The relationship between the gut microbiome and host gene expression: a review

Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.

Automated summary

The interaction between the gut microbiome and host gene expression is complex and bidirectional, influencing host pathways relevant for disease, such as immune development and energy metabolism. The gut microbiome can remodel host chromatin, cause differential splicing, alter the epigenetic landscape, and directly interrupt host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to enhance our understanding of this relationship in the future.