Substrate-Driven Differences in Tryptophan Catabolism by Gut Microbiota and Aryl Hydrocarbon Receptor Activation

Microbial tryptophan catabolism as an actionable target via diet-microbiome interactions

In recent years, the role of microbial tryptophan (Trp) catabolism in host-microbiota crosstalk has become a major area of scientific interest. Microbiota-derived Trp catabolites positively contribute to intestinal and systemic homeostasis by acting as ligands of aryl hydrocarbon receptor and pregnane X receptor, and as signaling molecules in microbial communities. Accumulating evidence suggests that microbial Trp catabolism could be therapeutic targets in treating human diseases. A number of bacteria and metabolic pathways have been identified to be responsible for the conversion of Trp in the intestine. Interestingly, many Trp-degrading bacteria can benefit from the supplementation of specific dietary fibers and polyphenols, which in turn increase the microbial production of beneficial Trp catabolites. Thus, this review aims to highlight the emerging role of diets and food components, i.e., food matrix, fiber, and polyphenol, in modulating the microbial catabolism of Trp and discuss the opportunities for potential therapeutic interventions via specifically designed diets targeting the Trp-microbiome axis.

Tempeh fermentation improves the nutritional and functional characteristics of Jack beans (Canavalia ensiformis (L.) DC)

The effect of two processing methods of Jack beans (i.e. cooked bean (CB) and cooked tempeh (CT)) on the in vitro digestibility of protein and starch, as well as the production of short chain fatty acids (SCFAs), γ-aminobutyric acid (GABA), and tryptophan (Trp) metabolites after in vitro colonic fermentation, was investigated. CT was obtained by fungal fermentation after cooking under acidic conditions. CT had significantly higher protein, lower digestible starch, lower total fiber, higher free phenolic compounds, and higher ash content compared to CB. CT exhibited better in vitro protein digestibility than CB and less glucose release during in vitro digestion than CB. A comparable concentration of total SCFAs and GABA was produced after in vitro fermentation of CB and CT, but CB produced more indole than CT, resulting in higher amounts of total Trp metabolites. In summary, our findings show that tempeh fermentation improves the nutritional quality of Jack beans and describe the impact of fermentation on the digestibility of nutrients and the formation of metabolites during colonic fermentation.

Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor

Aryl hydrocarbon receptor (AhR) is a transcription factor that regulates gene expression upon ligand activation, enabling microbiota-dependent induction, training, and function of the host immune system. A spectrum of metabolites, encompassing indole and tryptophan derivatives, have been recognized as activators. This work introduces an integrated, mass spectrometry-centric workflow that employs a bioassay-guided, fractionation-based methodology for the identification of AhR activators derived from human bacterial isolates. By leveraging the workflow efficiency, the complexities inherent in metabolomics profiling are significantly reduced, paving the way for an in-depth and focused mass spectrometry analysis of bioactive fractions isolated from bacterial culture supernatants. Validation of AhR activator candidates used multiple criteria─MS/MS of the synthetic reference compound, bioassay of AhR activity, and elution time confirmation using a C-13 isotopic reference─and was demonstrated for N-formylkynurenine (NFK). The workflow reported provides a roadmap update for improved efficiency of identifying bioactive metabolites using mass spectrometry-based metabolomics. Mass spectrometry datasets are accessible at the National Metabolomics Data Repository (PR001479, Project DOI: 10.21228/M8JM7Q).

Induction of AHR Signaling in Response to the Indolimine Class of Microbial Stress Metabolites

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that plays an important role in gastrointestinal barrier function, tumorigenesis, and is an emerging drug target. The resident microbiota is capable of metabolizing tryptophan to metabolites that are AHR ligands (e.g., indole-3-acetate). Recently, a novel set of mutagenic tryptophan metabolites named indolimines have been identified that are produced by M. morganii in the gastrointestinal tract. Here, we determined that indolimine-200, -214, and -248 are direct AHR ligands that can induce Cyp1a1 transcription and subsequent CYP1A1 enzymatic activity capable of metabolizing the carcinogen benzo(a)pyrene in microsomal assays. In addition, indolimines enhance IL6 expression in a colonic tumor cell line in combination with cytokine treatment. The concentration of indolimine-248 that induces AHR transcriptional activity failed to increase DNA damage. These observations reveal an additional aspect of how indolimines may alter colonic tumorigenesis beyond mutagenic activity.

