中药单体的增毒机制：肠道菌群介导的代谢活化

ETHNOPHARMACOLOGICAL RELEVANCE Euphorbia kansui (EK), a kind of toxic traditional Chinese medicine (TCM), is used in the treatment of edema, ascites and asthma. EK fry-baked with vinegar (VEK) is regularly used to reduce the toxicity in TCM. Previous studies have confirmed that fry-baking with vinegar could significantly reduce the significant gastrointestinal toxicity of EK. The toxic side-effects of EK are closely associated with intestinal tract, but existing research results could not provide practical measures for detoxification in terms of the biological effects of EK fry-baked with vinegar. AIM OF THE STUDY This study aimed to investigate the gastrointestinal toxicity of EK and detoxification of VEK through the regulation of gut microbiota. Thirty male Sprague Dawley (SD) rats were randomly divided equally into 3 groups and received by oral gavage 0.5% CMC-Na (C group), EK (EKC group) or VEK (VEKC group) powder at 680 mg/kg for seven consecutive days. RESULTS The ten toxic components in VEK were reduced significantly compared with those in EK. After fry-baked with vinegar, those side effects associated with VEK were significantly relieved in terms of histopathology and inflammatory injury indices of intestinal tissues, liver function and oxidative damage indices. The toxicity of EK might be highly correlated with Lactobacillus and Blautia genera. In addition, EK fry-baked with vinegar increased the production of short-chain fatty acids (SCFAs), which are regulated by gut microbiota. CONCLUSIONS The proportion of main probiotics increased and potentially pathogenic bacteria decreased after EK was fry-baked with vinegar. It turned out that effective detoxification could be achieved by fry-baking with vinegar.

Water decoction is the main form of traditional Chinese medicine (TCM) administered in clinics. Polysaccharides are major components of decoction. Recent studies reported that polysaccharides possess multiple pharmacological activities. However, the mechanism by which oral Chinese herbal polysaccharides play vital roles in the body remains uncertain. This review discussed the polysaccharides in Chinese herbal decoctions and their effects, direct and indirect. The direct impact of polysaccharides includes being absorbed into the body immunity regulation through Peyer’s patches; electrostatic adsorption, hydrophobic interaction, and glycoprotein receptors-induced antibacterial effects; prebiotic functions; gut microbiota structural regulation; and increasing the relative abundance of beneficial bacteria. The indirect effects of the polysaccharides in Chinese herbal decoctions include phytochemical toxicity reduction and activity enhancement. Finally, their clinical and research significance is summarized and future research directions are discussed.

Although the efficacy of herbal medicines (HMs) and traditional Chinese medicines (TCMs) in human diseases has long been recognized, their development has been hindered in part by a lack of a comprehensive understanding of their mechanisms of action. Indeed, most of the compounds extracted from HMs can be metabolized into specific molecules by host microbiota and affect pharmacokinetics and toxicity. Moreover, HMs modulate the constitution of host intestinal microbiota to maintain a healthy gut ecology. Dietary interventions also show great efficacy in treating some refractory diseases, and the commensal microbiota potentially has significant implications for the high inter-individual differences observed in such responses. Herein, we mainly discuss the contribution of the intestinal microbiota to high inter-individual differences in response to HMs and TCMs, and especially the already known metabolites of the HMs produced by the intestinal microbiota. The contribution of commensal microbiota to the inter-individual differences in response to dietary therapy is also briefly discussed. This review highlights the significance of intestinal microbiota-associated metabolites to the efficiency of HMs and dietary interventions. Our review may help further identify the mechanisms leading to the inter-individual differences in the effectiveness of HM and dietary intervention from the perspective of their interactions with the intestinal microbiota.

Xanthii Fructus (XF) not only has medicinal function in traditional Chinese medicine (TCM) but also contains rich oil and protein. The aim of this research was to develop the edible value of its protein based on the investigation on the extraction, basic characteristics and functions, safety, gut microbiota, and metabolomics, especially the effect of the concocting process. The proteins from raw and concocted XF were prepared using two methods: alkaline solubilization followed by acid precipitation and ammonium sulfate salting-out, respectively. The secondary structure and physicochemical properties of the proteins were characterized through spectroscopic analysis and property determination. The effects of alkaline and the concocting process on the proteins were systematically compared. The results indicated that the salting-out method could retain the protein activity better. Both alkali treatment and the concocting process altered the folding state of proteins. The toxicological results in mice indicated that a high dose (0.35 g/kg) of raw Xanthii Fructus protein (XFP) might cause damage to the liver and small intestine, and the concocting process could significantly alleviate the damage. The 16S rRNA sequencing technology was used to untangle their impact on gut microbiota in mice and the result showed that raw protein had a certain regulatory effect on Bifidobacterium, Rhodococcus, Lactococcus, and Clostridium, while the concocted protein had a smaller impact, mainly affecting Bacteroides and Bifidobacterium. The untargeted metabolomics using liquid chromatography-mass spectrometry (LC-MS) showed that the proteins of raw XF affected the metabolic level through cysteine and methionine metabolism, purine metabolism, amino sugar and nucleotide sugar metabolism pathways, and the concocted protein mainly involved histidine metabolism and purine metabolism pathways. Overall, XFP had potential development prospects, but the anti-nutritional factors might have some toxicity. The concocting process could significantly improve its safety, and the concocted proteins were worth developing as a food source. In the future, the processing conditions should be further optimized and more systematic investigation should be performed to ensure the safety of XF as a food source.

