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.

尽管关于宿主与微生物组相互作用的知识越来越多，但我们才刚刚开始了解肠道微生物组如何影响宿主基因表达以及如何受宿主基因表达影响。在这里，我们回顾了这两个领域交叉的最新文献，总结了各个研究的主题。模型生物、人体活检和细胞培养的研究表明，肠道微生物组是与疾病相关的多种宿主途径的重要调节者，包括免疫发育和能量代谢，反之亦然。肠道微生物组重塑宿主染色质，引起差异剪接，改变表观遗传景观，并直接中断宿主信号级联。单细胞 RNA 测序和类器官生成等新兴技术有可能在未来加深我们对肠道微生物组与宿主基因表达之间关系的理解。通过交叉微生物组和宿主基因表达，我们获得了了解生理过程的窗口，这对于促进广泛的跨界相互作用并最终促进我们的健康至关重要。