Effect of whole foods on the microbial production of tryptophan-derived aryl hydrocarbon receptor agonists in growing pigs

Effects of whole foods on the microbial production of tryptophan-derived aryl hydrocarbon receptor (AhR) ligands in the intestine were investigated in a pig model. Ileal digesta and faeces of pigs after feeding of eighteen different foods were analyzed. Indole, indole-3-propionic acid, indole-3-acetic acid, indole-3-lactic acid, kynurenine, tryptamine, and indole-3-aldehyde were identified in ileal digesta, which were also identified in faeces but at higher concentrations except indole-3-lactic acid, together with skatole, oxindole, serotonin, and indoleacrylic acid. The panel of tryptophan catabolites in ileal digesta and faeces varied across different foods. Eggs induced the highest overall concentration of catabolites in ileal digesta dominated by indole. Amaranth induced the highest overall concentration of catabolites in faeces dominated by skatole. Using a reporter cell line, we observed many faecal samples but not ileal samples retained AhR activity. Collectively, these findings contribute to food selection targeting AhR ligands production from dietary tryptophan in the intestine.

Impact of High-Fiber or High-Protein Diet on the Capacity of Human Gut Microbiota To Produce Tryptophan Catabolites

This study investigated the effect of high-fiber-low-protein (HF) and high-protein-low-fiber (HP) diets on microbial catabolism of tryptophan in the proximal colon (PC) and distal colon(DC) compartments of the Simulator of the Human Intestinal Microbial Ecosystem. The microbiota in PC and DC was dominated by Bacteroidetes and Firmicutes, in which Bacteroidetes were more abundant in DC (∼60% versus 50%) and Firmicutes were more abundant in PC (∼40% versus 25%). Most of the tryptophan catabolites were determined at a higher concentration in PC samples than in DC samples, but the overall concentration of tryptophan catabolites was over 10-fold higher in DC samples than that in PC samples. Interestingly, indole-3-propionic acid and oxindole were only identified in DC samples. A two-week dietary intervention by the HF diet enriched the abundance of Firmicutes in PC, whereas the HP diet enriched the abundance of Proteobacteria. Compared to the HP diet, the HF diet favored the microbial production of indole-3-acetic acid, indole-3-lactic acid, indole-3-aldehyde, and indole-3-propionic acid in both PC and DC compartments. To conclude, these findings increase the understanding of the effect of diets on the microbial production of tryptophan catabolites in the colon.

Cryo-EM structure of the cytosolic AhR complex

Aryl hydrocarbon receptor (AhR) is an important ligand-activated transcription factor involved in the regulation of various important physiological functions. Here, we report the cryo-EM structures of the Hsp90-AhR-p23 complex with or without bound XAP2, where the structure of the mouse AhR PAS-B domain is resolved. A highly conserved bridge motif of AhR is responsible for the interaction with the Hsp90 dimeric lumen. The ligand-free AhR PAS-B domain is attached to the Hsp90 dimer and is stabilized in the complex with bound XAP2. In addition, the DE-loop and a group of conserved pocket inner residues in the AhR PAS-B domain are found to be important for ligand binding. These results reveal the structural basis of the biological functions of AhR. Moreover, the protein purification method presented here allows the isolation of stable mouse AhR protein, which could be used to develop high-sensitivity biosensors for environmental pollutant detection.

