Gut Microbial Metabolism Research Articles

EGCG and catechin relative to green tea extract differentially modulate the gut microbial metabolome and liver metabolome to prevent obesity in mice fed a high-fat diet

Green tea extract (GTE) alleviates obesity, in part, by modulating gut microbial composition and metabolism. However, direct evidence regarding the catechin-specific bioactivities that are responsible for these benefits remain unclear. The present study therefore investigated dietary supplementation of GTE, epigallocatechin gallate (EGCG), or (+)-catechin (CAT) in male C57BL6/J mice that were fed a high-fat (HF) diet to establish the independent contributions of EGCG and CAT relative to GTE to restore microbial and host metabolism. We hypothesized that EGCG would regulate the gut microbial metabolome and host liver metabolome more similar to GTE than CAT to explain their previously observed differential effects on cardiometabolic health. To test this, we assessed metabolic and phenolic shifts in liver and fecal samples during dietary HF-induced obesity. Ten fecal metabolites and ten liver metabolites (VIP > 2) primarily contributed to the differences in the metabolome among different interventions. In fecal samples, nine metabolic pathways (e.g., tricarboxcylic acid cycle and tyrosine metabolism) were differentially altered between the GTE and CAT interventions, whereas three pathways differed between GTE and EGCG interventions, suggesting differential benefits of GTE and its distinctive bioactive components on gut microbial metabolism. Likewise, hepatic glycolysis / gluconeogenesis metabolic pathways were significantly altered between GTE and EGCG interventions, while only hepatic tyrosine metabolism was altered between CAT and GTE interventions. Thus, our findings support that purified catechins relative to GTE uniquely contribute to regulating host and microbial metabolic pathways such as central energy metabolism to protect against metabolic dysfunction leading to obesity.

Dissecting the relationship between plasma and tissue metabolome in a cohort of women with obesity: Analysis of subcutaneous and visceral adipose, muscle, and liver.

Untargeted metabolomics of blood samples has become widely applied to study metabolic alterations underpinning disease and to identify biomarkers. However, understanding the relevance of a blood metabolite marker can be challenging if it is unknown whether it reflects the concentration in relevant tissues. To explore this field, metabolomic and lipidomic profiles of plasma, four sites of adipose tissues (ATs) from peripheral or central depot, two sites of muscle tissue, and liver tissue from a group of nondiabetic women with obesity who were scheduled to undergo bariatric surgery (n=21) or other upper GI surgery (n=5), were measured by liquid chromatography coupled with mass spectrometry. Relationships between plasma and tissue profiles were examined using Pearson correlation analysis subject to Benjamini-Hochberg correction. Plasma metabolites and lipids showed the highest number of significantly positive correlations with their corresponding concentrations in liver tissue, including lipid species of ceramide, mono- and di-hexosylceramide, sphingomyelin, phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylethanolamine, dimethyl phosphatidylethanolamine, ether-linked PC, ether-linked PE, free fatty acid, cholesteryl ester, diacylglycerol and triacylglycerol, and polar metabolites linked to several metabolic functions and gut microbial metabolism. Plasma also showed significantly positive correlations with muscle for several phospholipid species and polar metabolites linked to metabolic functions and gut microbial metabolism, and with AT for several triacylglycerol species. In conclusion, plasma metabolomic and lipidomic profiles were reflective more of the liver profile than any of the muscle or AT sites examined in the present study. Our findings highlighted the importance of taking into consideration the metabolomic relationship of various tissues with plasma when postulating plasma metabolites marker to underlying mechanisms occurring in a specific tissue.

Intestinal Microecology of Mice Exposed to TiO2 Nanoparticles and Bisphenol A

Exposure to titanium dioxide nanoparticles (TiO2 NPs) and bisphenol A (BPA) is ubiquitous, especially through dietary and other environmental pathways. In the present study, adult C57BL/6J mice were exposed to TiO2 NPs (100 mg/kg), BPA (0, 5, and 50 mg/kg), or their binary mixtures for 13 weeks. The 16S rDNA amplification sequence analysis revealed that co-exposure to TiO2 NPs and BPA altered the intestinal microbiota; however, this alteration was mainly caused by TiO2 NPs. Faecal metabolomics analysis revealed that 28 metabolites and 3 metabolic pathways were altered in the co-exposed group. This study is the first to reveal the combined effects of TiO2 NPs and BPA on the mammalian gut microbial community and metabolism dynamics, which is of great value to human health. The coexistence of TiO2 NPs and BPA in the gut poses a potential health risk due to their interaction with the gut microbiota.

Gut microbiome/metabolome predicts response to immune checkpoint blockers (ICB) in patients with recurrent metastatic head and neck squamous cell cancer (RM HNSCC).

