Metagenomics: a path to understanding the gut microbiome

The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.

Automated summary

The gut microbiome plays a critical role in host health and advancements in next-generation sequencing have allowed for genomic level studies to be conducted in the past two decades. This has led to a better understanding of the microbial community and the functions encoded in their metagenome. Advances in sequencing technologies and computational approaches have revolutionized our ability to study the microbiome, highlighting the importance of ongoing technological developments in this field.