These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.īacteria catalyze fundamental steps of the geochemical cycles in almost every habitat on Earth and are partners in important ecological relationships with many eukaryotic organisms (that is, symbiosis, protocooperation, competition). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼16% of the total genes and ∼35% of the metabolic genes in some genomes (conservative estimation). Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed.

Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria.

Anaerobic bacteria shapes