Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

Abstract

<jats:p>Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.</jats:p>

The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil

“…Differences in hepatic and serum lipids have been previously observed to be diet and microbiota dependent [26,[29][30][31][32] and plasma lipids are well known to be directly influenced by dietary lipids [33][34][35][36]. Similar to a previous study, we observed more differential lipid molecules between conventional and germfree in the liver compared to plasma [26].…”

Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

“…Intriguingly, using cell culture, they showed that microbially-derived SPs are incorporated into mammalian SP pathways. More recently, Lee et al charted the pathways of dietary SPs in the gut microbiome ( Figure 1 ) [ 40 ]. Taking the Bioorthogonal labeling-Sort-Seq-Spec (BOSSS) approach, the authors found that dietary SPs were mainly consumed by Bacteroides.…”

“…Taking the Bioorthogonal labeling-Sort-Seq-Spec (BOSSS) approach, the authors found that dietary SPs were mainly consumed by Bacteroides. They also found that Bifidobacterium , which do not produce SPs, could process dietary SPs in a manner similar to that of SP-producer Bacteroides , suggesting that bioactive lipids which are metabolically-accessible to the gut microbiome could be the target for the host to control its gut microbial composition [ 40 ].…”

“…However, these dihydrocermides were absent in treatments with sphinganine (SA, green), vehicle or no treatment (red). Figure adapted from [ 40 ], with permission under CC BY 4.0 license.…”

A BOSSS platform: using functionalized lipids and click chemistry for new discoveries in lipid research

“…In this issue of the Journal, bioorthogonal click chemistry was cleverly used by Lee et al. ( 11 ) to interrogate the metabolism of sphinganine in the gut microbiome using a strategy that advanced the utility of click chemistry by incorporating flow cytometry and rRNA sequencing into their workflow. This study exploited several key features of click chemistry tools through a protocol that the authors describe as BioOrthogonal-Sort-Sequence-Spectrometry (BOSSS).…”