Diet-Specific Adaptations Mammalian Gut Microbiota Abundance and Host Glycan Degradation ( GlyDeR ) Analysis Predicts 2014

Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing degradation profiles for genomes in the Human Microbiome Project against KEGG reaction annotations. Next, we applied GlyDeR to the analysis of human and mammalian gut microbial communities, which revealed that the glycan degradation potential of a community is strongly linked to host diet and can be used to predict diet with higher accuracy than sequence data alone. Finally, we show that a microbe’s glycan degradation potential is significantly correlated (R 0.46) with its abundance, with even higher correlations for potential pathogens such as the class Clostridia (R 0.76). GlyDeR therefore represents an important tool for advancing our understanding of bacterial metabolism in the gut and for the future development of more effective prebiotics for microbial community manipulation. IMPORTANCE The increased availability of high-throughput sequencing data has positioned the gut microbiota as a major new focal point for biomedical research. However, despite the expenditure of huge efforts and resources, sequencing-based analysis of the microbiome has uncovered mostly associative relationships between human health and diet, rather than a causal, mechanistic one. In order to utilize the full potential of systems biology approaches, one must first characterize the metabolic requirements of gut bacteria, specifically, the degradation of glycans, which are their primary nutritional source. We developed a computational framework called GlyDeR for integrating expert knowledge along with high-throughput data to uncover important new relationships within glycan metabolism. GlyDeR analyzes particular bacterial (meta)genomes and predicts the potency by which they degrade a variety of different glycans. Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics. Received 24 June 2014 Accepted 25 June 2014 Published 12 August 2014 Citation Eilam O, Zarecki R, Oberhardt M, Ursell LK, Kupiec M, Knight R, Gophna U, Ruppin E. 2014. Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. mBio 5(4):e01526-14. doi:10.1128/mBio.01526-14. Editor Judith Berman, University of Minnesota Copyright © 2014 Eilam, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Address correspondence to Omer Eila, omereila@post.tau. ac.il. This article is a direct contribution from a Fellow of the American Academy of Microbiology. The human gastrointestinal tract harbors an extensive array of commensal microorganisms. Species composition is highly diverse both within and between individuals (1), and the activities of these organisms affect the host through many pathways, including the production of short-chain fatty acids (SCFA) that regulate epithelial cell growth and immune system development, displacement of potential pathogens, detoxification of protein fermentation products, and gas production (2–6). The beneficial or detrimental outcomes of these effects depend largely on the community structure, environmental factors, diet, and the genetic background of the host (7, 8). In order to gain a deeper understanding of the gut ecosystem as a whole, a systems biology approach integrating genomic, metabolic, and enzymatic information is an invaluable tool (9, 10). Large-scale sequencing analysis of the human gut microbiome has led to many tantalizing and highly important gut microbiome-human health associations, but typically little or no mechanistic insight is provided (11). Simplified in vitro models aim to bridge this gap, but the reliance of these models on a few strains and on defined culture media makes them difficult to relate to the complexities of the human gut (12, 13). A primary issue is the fact that very few simple metabolites escape digestion in the small intestine (14), which makes complex carbohydrates and their derivatives, collectively termed glycans, the predominant nutrients for microbes in the colon (15, 16). These glycans are poorly accounted for in any current systems biology or pathwayrelated frameworks or databases, and thus they represent a major hurdle in leveraging the full weight of systems biology methods in the gut microbiome field. Incorporating mechanisms into microbiome research will therefore first require a large-scale accounting and analysis of glycan degradation by the gut microbiota. While some human colonic bacteria simply require acetate or RESEARCH ARTICLE crossmark July/August 2014 Volume 5 Issue 4 e01526-14 ® mbio.asm. org 1 m b.asm . rg on O cber 3, 2014 P ubished by m b.asm . rg D ow nladed fom branched-chain fatty acids (17), the detailed growth requirements for the majority of gut bacteria remain unknown (18). Characterizing these requirements will shed light on the different metabolic niches organisms fill and may enable the design of dietary interventions that promote growth of particular beneficial microbes, an approach collectively termed “prebiotics” (19). While several glycans are currently marketed around the world as prebiotics, few have been validated through high-quality human trials (19, 20). Furthermore, dietary enrichment of a specific prebiotic compound may permit preferential expansion of a microbial group that is well adapted to its use, but the outcomes for the gut community as a whole can be unpredictable (21). In this study, we investigated the connections between diet and glycan metabolism of the human gut microbiota. Whereas the study of the metabolic activity conducted by gut microbiota has been the focal point of a wide range of computational studies (9, 11), current approaches have been highly limited in their ability to analyze glycan degradation. We present a novel algorithm (termed GlyDeR) for predicting the glycan degradation patterns of any bacterium with a sequenced genome. The algorithm is based on manual curation of nearly 150 carbohydrate-active enzymes (CAZymes) and is applied to a set of 10,000 glycan structures and 203 microbial genomes. Given a particular bacterial (meta)genome, GlyDeR can be used to reverse engineer the predicted potency by which a bacterium degrades a variety of different glycans. These predictions correlate with known KEGG reactions and expand upon the limited, previously available glycan degradation data 100-fold. We determined that the microbiota of herbivores and carnivores have stronger degradation affinities for plantderived and animal-derived glycans, respectively, and that a Western diet in humans correlates more strongly with meat-derived glycans than a non-Western diet. Finally, we show that speciesspecific glycan degradation profiles are associated with and can be used to predict bacterial species abundance, making GlyDeR a valuable tool for the future rational design of novel prebiotics, by deliberately manipulating the microbiome based on nutrient availability.