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No abstract available

Triclosan (TCS) and triclocarban (TCC) are widely used as antimicrobial agents in personal care products. Their widespread use has become a potential environmental contaminant. This review reviews the mechanisms of intestinal toxicity of TCS and TCC and their potential nutritional intervention strategies. TCS and TCC can be metabolized to glucuronic acid conjugates in the host and subsequently uncoupled by microorganisms in the intestine to regenerate free forms of TCS and TCC. TCS and TCC are unique metabolic pathways that lead to accumulation in the gut, altering the structure of intestinal flora, increasing the relative abundance of pathogenic bacteria, while reducing the abundance of beneficial bacteria, thereby disrupting the balance of intestinal flora. In addition, they can interfere with the self-renewal and differentiation of ISCs, thereby weakening intestinal barrier function. TCS and TCC can also activate the TLR4-NFκB signaling pathway, inducing and exacerbating inflammatory responses. These mechanisms together lead to intestinal toxicity and have a significant negative impact on intestinal health. In order to cope with the intestinal toxicity caused by these mechanisms of action, this paper believes that prebiotics, probiotics, vitamins, minerals and herbal extracts can be used as potential nutritional interventions to reduce the intestinal toxicity of TCS and TCC by regulating intestinal microbiota, enhancing intestinal barrier function and inhibiting inflammatory response. Although preliminary studies have shown the potential benefits of these interventions, their specific efficacy and safety still need further study.

Recent data clearly show that the gut microbiota plays a significant role in the biotransformation of many endogenous molecules and xenobiotics, leading to a potential influence of this microbiotic metabolism on activation, inactivation and possible toxicity of these compounds. To study the colonic biotransformation of xenobiotics by the gut microbiome, in vitro models are often used as they allow dynamic and multiple sampling overtime. However, the pre-analytical phase should be carefully optimized to enable biotransformation product identification representative for the in vivo situation. During this study, chlorogenic acid was used as a model compound to optimize a ready-to-use gut microbiome biotransformation platform using an in vitro gastrointestinal dialysis-model with colon phase together with an instrumental platform using liquid chromatography coupled to high resolution mass spectrometry (LC-QTOF-MS). Identification of the biotransformation products of chlorogenic acid was performed using complementary suspect and non-targeted data analysis approaches (MZmine + R and MPP workflow). Concerning the pre-analytical phase, (i) the influence of different incubation media (Wilkins-Chalgren Anaerobic Broth (WCB) and (versus) phosphate buffer) and different incubation times (prior to implementation in the colonic stage of the dialysis model) on fecal bacterial composition and concentration were investigated and (ii) four different sample preparation methods (centrifugation, extraction, sonication and freeze-drying) were evaluated targeting colonic biotransformation of chlorogenic acid. WCB as incubation medium showed to introduce substantial variation in the bacterial composition of the fecal samples, while the sterile phosphate buffer guaranteed a closer resemblance to the in vivo composition. Furthermore, incubation during 24 h in sterile phosphate buffer as medium showed no significant increase or decrease in anaerobic bacterial concentration, concluding that incubation prior to the colonic stage is not needed. Concerning sample preparation, centrifugation, sonication and extraction gave similar results, while freeze-drying appeared to be inferior. The extraction method was selected as an optimal sample preparation method given the quick execution together with a good instrumental sensitivity. This study optimized a ready-to-use platform to investigate colonic biotransformation of xenobiotics by using chlorogenic acid as a model compound. This platform can be used in the future to study differences in colonic biotransformation of xenobiotics using fecal samples of different patient groups.

Abstract There has been a growing recognition of the significant role played by the human gut microbiota in altering the bioavailability as well as the pharmacokinetic and pharmacodynamic aspects of orally ingested xenobiotic and biotic molecules. The determination of species-specific contributions to the metabolism of biotic and xenobiotic molecules has the potential to aid in the development of new therapeutic and nutraceutical molecules that can modulate human gut microbiota. Here we present “GutBugDB,” an open-access digital repository that provides information on potential gut microbiome-mediated biotransformation of biotic and xenobiotic molecules using the predictions from the GutBug tool. This database is constructed using metabolic proteins from 690 gut bacterial genomes and 363,872 protein enzymes assigned with their EC numbers (with representative Expasy ID and domains present). It provides information on gut microbiome enzyme-mediated metabolic biotransformation for 1439 FDA-approved drugs and nutraceuticals. GutBugDB is publicly available at https://metabiosys.iiserb.ac.in/gutbugdb/.

ABSTRACT STW 5, a blend of nine medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5’s differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n = 6; healthy controls, n = 10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4, and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid, and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective, or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5. IMPORTANCE STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5. STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5.