Insights into gut microbiota metabolism of dietary lipids: the case of linoleic acid

It has been recognized that, next to dietary fibre and proteins, gut microbiota can metabolize lipids producing bioactive metabolites. However, the metabolism of dietary lipids by human gut microbiota has been poorly explored so far. This study aimed to examine the change in lipids, particularly linoleic acid (LA), induced by the chemical form of lipids and the presence of the plant matrix. Short-chain fatty acid (SCFA) production was monitored to get an insight into microbial activity. Free LA, glyceryl trilinoleate and soybean oil as well as digested intact (DS) and broken (BS) soybean cells were subjected to in vitro fermentation using human faecal inoculums. Confocal microscopy was used to visualize the soybean cell integrity. Three LA metabolites, including two conjugated fatty acids (CLAs, 9z,11e and 9e,11e) and 12hydroxy, 9z C18:1, were identified and monitored. Free LA addition improved the LA metabolite production but reduced SCFA concentrations compared to trilinoleate and soybean oil. Breaking cell integrity had impacts on CLA, hydroxy C18:1 and SCFA production and free fatty acid release within the first 24 h of fermentation, but this effect vanished with time. In contrast, soybean oil only increased free LA release and hydroxy C18:1 production. The content of several FAs decreased during fermentation suggesting a substantial conversion in microbial metabolites. Besides, LA metabolites were also identified in the fermentation pellets suggesting the incorporation of microbial FA metabolites into bacterial cells. This study expands our understanding of microbial metabolism of dietary lipids with a special emphasis on the role of food- and diet-related factors.

Tryptophan Supplementation Increases the Production of Microbial-Derived AhR Agonists in an In Vitro Simulator of Intestinal Microbial Ecosystem

The aryl hydrocarbon receptor (AhR) plays an important role in intestinal homeostasis, and some microbial metabolites of tryptophan are known AhR agonists. In this study, we assessed the impact of tryptophan supplementation on the formation of tryptophan metabolites, AhR activation, and microbiota composition in the simulator of the human intestinal microbial ecosystem (SHIME). AhR activation, microbial composition, and tryptophan metabolites were compared during high tryptophan supplementation (4 g/L tryptophan), control, and wash-out periods. During tryptophan supplementation, the concentration of several tryptophan metabolites was increased compared to the control and wash-out period, but AhR activation by fermenter supernatant was significantly decreased. This was due to the higher levels of tryptophan, which was found to be an antagonist of AhR signaling. Tryptophan supplementation induced most microbial changes in the transverse colon including increased relative abundance of lactobacillus. We conclude that tryptophan supplementation leads to increased formation of AhR agonists in the colon.

Substrate-Driven Differences in Tryptophan Catabolism by Gut Microbiota and Aryl Hydrocarbon Receptor Activation

SCOPE

This study aims to investigate the effect of tryptophan sources on tryptophan catabolism by gut microbiota and the aryl hydrocarbon receptor (AhR) activation.

METHODS AND RESULTS

Four substrates (free tryptophan, soybean protein, single and clustered soybean cells) containing an equimolar amount of tryptophan, but with a different bioaccessibility are studied using in vitro batch fermentation. Tryptophan catabolites are identified by LC-MS/MS. AhR activity is measured by HepG2-Lucia AhR reporter cells. The total amount of tryptophan-derived catabolites increases with decreasing level of substrate complexity. Indole is the major catabolite produced from tryptophan and it is the most abundant in the free tryptophan fermentation. Indole-3-acetic acid and indole-3-aldehyde are abundantly generated in the soybean protein fermentation. The soybean cell fermentation produced high concentrations of tryptamine. Interestingly, large amounts of short-chain fatty acids (SCFAs) are also found in the soybean cell and protein fermentation. Both tryptophan-derived catabolites and SCFAs are able to increase AhR reporter activity over time in all four groups.

CONCLUSION

This study illustrates that bacterial catabolism of tryptophan and resulting AhR activation in the gut is modulated by the food matrix, suggesting a role for food design to improve gut health.