In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Abstract

The interactions between the gut microbiota and its host are of central importance to the health of the host. Outer membrane vesicles (OMVs) are produced ubiquitously by Gram-negative bacteria including the gut commensal Bacteroides thetaiotaomicron. These vesicles can interact with the host in various ways but until now their complement of small molecules has not been investigated in this context. Using an untargeted high-coverage metabolomic approach we have measured the small molecule content of these vesicles in contrasting in vitro conditions to establish what role these metabolites could perform when packed into these vesicles. B. thetaiotaomicron packs OMVs with a highly conserved core set of small molecules which are strikingly enriched with mouse-digestible metabolites and with metabolites previously shown to be associated with colonization of the murine GIT. By use of an expanded genome-scale metabolic model of B. thetaiotaomicron and a potential host (the mouse) we have established many possible metabolic pathways between the two organisms that were previously unknown, and have found several putative novel metabolic functions for mouse that are supported by gene annotations, but that do not currently appear in existing mouse metabolic networks. The lipidome of these OMVs bears no relation to the mouse lipidome, so the purpose of this particular composition of lipids remains unclear. We conclude from this analysis that through intimate symbiotic evolution OMVs produced by B. thetaiotaomicron are likely to have been adopted as a conduit for small molecules bound for the mammalian host in vivo.

Keywords: Bacteroides thetaiotaomicron VPI-5482; genome-scale metabolic modeling; host–microbe interaction; metabolomics; outer membrane vesicle.

FIGURE 1

Summary of metabolomics results. Venn diagrams of metabolomic results for B. thetaiotaomicron and its OMVs grown in vitro in rich and defined media. Subfigures (A) and (B) show overlap of all identified metabolites in each of the compartments considered in RM and DM, respectively. Subfigures (C) and (D) show cell and OMV contents that could be mapped to KEGG metabolites along with those metabolites inferred to be exported directly to the medium between TP1 and TP2, in RM and DM, respectively.

FIGURE 2

Summary of model expansion. The compartments of model iMM_BT_OMV that are affected by the presence of OMVs in the model. Numbers by solid arrows represent numbers metabolites that can cross compartment boundaries. Green dashed arrows represent the overlap between exported metabolites from one organism and imported metabolites to the other organism, along with the sizes of these overlaps. All OMV metabolites can potentially be transported from Bt to mouse. The cream dashed arrow represents the transfer from Bt to mouse via OMVs, and indicates the number of metabolites only transferrable via this route. The system boundary indicates how the model is connected to the dietary intake of nutrients and excretion from the GIT (via the lumen).

FIGURE 3

L-Methionine S-oxide (LMSO) transport and utilization pathway. The addition of reactions to model iMM_BT_OMV to represent transfer of LMSO by OMV from Bt to mouse and the enzyme found that could reduce LMSO to L-methionine in mouse. Squares represent reactions and circles represent metabolites, separated into their relevant compartments, “c,” “o,” and “cm,” in the model. Arrows show the direction of reaction flux; solid lines represent parts present in the original model, dash-single-dot lines represent parts added in OMV metabolism and dash-double-dot lines represent the reaction added during gap filling to link imported LMSO to mouse metabolism (by reduction). Reaction names and summaries are underlined.