Diet is a major determinant of gut microbiome composition, and variation in diet-microbiome interactions may contribute to variation in their health consequences. To mechanistically understand these relationships, here we map interactions between ∼150 small-molecule dietary xenobiotics and the gut microbiome, including the impacts of these compounds on community composition, the metabolic activities of human gut microbes on dietary xenobiotics, and interindividual variation in these traits. Microbial metabolism can toxify and detoxify these compounds, producing emergent interactions that explain community-specific remodeling by dietary xenobiotics. We identify the gene and enzyme responsible for detoxification of one such dietary xenobiotic, resveratrol, and demonstrate that this enzyme contributes to interindividual variation in community remodeling by resveratrol. Together, these results systematically map interactions between dietary xenobiotics and the gut microbiome and connect toxification and detoxification to interpersonal differences in microbiome response to diet.

The biotransformation of drugs by enzymes from the human microbiome can produce active or inactive products, impacting the bioactivity and function of these drugs inside the human host. However, understanding the biotransformation reactions of drug molecules catalyzed by bacterial enzymes in human microbiota is still limited. Hence, to characterize drug utilization capabilities across all the microbial phyla inside the human gut, we have used a knowledge-based approach to develop HgutMgene-Miner software which predicts xenobiotic metabolizing enzymes (XMEs) through genome mining. HgutMgene-Miner derives its predictive power from the MicrobiomeMetDB database, which systematically catalogs all known biotransformation reactions of xenobiotics and primary metabolites mediated by host-associated microbial enzymes. Over 10,000 isolate genomes from 830 different bacterial species found in the Unified Human Gastrointestinal Genome (UHGG) collection have been analyzed by HgutMgene-Miner. This led to the identification of 89,377 xenobiotic metabolizing enzymes (XMEs) across 13 phyla, with the greatest diversity in Bacteroidota, Firmicutes_A, Firmicutes, and Proteobacteria. Bacteroides, Clostridium, and Alitsipes were found to be the richest genera, while Actinomyces were found to encode the fewest XMEs, primarily metabolizing Diclofenac, a nonsteroidal anti-inflammatory drug. Overall, we discovered XMEs in 220 genera, exceeding the number experimentally reported in fewer than 10 genera. Notably, Eggerthella lenta's cgr2 involved in Digoxin inactivation was identified in very distant Holdemania genera, likewise Clostridium leptum's nitroreductase, involved in Nitrazepam metabolism, was found in Fusobacterium. These findings highlight the extensive and diverse distribution of XMEs across microbial taxa.

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No abstract available

Interspecies pathways in the gut microbiome have been shown to metabolize levodopa, the primary treatment for Parkinson’s disease, and reduce its bioavailability. While the enzymatic reactions have been identified, the ability to establish the resulting macromolecules as biomarkers of microbial metabolism remains technically challenging. In this study, we leveraged an untargeted mass spectrometry-based approach to investigate volatile organic compounds (VOCs) produced during levodopa metabolism by Enterococcus faecalis , Clostridium sporogenes , and Eggerthella lenta . We cultured these organisms with and without their respective bioactive metabolites and detected levodopa-induced shifts in VOC profiles. We then utilized bioinformatics to identify significant differences in 2,6-dimethylpyrazine, 4,6-dimethylpyrimidine, and 4,5-dimethylpyrimidine associated with its biotransformation. Supplementing cultures with inhibitors of levodopa-metabolizing enzymes revealed specific modulation of levodopa-associated diazines, verifying their relationship to its metabolism. Furthermore, functional group analysis depicts strain-specific VOC profiles that reflect interspecies differences in metabolic activity that can be leveraged to assess microbiome functionality in individual patients. Collectively, this work identifies previously uncharacterized metabolites of microbe-mediated levodopa metabolism to determine potential indicators of this activity and further elucidate the metabolic capabilities of different gut bacteria.

Mammalian gastrointestinal tract is inhabited by trillions of symbiotic microbiotas representing viruses, bacteria, archaea and eukaryotes including yeasts, fungi and protozoa. Compared to humans, the herbivores harbor a complex and metabolically efficient microbes which not only detoxify inadvertently consumed anti-nutritional phytochemicals, but also convert ingested tannin-polyphenols, saponins, phytoestrogens and alkaloids into metabolites which are more available and bioactive than their precursors. Some microbes detoxify toxicants and eliminate them from body. The resulting metabolites display a range of nutritional and therapeutic benefits besides their direct impact on enhancing diversity and functioning of the gut microbiome. Metabolically active gut microbiota and the metabolites generated might be the futuristic alternative biotherapeutics to develop nutraceuticals and plant-based health formulations primarily for ‘metabotype 0’ individuals. Further insights into novel microbial species, modes of microbial biotransformation of phytochemicals and botanicals will pave the way to develop futuristic non-antibiotic interventions to avert infections and boost human and veterinary health.     Keywords: Gut microbiome; Phytochemicals; Biotransformation; Biotherapeutics Highlights: Gut microbes and dietary phytochemicals prevent host against chronic diseases and infections.  Little is known about metabolism and modes of action of the GI metabolites of botanicals and herbal supplements.  Gut microbial metabolites having anti-inflammatory, anti-oxidative and anti-carcinogenic properties might be the futuristic therapeutics.

