We present a novel metabolic modeling framework assessing Glycan Degradation (GlyDe), a key nutrient source of microbial communities in the human gut. GlyDe predicts the usage patterns of thousands of glycans by each of the sequenced individual gut bacteria deposited at the Human Microbiome Project (HMP). These predictions strongly correlate with known biochemical information of the glycan degradation processes and are validated vs. in vitro growth data of two prominent gut Bacteroides species. Furthermore, Species belonging to the Bacteroidetes phylum have a rich and distinct glycan degradation profile, supporting their position as the main glycan degraders in the gut. Finally, microbiota originating from Herbivores has a stronger degradation affinity for plant-derived glycans, while the microbiota from carnivores prefers animal-derived glycans. GlyDE enables the systematic prediction of complex carbon sources utilization patterns for the first time and opens the door to better founded metabolic analysis of naturally occurring microbial communities.