6055 Background: Gut microbiome has emerged as an important predictor of response to ICB therapy in various cancers, most notably in melanoma. Due to functional redundancy of microbiota, there has been lack of consistency in gut microbial signature associated with ICB response. Microbial metabolites in addition to taxonomy may play a superior role in predicting response to ICB. Gut microbiome/metabolome signatures of ICB response is unknown in RM HNSCC patients. Methods: Two cohorts of patients were included (stool and plasma samples were collected)- cohort 1, newly diagnosed RM HNSCC patients starting first line ICB, for whom samples were collected before ICB initiation (baseline) and post-treatment at 3, 6, and 12 months. Cohort 2 with durable response (disease control lasting ≥ 6 months), with single sample collected at study entry. 16s rRNA sequencing was performed on stool samples while plasma metabolites were quantitated using Q Exactive plus Orbitrap mass spectrometer. Response was defined as partial response (PR) or complete response (CR) as per RECIST 1.1 Results: The 16-S sequence was carried on 31 samples (cohort 1- 16 baseline, 7 post treatment; cohort 2- 8 durable responders). Targeted metabolomics was completed on 92 plasma samples [cohort 1-27 baseline and 50 post-treatment, cohort 2- 15]. Responders had a significantly higher Shannon’s diversity index, lower Fermicutes to Bacteroidetes ratio, and were enriched with genus Bacteroides and Lachnospiracea incerate sedis at baseline and post treatment, compared to non-responders (p < 0.05). At species level, baseline and post treatment microbiome of responders was enriched with Eubacterium oxidoreducens and Bacteroides uniformis. Ruminococcus was preferentially enriched in durable responders. Targeted analysis of plasma metabolites (associated with gut microbial metabolism) showed that responders had a significantly lower baseline adenosine, Inosine and xanthine level as compared to non responders. Further, Inosine levels decreased with response, while levels increased in non-responders (p < 0.05), suggestive of consumption by re-activated T cells Further, ICB responders had significantly lower Kynurenine to tryptophan ratio compared to non responders Conclusions: This is the first study evaluating association of gut microbiome and metabolome on response to first line ICB, in RM HNSCC patients. We found higher diversity and specific gut microbial signatures associated with ICB response. Interestingly, we found that inosine and kynurenine/tryptophan pathways, both which play a crucial role in host as well as gut microbial metabolism were differentially expressed in ICB responders. Our results if validated in larger cohort, lays groundwork for gut microbiome and importantly microbial metabolite modulation to improve response to ICB in RM HNSCC.

Prebiotics as a Tool for the Prevention and Treatment of Obesity and Diabetes: Classification and Ability to Modulate the Gut Microbiota.

Diabetes and obesity are metabolic diseases that have become alarming conditions in recent decades. Their rate of increase is becoming a growing concern worldwide. Recent studies have established that the composition and dysfunction of the gut microbiota are associated with the development of diabetes. For this reason, strategies such as the use of prebiotics to improve intestinal microbial structure and function have become popular. Consumption of prebiotics for modulating the gut microbiota results in the production of microbial metabolites such as short-chain fatty acids that play essential roles in reducing blood glucose levels, mitigating insulin resistance, reducing inflammation, and promoting the secretion of glucagon-like peptide 1 in the host, and this accounts for the observed remission of metabolic diseases. Prebiotics can be either naturally extracted from non-digestible carbohydrate materials or synthetically produced. In this review, we discussed current findings on how the gut microbiota and microbial metabolites may influence host metabolism to promote health. We provided evidence from various studies that show the ability of prebiotic consumption to alter gut microbial profile, improve gut microbial metabolism and functions, and improve host physiology to alleviate diabetes and obesity. We conclude among other things that the application of systems biology coupled with bioinformatics could be essential in ascertaining the exact mechanisms behind the prebiotic–gut microbe–host interactions required for diabetes and obesity improvement.

The Short-Day Cycle Induces Intestinal Epithelial Purine Metabolism Imbalance and Hepatic Disfunctions in Antibiotic-Mediated Gut Microbiota Perturbation Mice

Intestinal microbiota dysbiosis is related to many metabolic diseases in human health. Meanwhile, as an irregular environmental light–dark (LD) cycle, short day (SD) may induce host circadian rhythm disturbances and worsen the risks of gut dysbiosis. Herein, we investigated how LD cycles regulate intestinal metabolism upon the destruction of gut microbes with antibiotic treatments. The growth indices, serum parameters, concentrations of short-chain fatty acids (SCFAs), and relative abundance of intestinal microbes were measured after euthanasia; intestinal contents, epithelial metabolomics, and hepatic transcriptome sequencing were also assessed. Compared with a normal LD cycle (NLD), SD increased the body weight, spleen weight, and serum concentration of aspartate aminotransferase, while it decreased high-density lipoprotein. Meanwhile, SD increased the relative abundance of the Bacteroidetes phylum while it decreased the Firmicutes phylum in the gut of ABX mice, thus leading to a disorder of SCFA metabolism. Metabolomics data revealed that SD exposure altered gut microbial metabolism in ABX mice, which also displayed more serious alterations in the gut epithelium. In addition, most differentially expressed metabolites were decreased, especially the purine metabolism pathway in epithelial tissue. This response was mainly due to the down-regulation of adenine, inosine, deoxyguanosine, adenylsuccinic acid, hypoxanthine, GDP, IMP, GMP, and AMP. Finally, the transcriptome data also indicated that SD has some negative effects on hepatic metabolism and endocrine, digestive, and disease processes. Overall, SD induced an epithelial and hepatic purine metabolism pathway imbalance in ABX mice, as well as the gut microbes and their metabolites, all of which could contribute to host metabolism and digestion, endocrine system disorders, and may even cause diseases in the host.