BACKGROUND STW 5-II is a combination of six herbal extracts with clinically proven efficacy in functional dyspepsia (FD) and irritable bowel syndrome (IBS). STW 5-II contains a wide variety of secondary plant constituents that may interact with the human gut microbiome. In addition to complex carbohydrates, secondary plant metabolites, such as polyphenols, are known to exert prebiotic-like effects. PURPOSE This study aimed to assess the bidirectional interactions between STW 5-II and the human gut microbiome. METHODS STW 5-II was incubated with human fecal microbiota in a short-term colonic model. In the samples, the impact of STW 5-II on microbial fermentation capacity (pH, gas production), short chain fatty acid (SCFA) production, and microbial composition (Illumina 16S rRNA gene sequencing) was analyzed. In addition, the biotransformation of STW 5-II constituents by the fecal microbiota was assessed by UHPLCHRMS-based metabolite profiling. Furthermore, Caco-2/THP1 co-culture assay was used to explore the effect on gut barrier integrity and inflammatory markers. RESULTS Fermentation of STW 5-II by fecal microbiota led to consistent changes in pH and gas production and increased production of SCFAs (acetate, propionate, and butyrate). STW 5-II promoted the enrichment of Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Eggerthellaceae and suppressed the growth of pathogenic species from the Enterobacteriaceae family. In Caco2/THP1 culture, treatment with STW 5-II-incubated samples resulted in significantly increased transepithelial electrical resistance, indicating enhanced barrier function. Among inflammatory markers, STW 5-II-incubated samples increased LPS-induced secretion of the anti-inflammatory cytokine IL-10, as well as NF-κB activity, and significantly decreased the secretion of the pro-inflammatory chemokine MCP-1. UHPLCHRMS analysis identified 110 constituents of STW 5-II with changed levels during incubation with fecal microbiota: 63 constituents that were metabolized, 22 intermittently increased metabolites, and 25 final metabolites, including compounds with established anti-inflammatory activity, such as 18β-glycyrrhetinic acid. CONCLUSION These findings indicate a microbiome-mediated digestive health-promoting effect of STW 5-II via three different routes, namely enhanced microbial SCFA production, microbial production of potentially bioactive metabolites from STW 5-II constituents, and prebiotic-like action by promoting the proliferation/growth of beneficial bacteria.

Introduction: Although pharmacogenetics and pharmacogenomics have been at the forefront of research aimed at finding novel personalized therapies, the focus of research has recently extended to the potential of intestinal microbiota to affect drug efficacy. Complex interplay of gut microbiota with bile acids may have significant repercussions on drug pharmacokinetics. However, far too little attention has been paid to the potential implication of gut microbiota and bile acids in simvastatin response which is characterized by large interindividual variations. The Aim: In order to gain more insight into the underlying mechanism and its contribution in assessing the clinical outcome, the aim of our study was to examine simvastatin bioaccumulation and biotransformation in probiotic bacteria and the effect of bile acids on simvastatin bioaccumulation in in vitro conditions. Materials and methods: Samples with simvastatin, probiotic bacteria and three different bile acids were incubated at anaerobic conditions at 37°C for 24 h. Extracellular and intracellular medium samples were collected and prepared for the LC-MS analysis at predetermined time points (0 min, 15 min, 1 h, 2 h, 4 h, 6 h, 24 h). The concentrations of simvastatin were analyzed by LC-MS/MS. Potential biotransformation pathways were analyzed using a bioinformatics approach in correlation with experimental assay. Results: During the incubation, simvastatin was transported into bacteria cells leading to a drug bioaccumulation over the time, which was augmented upon addition of bile acids after 24 h. A decrease of total drug level during the incubation indicates that the drug is partly biotransformed by bacterial enzymes. According to the results of bioinformatics analysis, the lactone ring is the most susceptible to metabolic changes and the most likely reactions include ester hydrolysis followed by hydroxylation. Conclusion: Results of our study reveal that bioaccumulation and biotransformation of simvastatin by intestinal bacteria might be the underlying mechanisms of altered simvastatin bioavailability and therapeutic effect. Since this study is based only on selected bacterial strains in vitro, further more in-depth research is needed in order to elicit completely the contribution of complex drug-microbiota-bile acids interactions to overall clinical response of simvastatin which could ultimately lead to novel approaches for the personalized lipid-lowering therapy.

ABSTRACT Biotransformation of Fipronil forms three metabolites: fipronil sulfone, fipronil sulfide and fipronil desulfinyl. Among the triad of metabolites, fipronil sulfone exhibits quantitatively predominant production. Research on Fipronil and its relationship with Parkinson's disease (PD) has exclusively focused on the parent compound (fipronil), with no consideration given to its metabolites. We aim to investigate the effect of fipronil sulfone, on gut bacterial proteins involved in metabolite production, adversely affect patients with Parkinson’s disease. The proteins Diaminopimelate epimerase (Q88V90) (DapF) from Lactobacillus sp., and. Tyrosine Decarboxylase (P0DTQ4) (TDC) from Enterococcus sp. are involved in cellular mechanisms help bacteria maintain a normal functional state & cell population to produce metabolites. The interaction of FS with DapF and TDC for each bacterial species was simulated. A concentration-based simulation was performed for 100 ns at 92 mg/L, half the LD50 value (184 mg/L) of Fipronil sulfone. The values of molecular simulation analysis of TDC and DapF respectively were: RMSD = 4.9846 nm & 2.0648 nm and RMSF = 1.788071 nm & 1.237829 nm. The aforementioned interaction studies indicate conformation change in the protein structures of DapF and TDC could potentially inhibit the functioning of the bacteria, thereby reducing amount of metabolites produced possibly influencing Parkinson’s Disease. Highlights Fipronil is metabolised by the human body into Fipronil sulfone (FPS) which is potentially more toxic than its parent compounds. FPS binds to proteins that are involved in essential biochemical pathways that are responsible for the survival or production of neurotransmitters. FPS shows strong binding to these proteins possibly leading to a change in the 3D structure which would indicate the compromise in the functionality of these proteins. This way, due to the failure of survival or an essential pathway being blocked, the amount of neurotransmitters produced could eventually reduce and affect the enteric nervous system, leading to worsening the symptoms of PD.

