The human microbiome is a consortium of microorganisms living on and in our bodies. There are more microbial cells in our body than human cells and microbial genes outnumber our own 30:1. These microbial symbionts contribute to our health and homeostasis, but sometimes, the microbiome becomes perturbed resulting in dysbiosis and chronic disease. Understanding how changes in our microbiome lead to disease has immense implications for human health. My laboratory studies how metabolites from the microbiome shape our health and disease and specifically how changes in the cystic fibrosis (CF) lung microbiome cause disease in patients. Using mass spectrometry-based metabolomics, nucleic acid sequencing, and novel microbial culture techniques, our work has shown how changes in metabolite production from the microbiome lead to acute flares of chronic disease. For example, in the CF lung, changes in the core metabolism of the microbiome to anaerobic fermentation results in the production of acidic products that damage the lung (Fig. 1). In the human gut, bacteria alter molecules we consume in our food (Fig. 2) and also those that we produce, such as bile acids, however, we have little understanding of how these molecules affect human health. My laboratory also focuses on translating bioinformatic tools to clinical medicine. The software and data analysis pipelines developed for microbiome and metabolome research are now so advanced that this big-data science can be done in clinically relevant timeframes. My laboratory will use metabolomics and microbiome sequencing as a precision medicine approach for microbiome-related diseases with sample-to-data turnaround times as fast as 48 hours (Fig. 3). By combining multi-omics tools with microbial ecology theory, we aim to understand the causes of microbiome dysbioses and develop new therapeutic approaches to manipulate the microbiome to benefit human health.