Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota

Abstract

A common human gut bacterium, Bacteroides fragilis, produces a sphingolipid ligand for the conserved host receptor CD1d and can modulate natural killer T cell activity.

Abstract

While the human gut microbiota are suspected to produce diffusible small molecules that modulate host signaling pathways, few of these molecules have been identified. Species of Bacteroides and their relatives, which often comprise >50% of the gut community, are unusual among bacteria in that their membrane is rich in sphingolipids, a class of signaling molecules that play a key role in inducing apoptosis and modulating the host immune response. Although known for more than three decades, the full repertoire of Bacteroides sphingolipids has not been defined. Here, we use a combination of genetics and chemistry to identify the sphingolipids produced by Bacteroides fragilis NCTC 9343. We constructed a deletion mutant of BF2461, a putative serine palmitoyltransferase whose yeast homolog catalyzes the committed step in sphingolipid biosynthesis. We show that the Δ2461 mutant is sphingolipid deficient, enabling us to purify and solve the structures of three alkaline-stable lipids present in the wild-type strain but absent from the mutant. The first compound was the known sphingolipid ceramide phosphorylethanolamine, and the second was its corresponding dihydroceramide base. Unexpectedly, the third compound was the glycosphingolipid α-galactosylceramide (α-GalCer _Bf), which is structurally related to a sponge-derived sphingolipid (α-GalCer, KRN7000) that is the prototypical agonist of CD1d-restricted natural killer T (iNKT) cells. We demonstrate that α-GalCer _Bf has similar immunological properties to KRN7000: it binds to CD1d and activates both mouse and human iNKT cells both in vitro and in vivo. Thus, our study reveals BF2461 as the first known member of the Bacteroides sphingolipid pathway, and it indicates that the committed steps of the Bacteroides and eukaryotic sphingolipid pathways are identical. Moreover, our data suggest that some Bacteroides sphingolipids might influence host immune homeostasis.

Author Summary

While human gut bacteria are thought to produce diffusible molecules that influence host biology, few of these molecules have been identified. Species of Bacteroides, a Gram-negative bacterial genus whose members often comprise >50% of the gut community, are unusual in that they produce sphingolipids, signaling molecules that play a key role in modulating the host immune response. Sphingolipid production is ubiquitous among eukaryotes but present in only a few bacterial genera. We set out to construct a Bacteroides strain that is incapable of producing sphingolipids, knocking out a gene predicted to encode the first enzymatic step in the Bacteroides sphingolipid biosynthetic pathway. The resulting mutant is indeed deficient in sphingolipid production, and we purified and solved the structures of three sphingolipids that are present in the wild-type strain but absent in the mutant. To our surprise, one of these molecules is a close chemical relative of a sponge sphingolipid that is the prototypical ligand for a host receptor that controls the activity of natural killer T cells. Like the sponge sphingolipid, the Bacteroides sphingolipid can modulate natural killer T cell activity, suggesting a novel mechanism by which Bacteroides in the gut might influence the host immune response.