Q02: Integrative microbiota analysis
In project Q02, Thomas Clavel and his team provide expertise in microbiota analysis to the consortium.
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. Q02 relies on established wet lab protocols and in-house developed analysis pipelines for generating microbiota profiles from all relevant samples collected by the consortium. Q02 will thereby be the basis for harmonized analysis of microbiota profiles for the consortium.
Q02 also educates young researchers on good practices in microbiota analysis by organizing workshops.
In parallel, as annotation of sequencing datasets is still limited by the quality of reference databases, Q02 implements culture techniques for isolating novel taxa and subsequent amendment of reference datasets for better sequence classification. Most importantly, there are no well-curated databases of 16S rRNA-based microbial profiles available to date that allow comparison of newly generated profiles to already stored data. Along the lines of an already published system (www.imngs.org), we will create a well-curated, searchable database dedicated to fecal microbiota profiles from patients and models with disorders of the gut-liver axis.
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).