The human microbiome and its metabolic output play an important role in shaping human health and disease. The host-microbe crosstalk is often characterised using metabolomics and metagenomics, yet a large proportion of microbial metabolites and the molecular functions of gut microbes remain unknown. This review summarises the strategies for annotation and discovery of the novel metabolites from the human gut microbiome, either using metabolomics alone or in combination with metagenomics, and presents data analysis methods for combining these two types of data to obtain biological insights. Applications of the gut microbiome research in biomarker screening, precision medicine, microbiome medicine, and drug discovery are also discussed, along with the perspectives, challenges and limitations of this research field.