Research

The human microbiome is a consortium of microorganisms living on and in our bodies. 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. Our laboratory studies how metabolites from the microbiome shape our health and disease.

We focus our research on the cystic fibrosis (CF) lung microbiome to understand how bacteria living in the lungs of CF patients cause disease, but also study the gut microbiome and microbial communities associated with marine organisms, fermented foods and anything else we find interesting. 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. In the CF lung for example, changes in the core metabolism of the microbiome to anaerobic fermentation results in the production of acidic products that damage the lung. In the human gut, bacteria alter molecules we consume in our food 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. We 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. 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.

Cystic Fibrosis Research

Our CF research aims to determine how the lung microbiome contributes to CF disease and develop novel methods to treat these complex infections. We are particularly interested in understanding how the lung microbiome may contribute to CF pulmonary exacerbations. Exacerbations are periodic flares of CF disease symptoms that cause significant lung damage and are treated aggressively with antibiotics. We currently do not know the cause of exacerbations in most cases, but believe the lung microbiome is involved. By analyzing the lung microbiome with multi-omics methods supported by experimental microcosms and mathematical modeling we have developed the "Fermentation and Exacerbation Hypothesis". This hypothesis proposes that exacerbations are caused by a hidden group of bacteria in the lungs of CF patients: the anaerobes. These bacteria grow by fermentation in anaerobic environments and are not routinely detected in clinical laboratories. As patients develop an exacerbation we have observed blooms of anaerobic bacteria and their fermentative metabolism. We are currently trying to understand how these bacteria play a role in CF exacerbations and interact with classic pathogens such as Pseudomonas aeruginosa.

Microbiomes Research

Dr. Quinn has studied the microbiomes of salmon, lobsters, corals, mice, lungs, guts, fermented foods, and well, whatever else he becomes interested in. Our main focus is understanding how metabolites from the microbiome shape community function and interactions with the host. We apply high-throughput metabolomics methods to profile the chemical repetoire of the microbiome during health and disease to indentify metabolites important for community function and the microbes responsible for making them. Recently, we discovered that our microbiome produces a unique set of bile acids that are conjugated with various amino acids. By applying advanced bioinformatic approaches for mass spectrometry through the GNPS infrastructure (gnps.ucsd.edu) we identified these molecules that have evaded discovery despite 170 years of research on bile acid chemistry. These molecules have strong effects on host physiology through signalling of bile acid receptors in the gut, and are elevated in those with diseased guts, but outside of that, their role is almost completely unknown. We are intensly studying how these compounds are produced and why microbes make them.

Coral Reef Research

We also have projects on the metabolomics and microbiome dynamics of coral reefs. We use these same multi-omics methods to monitor changes on natural reefs during disease events, such as bleaching. Collaborators at the Universtiy of Hawaii at Manoa sample corals in the natural environment and in the laboratory to peer deep inside the complex and beautiful symbiotic organisms that are in peril across the world due to a changing climate.

Microbial Bile Acids

The Quinn lab is currently investigating how bile acids are produced by our microbiota and their effects on our physiology.