The relationship between the gut microbiome and host gene expression: a review
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REVIEW
The relationship between the gut microbiome and host gene expression: a review Robert G. Nichols1 · Emily R. Davenport1,2 Received: 3 September 2020 / Accepted: 6 November 2020 © The Author(s) 2020
Abstract 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.
Introduction The human body plays host to large numbers of bacteria, fungi and other microorganisms—commonly referred to as the microbiota (Shreiner et al. 2015). These microbes are important to our health. They assist in establishing host immunity (Kamada et al. 2013), strengthen the gut barrier (Leclercq et al. 2014), and provide beneficial metabolites (Lukovac et al. 2014). Consequently, the microbiota is associated with a large number of complex diseases in humans, including inflammatory bowel disease (IBD) (Aleksandrova et al. 2017), cardiovascular disease (CVD) (Tang et al. 2017), and colon cancer (Nelson and Chia 2019). Whether shifts in the microbiota lead to or are the cause Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00439-020-02237-0) contains supplementary material, which is available to authorized users. * Emily R. Davenport [email protected] Robert G. Nichols [email protected] 1
Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
2
of disease remains largely unknown. Although, it has been demonstrated that the microbiota play causal roles in several diseases, including obesity (Ridaura et al. 2014; Turnbaugh et al. 2006) and diabetes (Wen et al. 2008). Given the importance for our health, it is necessary to characterize the physiological relationships between the microbiota and human host to understand disease etiology and design therapeutics involving the microbiome. There is much to be learned about human–microbiome interactions by studying the genetic components of each. The human genome contains approximately 20
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