(70f) Discovery of Immunomodulatory Gut Bacterial Metabolites Using Metabolomics and Metabolic Modeling

Cellular reactions produce small molecule compounds that are structurally diverse and interact with cellular components such as enzymes and receptors to modulate cellular activity. We are interested in studying the regulatory and signaling roles of these metabolites. The first part of this presentation describes tools for global analysis of metabolites present in a biological sample. A typical mass spectrometry experiment aimed at detecting small molecules generates 10³~10⁴ data features. Despite progress, the identification of metabolites from spectral data, i.e., assignment of chemical structures, remains a daunting task. To address this bottleneck, we assembled a novel computational workflow that utilizes the biological context of a sample to annotate and interpret the metabolomics data. The accuracy and utility of our workflow are illustrated through an analysis of industrial Chinese hamster ovary (CHO) cell lines.

The second part of this presentation describes an ongoing project that uses metabolomics to discover potentially therapeutic metabolites that are produced by commensal gut bacteria. The mammalian gastrointestinal (GI) tract harbors microbial communities that impact a wide array of physiological functions, including digestion, immune system development, and defense against pathogens. Alterations in the microbiota composition leading to functional imbalance, or dysbiosis, have been linked to various chronic diseases and disorders. This presentation will focus on non-alcoholic fatty liver disease (NAFLD), the most prevalent chronic liver disease globally. In a subset of the population, NAFLD develops into steatohepatitis (NASH), which substantially raises the risk for cirrhosis and liver cancer. Currently, there is no effective treatment for NASH.

We have shown that a high-fat diet (HFD) depletes the body of protective immunomodulatory metabolites derived from tryptophan, priming the liver for inflammatory insults. Administered to mice, one of these metabolites, reduced Western diet (WD)-induced weight gain and protected the liver against fat accumulation and inflammation. Applied to cultured liver and adipose cells, the metabolite suppressed pro-inflammatory responses, including secretion of immune cell recruitment and activation, via receptor-mediated pathways. These results suggest that microbiome-based therapies could be effective against NASH, and that the chemical products of gut bacteria could represent an attractive, inherently safe alternative to conventional drug molecules.

Finally, we are developing strategies to shape the intestinal microbiome using mucin mimetics as substrates that can selected enrich the microbiome with desired species. To this end, we built a fast, protein language-based machine learning (ML) model that can identify mucin O-glycan grazing species based on the species’ enzymatic profile. Anaerobic culture experiments confirmed selective growth enhancement of species predicted to have mucin O-glycan metabolizing enzymes compared to other gut bacteria lacking these enzymes. Simulations of community-level metabolic behavior suggest that it is possible to modulate the production of a desired immunomodulatory metabolite by adjusting the availability of O-glycan derived substrates through the activity of mucin grazing species.