Dietary components and bioactive molecules present in functional foods and nutraceuticals provide various beneficial effects including modulation of host gut microbiome. These metabolites along with orally administered drugs can be potentially bio-transformed by gut microbiome, which can alter their bioavailability and intended biological or pharmacological activity resulting in individual or population-specific variation in drug and dietary responses. Experimental determination of microbiome-mediated metabolism of orally ingested molecules is difficult due to the enormous diversity and complexity of the gut microbiome. To address this problem, we developed "GutBug", a web-based resource that predicts all possible bacterial metabolic enzymes that can potentially biotransform xenobiotics and biotic molecules using a combination of machine learning, neural networks and chemoinformatic methods. Using 3,457 enzyme substrates for training and a curated database of 363,872 enzymes from ∼700 gut bacterial strains, GutBug can predict complete EC number of the bacterial enzymes involved in a biotransformation reaction of the given molecule along with the reaction centres with accuracies between 0.78 and 0.97 across different reaction classes. Validation of GutBug's performance using 27 molecules known to be biotransformed by human gut bacteria, including complex polysaccharides, flavonoids, and oral drugs further attests to GutBug's accuracy and utility. Thus, GutBug enhances our understanding of various metabolite-gut bacterial interactions and their resultant effects on the human host health across populations, which will find enormous applications in diet design and intervention, identification and administration of new prebiotics, development of nutraceutical products, and improvements in drug designing. GutBug is available at https://metabiosys.iiserb.ac.in/gutbug.

Individuals vary widely in their responses to drugs, and growing evidence implicates the gut microbiome as a contributor to this variability. While prior studies show that gut bacteria can metabolize drugs, how differences in microbial community composition influence drug metabolism remains poorly understood. Here, we characterize the biotransformation of 271 drugs by 89 gut microbial communities derived from human donors and preclinical animal models. Over 90% of tested drugs were metabolized by at least one microbiome. We identified 66 drugs exhibiting highly variable metabolism across human-derived microbiomes and several drugs whose biotransformation differed markedly between human and animal microbiomes. To enable prediction of microbiota-mediated drug metabolism, we developed and compared multiple modeling approaches based on metagenomic data. These results, together with the provided data and analytical resources contribute to a better understanding of microbiome-drug interactions and support their future integration into drug discovery, personalized prescription, and therapeutic drug monitoring.

Background The pseudo germ-free (PGF) model has been widely used to research the role of intestinal microbiota in drug metabolism and efficacy, while the modelling methods and the utilization of the PGF model are still not standardized and unified. A comprehensive and systematic research of the PGF model on the composition and function of the intestinal microbiota, changes in host cytochrome P450 (CYP450) enzymes expression and intestinal mucosal permeability in four different modelling cycles of the PGF groups are provided in this paper. Results 16S rRNA gene amplicon sequencing was employed to compare and analyze the alpha and beta diversity, taxonomic composition, taxonomic indicators and predicted function of gut microbiota in the control and PGF groups. Bacterial richness and diversity decreased significantly in the PGF group beginning after the first week of establishment of the PGF model with antibiotic exposure. The PGF group exposed to antibiotics for 4-week-modelling possessed the fewest indicator genera. Moreover, increased intestinal mucosal permeability occurred in the second week of PGF model establishment, indicating that one week of antibiotic exposure is an appropriate time to establish the PGF model. The results of immunoblots revealed that CYP1A2, CYP2C19 and CYP2E1 expression was significantly upregulated in the PGF group compared with the control group, implying that the metabolic clearance of related drugs would change accordingly. The abundance of functional pathways predicted in the gut microbiota changed dramatically between the control and PGF groups. Conclusions This study provides information concerning the microbial and CYP450 enzyme expression profiles as a reference for evaluating drug metabolism differences co-affected by gut microbiota and host CYP450 enzymes in the PGF model.

