MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology
At a glance
- Co-project leader : Dr. Joël Pothier, Dr. Fabio Rezzonico
- Project budget : CHF 40'000
- Project status : completed
- Funding partner : Internal
- Project partner : Université de Genève / Unité de Microbiologie, MALDI-ID, Mabritec AG, Murdoch University
- Contact person : Fabio Rezzonico
Description
Rhizobia are bacterial symbionts associated with legumes that are of paramount importance for the fixation of atmospheric nitrogen in the soil. The success of this process (and ultimately the performance of the plant) depends on the type of root nodule bacteria, which should be adequate to each plant species. The objective of this project is to establish a quick and effective identification tool for rhizobial symbionts within the most important grain legumes. Our approach combines next generation sequencing (NGS) data and MALDI-TOF MS protein markers to identify the different inoculant strains based on their unique fingerprints. During this project we will introduce the nanopore-based MinION device as routine tool for genomic and amplicon sequencing in our laboratory, testing various protocols and establishing the associated bioinformatics infrastructure and data analysis pipeline. Together with the gain of expertise, this will enable us to refine and expand the available genomic data on rhizobia, which will allow the precise identification of individual protein signals obtained with MALDI-TOF MS, thus enabling the selection of the best discriminatory markers for the different bacterial species and improving the accuracy of the proteomics approach.
Publications
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Fossou, Romain K.; Pothier, Joël F.; Zézé, Adolphe; Perret, Xavier,
2020.
International Journal of Systematic and Evolutionary Microbiology.
70(2), pp. 1421-1430.
Available from: https://doi.org/10.1099/ijsem.0.003931