Commensal microbes are established in gut at and after birth. There is always crosstalk between innate cells and gut microbiome. Homeostasis is established and immune priming (innate immune memory) occurs. If diet, disease, etc alter gut microbiome for a long duration, innate cells may lose healthy primed state. Here are three good places to start reading into details of various molecular mechanisms:

https://www.frontiersin.org/articles/10.3389/fimmu.2020.00282/full

https://www.tandfonline.com/doi/full/10.1080/19490976.2021.1939598

https://www.cell.com/immunity/pdfExtended/S1074-7613(22)00177-7