Cetilistat is a pancreatic lipase inhibitor approved for management of obesity, following the serious adverse effects exhibited by its analogueorlistat. Exhaustive literature review reveals lack of comprehensive reports on itsbiotransformation. With a view to undertake the same, present study reports the identification and characterization of metabolites of cetilistat in rats using UPLC-MS/MS. Since, the site of action for cetilistat is the small intestine, it was of paramount importance that the role of microbial flora in the metabolism of cetilistat was explored. To achieve so, the metabolic profile of cetilistat was compared in normal vs pseudo germ free rats. The study involved administration of drug suspension to male Sprague-Dawleypseudo germ free and normal untreated rats followed by collection of urine, feces, and blood at specific intervals. Sample preparation was performed through liquid-liquid extraction and concentration of samples followed by analysis using LC-MS/MS. Lastly, an in silicostudy was performed on the drug and metabolites to predict their toxicological properties by ADMET Predictor TM software. Four metabolites of Cetilistat were observed in in vivomatrices. Conforming to anticipation,significant changes were observed both qualitatively as well as quantitatively implying that formation of metabolites was both CYP enzymes and gut microflora mediated.

Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.

The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.

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Our microbiome harbours a metabolic capacity far beyond our own. Moreover, its gene pool is highly adaptable and subject to selective pressure, including host exposure to xenobiotics. Yet, the resulting adaptations do not necessarily follow host well-being and can therefore contribute to disease or unfavourable metabolite production. This review provides an overview of our host-microbiome relationship in light of bacterial (xenobiotic) metabolism, community dynamics, entero-endocrine crosstalk, dysbiosis and potential therapeutic targets. In addition, it will highlight the need for a systematic analysis of the microbiome's potential for substance toxification. The influence of our microbiota reaches from primary metabolites to secondary effects such as substrate competition or the activation of eukaryotic Phase I and Phase II enzymes. Further on it plays a hitherto underestimated role in drug metabolism, toxicity and pathogenesis. These effects are partly caused by entero-endocrine crosstalk and interference with eukaryotic regulatory networks. On first sight, the resulting concept of a metabolically competent microbiome adds enormous complexity to human physiology. Yet, the potential specificity of microbial targets harbours therapeutic promise for diseases such as diabetes, cancer and psychiatric disorders. A better physiological and biochemical understanding of the microbiome is thus of high priority for academia and biomedical research.

Exposure to environmental pollutants and human microbiome composition are important predisposition factors for tumour development

Patients with renal failure suffer from symptoms caused by uraemic toxins, possibly of gut microbial origin, as deduced from studies in animals. The aim of the study is to characterise relationships between the intestinal microbiome composition, uraemic toxins and renal failure symptoms in human end-stage renal disease (ESRD). Characterisation of gut microbiome, serum and faecal metabolome and human phenotypes in a cohort of 223 patients with ESRD and 69 healthy controls. Multidimensional data integration to reveal links between these datasets and the use of chronic kidney disease (CKD) rodent models to test the effects of intestinal microbiome on toxin accumulation and disease severity. A group of microbial species enriched in ESRD correlates tightly to patient clinical variables and encode functions involved in toxin and secondary bile acids synthesis; the relative abundance of the microbial functions correlates with the serum or faecal concentrations of these metabolites. Microbiota from patients transplanted to renal injured germ-free mice or antibiotic-treated rats induce higher production of serum uraemic toxins and aggravated renal fibrosis and oxidative stress more than microbiota from controls. Two of the species, Aberrant gut microbiota in patients with ESRD sculpts a detrimental metabolome aggravating clinical outcomes, suggesting that the gut microbiota will be a promising target for diminishing uraemic toxicity in those patients. This study was registered at ClinicalTrials.gov (NCT03010696).

Complex interactions between the host and the gut microbiota govern intestinal homeostasis but remain poorly understood. Here we reveal a relationship between gut microbiota and caspase recruitment domain family member 9 (CARD9), a susceptibility gene for inflammatory bowel disease (IBD) that functions in the immune response against microorganisms. CARD9 promotes recovery from colitis by promoting interleukin (IL)-22 production, and Card9(-/-) mice are more susceptible to colitis. The microbiota is altered in Card9(-/-) mice, and transfer of the microbiota from Card9(-/-) to wild-type, germ-free recipients increases their susceptibility to colitis. The microbiota from Card9(-/-) mice fails to metabolize tryptophan into metabolites that act as aryl hydrocarbon receptor (AHR) ligands. Intestinal inflammation is attenuated after inoculation of mice with three Lactobacillus strains capable of metabolizing tryptophan or by treatment with an AHR agonist. Reduced production of AHR ligands is also observed in the microbiota from individuals with IBD, particularly in those with CARD9 risk alleles associated with IBD. Our findings reveal that host genes affect the composition and function of the gut microbiota, altering the production of microbial metabolites and intestinal inflammation.

The composition of the microbial community in the intestine may influence the functions of distant organs such as the brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to the hypothesis that microbes in the gut explain the co-occurrence of intestinal and skin diseases. Here, we show that the reverse can occur, and that skin directly alters the gut microbiome. Disruption of the dermis by skin wounding or the digestion of dermal hyaluronan results in increased expression in the colon of the host defense genes Reg3 and Muc2, and skin wounding changes the composition and behavior of intestinal bacteria. Enhanced expression Reg3 and Muc2 is induced in vitro by exposure to hyaluronan released by these skin interventions. The change in the colon microbiome after skin wounding is functionally important as these bacteria penetrate the intestinal epithelium and enhance colitis from dextran sodium sulfate (DSS) as seen by the ability to rescue skin associated DSS colitis with oral antibiotics, in germ-free mice, and fecal microbiome transplantation to unwounded mice from mice with skin wounds. These observations provide direct evidence of a skin-gut axis by demonstrating that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome.

