival advantage upon H. pylori strains, making them fitter in different human and animal hosts and, as a result, the pathogen may have spread selectively in a geographically compartmentalized manner.doi:10.1128/9781555817213.ch03f04

Arrangement of ORFs under different types of plasticity zone-encoded transposable elements (TnPZs) in H. pylori (from Kersulyte et al., 2009 ). Different regions/ORFs of the TnPZs have been color coded as per the conventions detailed by Kersulyte et al. (2009) .doi:10.1128/9781555817213.ch03f05