Q02: Functional microbiota analysis
In project Q02, Thomas Clavel and his team provide expertise in microbiota analysis to the consortium.
Please find detailed information on our protocols and resources on a separate page as follows:
Although high-throughput sequencing of 16S rRNA genes has become a widespread method for rapid profiling of microbial communities, it is crucial to have a common ground of analysis to be able to compare results. This also applies to shotgun metagenomic workflows that are used in Q02. The project relies on established wet-lab protocols and in-house developed bioinformatic pipelines for generating and comparing microbiota profiles from all relevant samples collected by the consortium. Q02 is thereby the basis for harmonized analysis of microbiota profiles for the consortium. This includes the education of young researchers within and outside the consortium on good practices in microbiota analysis by organizing hands-on data analysis workshops.
In parallel, as annotation of sequencing datasets is still limited by the quality of reference databases and because it is necessary to test hypotheses generated via sequencing by performing functional studies with isolates, Q02 also implements culture techniques for isolating gut bacteria and described novel taxa for subsequent amendment of reference datasets.
Overall structure of the CRC core project Q02. It follows four main aims (numbered boxes): (1) Expert service for sample processing and generation of microbiota profiles by 16S rRNA amplicon sequencing; (2) Bioinformatic data analysis by providing individualized support adapted to the particular needs of each project and also by educating young scientists to good practices in the field; (3) Establish collections of bacterial strains from the mouse and human gut in order to improve annotation power of 16S rRNA amplicon datasets and to prepare the ground for future functional studies in CRC projects using isolates; (4) Benefit from the unique pool of samples and corresponding sequence datasets generated by the consortium to create a new database of microbiota profiles in the context of gut- and liver-associated pathological conditions. This core project serves primarily the purpose of CRC partners (left-hand box), who will interact with Q02 via sample exchange, data interpretation, and training of young scientists. However, external groups (research community in the right-hand box) will also benefit from the resources created in Q02 (strain collections and sequence database).