Dimeric IgA secreted across mucous membranes in response to nonpathogenic taxa of the microbiota accounts for most antibody production in mammals. Diverse binding specificities can be detected within the polyclonal mucosal IgA antibody response

Balanced interactions between the enteric microbiota and enterohepatic organs are essential to bile acid homeostasis, and thus normal gastrointestinal function. Disruption of these interactions by cancer treatment instigates bile acid malabsorption, leading to treatment delays, malnutrition, and decreased quality of life. However, the nature of chemotherapy-induced bile acid malabsorption remains poorly characterized with limited treatment options. Therefore, this study sought to characterize changes in hepatic, enteric, and microbial bile acid metabolism in a mouse model of chemotherapy-induced toxicity. Consistent with clinical bile acid malabsorption, chemotherapy increased fecal excretion of primary bile acids and water, while diminishing microbiome diversity, secondary bile acid formation, and small intestinal bile acid signaling. We identified new contributors to pathology of bile acid malabsorption in the forms of lipopolysaccharide-induced cholestasis and colonic crypt hyperplasia from reduced secondary bile acid signaling. Chemotherapy reduced markers of hepatic bile flow and bile acid synthesis, elevated markers of fibrosis and endotoxemia, and altered transcription of genes at all stages of bile acid metabolism. Primary hepatocytes exposed to lipopolysaccharide (but not chemotherapy) replicated chemotherapy-induced transcriptional differences, while gut microbial transplant into germ-free mice replicated very few differences. In the colon, chemotherapy-altered bile acid profiles (particularly higher tauromuricholic acid and lower hyodeoxycholic acid) coincided with crypt hyperplasia. Exposing primary colonoids to hyodeoxycholic acid reduced proliferation, while gut microbiota transplant enhanced proliferation. Together, these investigations reveal complex involvement of the entire microbiota-enterohepatic axis in chemotherapy-induced bile acid malabsorption. Interventions to reduce hepatic lipopolysaccharide exposure and enhance microbial bile acid metabolism represent promising co-therapies to cancer treatment.

Interactions between gut microbiota and environmental chemicals critically influence toxicological outcomes, yet mechanistic insights remain limited. Here, we combine developmental toxicity with full-length 16S rRNA gene sequencing, transcriptomic, and metabolomic analyses in germ-free (GF) and conventionally colonized wild-type (WT) zebrafish embryos to elucidate the microbiota's role in modulating chemical toxicity. Using representative compounds from major classes of environmental contaminants, we show that microbial presence significantly alters toxicity profiles in a compound-specific manner. The perfluorinated contaminant PFOS (perfluorooctanesulfonic acid) induced the strongest microbiota-dependent effects, with a greater number of differentially expressed genes in WT embryos and pronounced changes in immune and stress-related pathways. The pesticide boscalid and bisphenol F elicited distinct microbiota-modulated transcriptional and metabolic responses. Gene network analysis identified baseline microbial regulation of immune and metabolic programs, while metabolomics showed PFOS-dependent changes in L-tryptophan and its microbe-associated metabolites, including inosine, indoxyl sulfate and indole acetaldehyde, exclusively in WT embryos. These findings establish a mechanistically grounded framework for microbiota-chemical interactions and highlight the importance of integrating microbiome context into environmental health assessments.

Although genetic background is known to contribute to colon carcinogenesis, the exact etiology of the disease remains elusive. The organ's extensive interaction with microbes necessitated research on the role of microbiota on development of colon cancer. In this review, we summarized the defense mechanism of colon from foreign organism, and germ-free animal models that have been employed to elucidate microbial effect. We also comprehensively discussed the metabolic property of microbiota such as butyrate production, facilitation of heme toxicity, bile acid transformation, and nitrate reduction that has been shown to contribute to the development of the tumor. Finally, up-to-date subjects such as the effect of age and gender on microbiota are briefly discussed.

Triclosan (TCS) is a widespread antimicrobial agent that is associated with many adverse health outcomes. Its gut toxicity has been attributed to the molecular modifications mediated by commensal microbes, but microbial transformations of TCS derivatives in the gut lumen are still largely unknown. Aromatic hydroxylation is the predominant oxidative metabolism of TCS that linked to its toxicological effects in host tissues. Here, we aimed to reveal the biological fates of hydroxyl-TCS (OH-TCS) in the colon, where intestinal microbes mainly reside. Unlike the profiles generated via host metabolism, OH-TCS species remain unconjugated in human stools from a cohort study. Through tracking molecular compositions in mouse intestinal tract, elevated abundance of free-form OH-TCS while reduced abundance of conjugated forms was observed in the colon digesta and mucosa. Using antibiotic-treated and germ-free mice, as well as in vitro approaches, we demonstrate that gut microbiota-encoded enzymes efficiently convert glucuronide/sulfate-conjugated OH-TCS, which are generated from host metabolism, back to their bioactive free-forms in colon tissues. Thus, host-gut microbiota metabolic interactions of TCS derivatives were proposed. These results shed light on the crucial roles of microbial metabolism in TCS toxicity, and highlight the importance of incorporating gut microbial transformations in health risk assessment of environmental chemicals.

