With the rapid increase of the microbiome samples and sequencing data, more and more knowledge about microbial communities has been gained. However, there is still much more to learn about microbial communities, including billions of novel species and genes, as well as countless spatiotemporal dynamic patterns within the microbial communities, which have formed the microbial dark matter. In this talk, I will summarize this dark matter in the microbiome research, and introducing our current work on microbiome data mining, especially artificial intelligence (AI) methods for different types of knowledge discovery from microbial dark matter. We also provided case studies on using these AI methods for microbiome data mining and knowledge discovery.