Deciphering the human intestinal tract microbiome using metagenomic computational methods

In 2010, the MetaHIT consortium published a 3.3M microbiota gene catalog generated by whole genome shotgun metagenomic sequencing, representing a mixture of bacteria, archaea, parasites and viruses coming from 124 human stool metagenomic samples [Qin et al, Nature 2010].
However most of the genes were fragmented, taxonomically and functionally unknown, making it difficult to define and select biomarkers of interest for genome-wide association studies.
Since that, this human gene catalog was improved multiple times, with the last update by [Li et al, Nature Biotechnology, 2014], which generated a 10M gene catalog using more than 1000 metagenomic samples and including some prevalent human microbe genome available at that time. Along with the catalog update, the scientific community developed new tools to challenge the complexity of this dataset and provided new ways to assemble, annotate, quantify and classify the genes coming from these catalogs.
In this talk we will discuss the main approaches related to the computational treatment of the different gene catalog other the time, illustrated by the different papers that deciphered step by step the hidden information of our microbiota and his link with our health.