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

Robert G. Nichols, Emily R. Davenport

Research output: Contribution to journalReview articlepeer-review

66 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)747-760
Number of pages14
JournalHuman genetics
Issue number5
StatePublished - May 2021

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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