Analysis of microbial diversity in metagenomic datasets
Many metagenomic shotgun methods have been developed to get a precise view of the composition of these ecosystems. The huge number of metagenomes and genomes available open the way to study population genetics of microbial species at short evolutionary scales in metagenomic datasets. For that purpose, a pipeline is currently being developed in the team to analyse metagenomic samples. It computes two genomic diversity indices, based on diversity indices used in population genetics. The first index evaluates the diversity for each species the metagenomes into a dataset, and the second one allow to evaluate the diversity between metagenomes of two datasets.
The aim of the M2 internship is to apply the whole pipeline on one or two published metagenomic dataset(s) of children gut microbiota, and design relevant approaches to visualize, analyse and interpret the obtained results. These analyses will be a first step to test and evaluate our approach to study the diversity of species of the gut microbiota on a complete biological dataset.