Categorization of bacterial habitats linking 16S RNA amplicon sequencing to biotope information

During the last decade we have witnessed a rapid expansion of DNA sequencing technologies and their applications, leading to the development of culture-independent methods for the identification and characterization of microbial ecosystems. The resulting massive amount of DNA sequence data forced us to revise the scale of estimated bacterial species diversity and of the diversity of biotopes colonized by bacteria. Still, there are gaps in our knowledge on the distribution of bacteria species in these different biotopes. This information is important for different areas such as in human and animal health, environmental science and technology and agri-food sector.

The aim of this work is to develop a database linking bacterial taxonomy (based on 16S RNA amplicon) and the species detection in ecosystems/biotope information. This database is intended to be fully compatible with amplicon sequencing and metagenetic designs.

During the first steps, we created a tool for cataloging the biotopes in which each bacterial species is found, with the primary focus on host related environment and food. This consisted of a comprehensive search on existing bacterial sequence database and associated metadata, to provide a set of 5 million published 16S RNA sequences for which taxonomic identity is validated. Each 16S RNA sequence was subsequently labelled with publication and biotope information, when available.
The next stage of this work is to use text mining tools to enrich the database by extracting pertinent information from sequence associated publications and to format the subsequent biotope information using a hierarchical ontologic design.

The database will be validated by the exploration of metagenetic data of target/specific ecosystems. The final phase of the project will consist of automating the updating of the database and rendering it accessible via the web interface.