Related Experiment Video
Updated: Jun 7, 2026

An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota
Published on: July 31, 2019
Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the
Nick Quinn-Bohmann1,2, Tomasz Wilmanski1, Katherine Ramos Sarmiento1
1Institute for Systems Biology, Seattle, WA 98109, USA.
Abstract:
Microbially-derived short chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. A systems-scale mechanistic understanding of this heterogeneity is lacking. We present a microbial community-scale metabolic modeling (MCMM) approach to predict individual-specific SCFA production profiles. We assess the quantitative accuracy of our MCMMs using in vitro, ex vivo, and in vivo data. Next, we show how MCMM SCFA predictions are significantly associated with blood-derived clinical chemistries, including cardiometabolic and immunological health markers, across a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic, and probiotic interventions that optimize SCFA production in the gut. Our results represent an important advance in engineering gut microbiome functional outputs for precision health and nutrition.
Related Concept Videos
Introduction to the Human Microbiota
Development of Human Microbiota
Microbiota of the Large Intestine
Functions of the Gut Microbiota
Dysbiosis of the Gut Microbiota
Microbiota Modulation by Antibiotics

