The study of microbiota and their actions on the environment and their living hosts is a major field of biology, today and for decades to come. Understanding and controlling the microbiota associated with plants, animals, food is a lever for achieving the objectives of the transition to sustainable agricultural production systems. In this field, which requires looking at complex systems in a holistic way, research faces many technical challenges that must be overcome before to reach meaningful and reproducible biological conclusions. In this context, biological resource centres (BRCs) must be prepared to the processing and characterization of microbiota-oriented samples, in the continuity of their missions of collection, preservation and distribution of perfectly characterized biological resources. Furthermore, they can play a structuring role by offering the scientific community standardized procedures.
The thrust of RARE is to bring together BRCs working on different biological systems to optimize resources and benefit from the experience gained within the infrastructure before making it available to the wider community. The idea of the HARMONI project is to bring together 5 BRCs working in different fields (Environment, Animal, Food), all belonging to the national infrastructure RARe (Resources for Agronomical Research) to work collaboratively on the development of procedures for microbiota characterization. One of the expected added values of the project is to share experience between very experienced BRC and others whose experience is more recent in the field and thus to increase competence within the infrastructure.
BRCs are particularly concerned by the initial steps of microbiota studies: the handling and conservation of samples, the nucleic acids extraction and quality check procedures, the impact of conservation on nucleic acids integrity, the sequencing strategies and data analytical pipelines for microbial community characterization. By mastering technical steps, the BRCs could also develop new services like the offer to their catalogue of specific mock communities as ‘positive controls’ that can be used in each sequencing library to help in testing the quality of sequencing run and analytical workflow. Hence, the business models of BRCs could be positively impacted by such new developments in their expertise. The project is structured in two technical work packages and one transversal WP:
WP1- Conserving samples and extracting DNA
This WP will focus on handling samples and comparison of DNA extraction protocols specific to each BRC with the development of common quality check procedures.
WP2- Evaluating sequencing strategies
This WP will implement several sequencing approaches: classical (16S/ITS metabarcoding) and exploratory (shallow sequencing, SMRT) that will make possible to evaluate the robustness of the extraction procedures. The results of comparative analysis between the analytical pipelines will give to the BRCs an expertise in the basic characterization of microbial community associated to the samples they are in charge of.
WP3- Internal communication and dissemination
The success of the HARMONI project relies on close collaboration between the partners, whether it be the critical evaluation of the initial experimental protocols or the choice of metrics to be used in the analysis of the sequencing data. This objective will be achieved through the setting up of workshops in the course of the project during which protocol proposals and results will be presented and discussed in depth. The major outputs of the project will be the elaboration of guidelines for processing and characterizing microbiota-oriented samples. These guidelines will be available on the RARe portal and published. A closing seminar widely open to the community will be organized to disseminate the results.
It is the guiding idea of RARE to have BRCs working on different biological systems collaborate in order to optimize resources and benefit from the experience gained within the infrastructure before making it available to the wider community. The HARMONI project is an opportunity to put this idea into action.