Expert’s view: 3 questions to Caroline Achard on metagenomics

Caroline Achard is a research scientist at the Lallemand Monogastric Center of Excellence in Toulouse, and she is an expert in molecular biology and metagenomics.

 

Caroline, we see more and more metagenomics studies, what does it bring animal production in practice?

It is well accepted today that the gut microbiota interacts closely with its host and plays a crucial role in the maintenance of gut health. In humans, microbiota imbalance has been associated with multiple disorders and diseases. We believe that the establishment of beneficial microbiota in young animals can improve robustness, health, and finally lead to better performance. It is thus important to have a better understanding of the microbiota dynamics. Metagenomics studies give us a better insight into the composition and the potential function of the microbiota. Most of the studies published today are using amplicon sequencing, also called barcoding or 16S rRNA sequencing. Such studies use only one marker gene, as some kind of bacteria ID cards. They give us access to the composition of the microbiota without the need for complete sequencing of the metagenome. These studies help us better understand the impact of our solutions on the host microbiota and potentially discover the solutions of tomorrow.

How can we link metagenomics studies to microorganisms’ functions?

Metagenomics is a great tool to predict the potential functions of the bacteria present in an ecosystem, based on the comparison of functional pathways database. It is important to keep in mind that these databases are generated and maintained thanks to what was observed for cultivable representative strains of bacteria. In order to confirm that these functions are really expressed, we are using other techniques such as metabolomics, which is the characterization of an entire set of metabolites synthesized by the microbiota).

Can you share some of the most recent results you have been working on?

Using 16S rRNA sequencing analyses, we have demonstrated that feeding the probiotic yeast Saccharomyces cerevisiae boulardii CNCM I-1079 (LEVUCELL SB) to sows during gestation and lactation had a beneficial impact on the gut microbiota composition as reflected in sow performance. Interestingly, it also modulated the microbiota of the piglets. This so-called maternal imprinting on the piglet microbiota lasted even after weaning and is associated with improved piglet performance. Our team is currently conducting studies in all the applications we cover with our solutions, in various species of microbiota, but also in silage or animal environments.