Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence.

Edward G. Ruby,Yunus E. Tuncil,Bradley L. Reuhs,Bruce R. Hamaker,Jens Walter,Yao Xiao,Nathan T. Porter,Eric C. Martens

doi:10.1128/mbio.01068-17

Edward G. Ruby, Yunus E. Tuncil

Open Access

https://doi.org/10.1128/mbio.01068-17

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Abstract

ABSTRACTWhen presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. However, it is unclear how closely these observed physiological changes, often measured by altered transcription of glycan utilization genes, mirror actual glycan depletion. To understand the glycan prioritization strategies of two closely related human gut symbionts, Bacteroides ovatus and Bacteroides thetaiotaomicron, we performed a series of time course assays in which both species were individually grown in a medium with six different glycans that both species can degrade. Disappearance of the substrates and transcription of the corresponding polysaccharide utilization loci (PULs) were measured. Each species utilized some glycans before others, but with different priorities per species, providing insight into species-specific hierarchical preferences. In general, the presence of highly prioritized glycans repressed transcription of genes involved in utilizing lower-priority nutrients. However, transcriptional sensitivity to some glycans varied relative to the residual concentration in the medium, with some PULs that target high-priority substrates remaining highly expressed even after their target glycan had been mostly depleted. Coculturing of these organisms in the same mixture showed that the hierarchical orders generally remained the same, promoting stable coexistence. Polymer length was found to be a contributing factor for glycan utilization, thereby affecting its place in the hierarchy. Our findings not only elucidate how B. ovatus and B. thetaiotaomicron strategically access glycans to maintain coexistence but also support the prioritization of carbohydrate utilization based on carbohydrate structure, advancing our understanding of the relationships between diet and the gut microbiome.

Highlights

When presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression
In vitro time course studies were conducted for B. ovatus and B. thetaiotaomicron grown either individually or together in a glycan mixture containing chondroitin sulfate (CS), polygalacturonic acid (PGA), pectic galactan (PG), RGI, ARAB, and amylopectin (AP), each at an equal concentration so that the total carbohydrate concentration was 5 g/liter
To make sure there were no contaminating sugars produced by B. ovatus or B. thetaiotaomicron over time, we performed parallel measurements in cultures grown on medium with mannose (Fig. S2), a sugar not contained in any of the glycans in our mixture, and we found that glucose was the only sugar detected during the active growth period (Fig. S2a and c) and was detected in only a negligible amount (Fig. S2b and d)

Summary

Introduction

When presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. Transcriptional sensitivity to some glycans varied relative to the residual concentration in the medium, with some PULs that target high-priority substrates remaining highly expressed even after their target glycan had been mostly depleted Coculturing of these organisms in the same mixture showed that the hierarchical orders generally remained the same, promoting stable coexistence. Based on direct carbohydrate measurements and corresponding transcriptional analyses, our findings showed that individual bacterial species exhibit different preferences for the same set of glycans and that this prioritization is maintained in a competitive environment, which may promote stable coexistence. Such understanding of gut bacterial glycan utilization will be essential to eliciting predictable changes in the gut microbiota to improve health through the diet. Bacteroides species possess cognate PULs for all glycans that they are capable of degrading [16, 20, 21], and expression of a given PUL is activated by either an oligosaccharide derived from a larger glycan [21] or its monosaccharide units [5]

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