The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host’s mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host–microbiome ‘conversation’ in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.

肠道微生物组是一个生态系统。自然选择偏爱适合肠道的微生物，它们可以利用和转化宿主产生的分子，为自己谋取利益。但自然选择也有利于宿主感知和响应微生物生态系统的机制，以谋取自身利益。我们可以在微生物组和宿主对强烈扰动的同时响应中监听宿主-微生物组的“对话”。在实验室动物中，可以进行扰动以进行研究；在人类患者中，扰动可能是由疾病或治疗引起的。宏基因组学、代谢组学和计算方面的进步扩大了我们倾听肠道微生物组与其宿主之间对话的手段。