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.

The purpose of this document is to describe the procedures for screening samples on the Hutu-80 and NCI h 716 GCaMP reporter cell line and the quality controls to be carried out on this line prior to initiating thescreenings.

This protocol describe the treatment of human enteroendocrine cell models Hutu80 and NCI h716 parental cells with SCFAs and GCase inhibitor (CBE) in order to detect the impact of SCFAs and GCAse inhibition on alpha synuclein protein expression by immunoblotting.