PopMet · Investigating bacterial strain evolution through metagenomic genome assemblies

Investigating bacterial strain evolution through metagenomic genome assemblies

In microbial genomics classical reductionist approaches, focusing on single species, genes and genomes, are increasingly replaced by holistic “whole-community” metagenomic studies. In this approach, DNA of all genomes found in a given ecosystems is randomly sequenced, and the genomic content of the microorganisms within the environment are reconstructed, in order to enable quantification of the taxonomic and functional diversity within a given community. Earlier metagenomic studies relied mostly on identifying taxa at genus or broader taxonomic levels, typically using highly conserved genes found in all bacteria (marker genes). However, theoretical advances in using single nucleotide variants (SNVs) allow currently for the distinction of single bacterial species, or even strains. These advances are critically important, as pathogenicity and metabolism of bacteria are often strain specific. SNVs can also guide the reconstruction of the bacterial genomes, thus linking taxonomy to specific functions. In this project, we exploited the information in SNVs to get an understanding of the bacteria and their functional capacities in a diverse set of environments. This is different from classical metagenomics, in that we have a higher resolution to differentiate between single strains and in that we can recover part of the genomes and link this to the taxonomic identity of a bacterium, giving us more information about what who is doing at a given environment. This is important to understand how pathogenic bacteria are distributed in the environment, where they normally occur and when they turn from a “bystander” to an “aggressor” that is trying to damage the host. This kind of switch is known for many bacteria, e.g. E. coli is often found in the gut ecosystem, but is also often causing diarrhea, given opportunistic circumstances. Understanding the bacterial distribution and what can be considered as normal was thus an important scientific research goal in this project. A second part was to investigate how bacterial genomes evolve over time, as this is important to understand how the phenotype of a bacteria can change. Normally these changes in phenotype are not harmful to the host, but in some rare cases this can also lead to a switch from bystander to aggressor strain.

Data: CORDIS, © European Union