Arsenobetaine (AB), a major organic arsenic (As) species in seafood, is regarded as safe by current regulatory assessments due to low toxicity and rapid unmodified urinary excretion. This notion has been challenged by reports of AB metabolism by intestinal bacteria in vitro and more recent evidence of in vivo AB metabolism in mice. However, these studies did not establish the causal role of intestinal bacteria in AB transformation in vivo. To address this, we employed gnotobiology and compared the biotransformation of As from naturally AB-rich rodent diet in mice that were either germ-free or colonized with gut microbiota of varying microbial diversity. Our results confirm the in vivo metabolism of AB in the intestine under chronic dietary exposure. The transformation of ingested As was dependent on the presence/absence and complexity of the gut microbiota. Notably, specific toxic As species were absent under germ-free condition. Furthermore, gut microbial colonization was linked to increased As accumulation in the intestinal lumen as well as systemically, along with delayed clearance from the body. These findings emphasize the mammalian gut microbiota as a critical factor in evaluating the safety of AB-accumulating seafoods.

The human gut microbiota produces dozens of small molecules that circulate in blood, accumulate to comparable levels as pharmaceutical drugs, and influence host physiology. Despite the importance of these metabolites to human health and disease, the origin of most microbially-produced molecules and their fate in the host remains largely unknown. Here, we uncover a host-microbe co-metabolic pathway for generation of hippuric acid, one of the most abundant organic acids in mammalian urine. Combining stable isotope tracing with bacterial and host genetics, we demonstrate reduction of phenylalanine to phenylpropionic acid by gut bacteria; the host re-oxidizes phenylpropionic acid involving medium-chain acyl-CoA dehydrogenase (MCAD). Generation of germ-free male and female MCAD

Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many different physiologic responses, including nervous system function. Recently, host-associated microbiota have been shown to influence neurodevelopment. Here, we hypothesized that microbiota may biotransform exogenous 17-βestradiol (E2) and modify E2 effects on swimming behavior. Colonized zebrafish were continuously exposed to non-teratogenic E2 concentrations from 1 to 10 days post-fertilization (dpf). Changes in microbial composition and predicted metagenomic function were evaluated. Locomotor activity was assessed in colonized and axenic (microbe-free) zebrafish exposed to E2 using a standard light/dark behavioral assay. Zebrafish tissue was collected for chemistry analyses. While E2 exposure did not alter microbial composition or putative function, colonized E2-exposed larvae showed reduced locomotor activity in the light, in contrast to axenic E2-exposed larvae, which exhibited normal behavior. Measured E2 concentrations were significantly higher in axenic relative to colonized zebrafish. Integrated peak area for putative sulfonated and glucuronidated E2 metabolites showed a similar trend. These data demonstrate that E2 locomotor effects in the light phase are dependent on the presence of microbiota and suggest that microbiota influence chemical E2 toxicokinetics. More broadly, this work supports the concept that microbial colonization status may influence chemical toxicity.

Gut microbiota are important factors in obesity and diabetes, yet little is known about their role in the toxicodynamics of environmental chemicals, including those recently found to be obesogenic and diabetogenic. We integrated evidence that independently links gut ecology and environmental chemicals to obesity and diabetes, providing a framework for suggesting how these environmental factors may interact with these diseases, and identified future research needs. We examined studies with germ-free or antibiotic-treated laboratory animals, and human studies that evaluated how dietary influences and microbial changes affected obesity and diabetes. Strengths and weaknesses of studies evaluating how environmental chemical exposures may affect obesity and diabetes were summarized, and research gaps on how gut ecology may affect the disposition of environmental chemicals were identified. Mounting evidence indicates that gut microbiota composition affects obesity and diabetes, as does exposure to environmental chemicals. The toxicology and pharmacology literature also suggests that interindividual variations in gut microbiota may affect chemical metabolism via direct activation of chemicals, depletion of metabolites needed for biotransformation, alteration of host biotransformation enzyme activities, changes in enterohepatic circulation, altered bioavailability of environmental chemicals and/or antioxidants from food, and alterations in gut motility and barrier function. Variations in gut microbiota are likely to affect human toxicodynamics and increase individual exposure to obesogenic and diabetogenic chemicals. Combating the global obesity and diabetes epidemics requires a multifaceted approach that should include greater emphasis on understanding and controlling the impact of interindividual gut microbe variability on the disposition of environmental chemicals in humans.

The gut microbiota is implicated in the metabolism of many medical drugs, with consequences for interpersonal variation in drug efficacy and toxicity. However, quantifying microbial contributions to drug metabolism is challenging, particularly in cases where host and microbiome perform the same metabolic transformation. We combined gut commensal genetics with gnotobiotics to measure brivudine drug metabolism across tissues in mice that vary in a single microbiome-encoded enzyme. Informed by these measurements, we built a pharmacokinetic model that quantitatively predicts microbiome contributions to systemic drug and metabolite exposure, as a function of bioavailability, host and microbial drug-metabolizing activity, drug and metabolite absorption, and intestinal transit kinetics. Clonazepam studies illustrate how this approach disentangles microbiome contributions to metabolism of drugs subject to multiple metabolic routes and transformations.