An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food–Microbiota–Host Interactions in the Human Gut

Author:

Mathieu Elliot1,Léjard Véronique1,Ezzine Chaima1ORCID,Govindin Pauline1,Morat Aurélien1,Giat Margot1,Lapaque Nicolas2ORCID,Doré Joël12,Blottière Hervé M.13ORCID

Affiliation:

1. Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France

2. Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France

3. Nantes Université, INRAE, UMR 1280, PhAN, 44000 Nantes, France

Abstract

Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the “self” was not only defined by our genetic patrimony but also by the genomes of bugs living in us. The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives. In the present chapter, we will describe the advances of functional metagenomics to decipher food–microbiota and host–microbiota interactions. This powerful high-throughput approach allows for the assessment of the microbiota as a whole (including non-cultured bacteria) and enabled the discovery of new signaling pathways and functions involved in the crosstalk between food, the gut microbiota and its host. We will present the pipeline and highlight the most important studies that helped to develop the field. To conclude, we will emphasize the most recent developments and hot topics in functional metagenomics.

Funder

French National Research Agency

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

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