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Apr 30, 2019

Lallemand takes part in large-scale research project to advance metagenomics research

Apr 30, 2019

SeqOccIn © INRA GeT-PlaGe

Photo © INRA GeT-PlaGe

SeqOccIn research project aims to acquire advanced expertise of the latest sequencing technologies

We are proud to announce our participation in a large-scale research project led by INRA Occitanie-Toulouse, aimed at developing new approaches based on the latest sequencing technologies. This project, called SeqOccIn (Sequencing Occitanie Innovation),  is mainly oriented towards the development of advanced expertise in the use of different sequencing technologies, particularly those allowing the sequencing of long DNA fragments into single molecules. It is led by Genotoul’s INRA platforms GeT-PlaGe (Genome and Transcriptome platform) and Bioinfo (Bioinformatics Platform), based in Toulouse, France, and also involves 4 INRA laboratories and 14 private companies, including Lallemand, and was selected to receive public funding from the Occitanie region.

Caroline Achard, Research Scientist at Lallemand Animal Nutrition and in charge of the project coordination for Lallemand, commented:

photo of Caroline Achard, research scientist at LAN and in charge of the project coordination for Lallemand“Dr. Caroline Achard, research scientist in charge of the project coordination for Lallemand Animal Nutrition commented: “This ambitious project aims at acquiring advanced expertise of long fragment sequencing technologies in three fields of study: genome polymorphism, epigenome, and metagenomics, which refers to the analysis of all the microbial genes within an ecosystem. Metagenomics is an important area of investigation for us as it allows a better understanding of microbial ecosystems such as the gut microbiota. The current classical metabarcoding approach for microbiota studies uses short DNA fragments sequenced by the Illumina technology to characterize the taxonomic affiliation of the gut microbes and to decipher the effects of various external factors, such as animal’s age, diet, stress, weaning, probiotics feeding, and more. However, short sequences are not always sufficient to identify bacteria at the species level, and thus, predicting their functions remains challenging. New long-read sequencing technologies could enable more accurate identification of the bacteria. Those sequencing technologies can also be used for whole genome sequencing. Long DNA fragments indeed drastically facilitate the assembly process and thus the prediction of bacterial genes and the functional annotation.” She added: “Major obstacles need to be overcome, such as the production of high quality DNA, the sequencing high error rate, the high cost, the development of adequate bioinformatics pipeline etc. Nevertheless, we believe in cost-effective access to these technologies in the future, to be used routinely and directly on sites, for a better characterization of microbiota in the context of animal health and performance.

With a total budget of €6 million over a period of 3 years, the project will finance in particular a team of a dozen people and the acquisition of expertise through the production and analysis of data sets of interest to all partners.

For more information on SeqOccIn project, visit INRA’s website.