Mapping microbiome diversity in the age of big(gish) data

The field of microbial ecology has gone through significant changes in the past 15 years, with the development of culturing-free techniques such as metagenomics accompanied by dramatic improvements in DNA sequencing technologies. Advanced bioinformatics programs now enable the large-scale recovery of genomes from metagenomic samples. The analysis of these genomes expands our understanding of the vast majority of microorganisms on Earth that cannot be cultured. Despite these advancements, we still struggle to answer basic questions in microbial ecology, such as what species can be found in a given environment and what are their metabolic capabilities. This is true even for the most studied environments, such as the human body.

In this talk, I will describe our efforts to understand microbial diversity in the human microbiome. We aim to identify all the species that are associated with the human body, understand their potential contribution to the human microbiome, and find patterns in their appearance across different human populations. To achieve these goals, we take advantage of the thousands of metagenomes and hundreds of thousands of assembled genomes that are publicly available. Our results suggest that the actual number of species in the human microbiome may be smaller than previously estimated. Also, the functional diversity represented by strain-specific genes significantly expands the functionality exhibited by the core genes of a species. We anticipate that similar approaches to the ones we apply may be useful for other environments.