Ginsenoside Rg1 Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Microbial Tryptophan Metabolism.

Ulcerative colitis (UC) is a chronic and recurrent inflammatory disorder in the gastrointestinal tract. Here, we examined the pharmacological effects of ginsenoside Rg1, a natural compound with low bioavailability, on the acute experimental colitis mice induced by dextran sulfate sodium (DSS) and explored underlying mechanisms. Acute UC was induced in C57BL/6 mice by 2.5% DSS for 7 days, meanwhile, 2 mg/10 g b.w. ginsenoside Rg1 was administrated to treat the mice. Body weight, colon length, colon tissue pathology, and colon tissue inflammatory cytokines were assessed. The composition structure of gut microbiota was profiled using 16s rRNA sequencing. Global metabolomic profiling of the feces was performed, and tryptophan and its metabolites in the serum were detected. The results showed that Rg1 significantly ameliorated DSS-induced colonic injury and colonic inflammation. In addition, Rg1 also partly reversed the imbalance of gut microbiota composition caused by DSS. Rg1 intervention can regulate various metabolic pathways of gut microbiota such as valine, leucine, and isoleucine biosynthesis and vitamin B6 metabolism and the most prominent metabolic alteration was tryptophan metabolism. DSS decreased the levels of tryptophan metabolites in the serum, including indole-3-carboxaldehyde, indole-3-lactic acid, 3-indolepropionic acid, and niacinamide and Rg1 can increase the levels of these metabolites. In conclusion, the study discovered that Rg1 can protect the intestinal barrier and alleviate colon inflammation in UC mice, and the underlying mechanism is closely related to the regulation of gut microbiota composition and microbial tryptophan metabolism.

LC‐MS based urine metabolomic profiling indicate altered gut microbiome and host lipid metabolites in Parkinson’s disease

Evidence indicates that host and gut microbial metabolism are dysregulated prior to the onset of motor symptoms, in the prodromal phase of Parkinson’s disease (PD). There is currently no definitive test for the diagnosis of Parkinson’s disease; this represents an urgent, unmet medical need to enable the effectiveness of current and future therapeutic interventions for PD. The aim of this study was to understand changes in host and microbial metabolism in PD patient biofluids which could reflect a transition from the healthy to diseased state. We performed a comprehensive untargeted metabolomics analysis of urinary lipid metabolites together with altered metabolites associated with the gut microbiota. A total of 64 urine samples consisting of 31 from age matched healthy controls and 33 from PD patients were used in this study. Samples were deproteinized and analysed by reverse phase (RP)/UPLC‐MS/MS methods with positive and negative ion mode electrospray ionization (ESI) and HILIC/UPLC‐MS/MS with negative ion mode ESI. 14 lipid metabolites were significantly altered in PD patients. Five metabolites were associated with bile acid metabolism and nine were from the cholesterol pathway. Changes in secondary bile acid metabolism, particularly secondary bile acids indicative of microbial metabolism changes, were evident in PD patients, with 11 altered metabolites associated with the gut microbiota being significantly altered. Interestingly, several lipid metabolites that were altered in PD patients correlated with specific gut microbiome metabolites. Our results provide new insights into altered lipid metabolism and gut dysbiosis in PD, however, confirmation in a larger cohort would be needed.

P380. Genetic Deficiency in Serotonin Transporter in Mice Alters Effects of Western Diet on Gut Microbiota

Serotonin transporter expression, besides implicated in serotonergic neurotransmission, is also involved in regulation of metabolic health. Animal work has shown gene x environment interactions, where serotonin transporter deficiency aggravated the effects of Western diet (a diet high in calories, saturated fat, sugar and cholesterol) on metabolic health and hippocampal-dependent behaviour. This transporter-dependent increased metabolic sensitivity to Western diet may be driven by the gut microbiota, as its expression affects gut microbial composition and metabolism of serotonin, lipids and steroids. Hence, variation in the gut microbiota due to differential serotonin transporter expression may result in differential susceptibility to the effects of Western diet on the gut microbiota and metabolic syndrome.

Metabolic Basis of Cognitive Improvement Associated With Active B Vitamin Supplementation in Cognitively Impaired Elderly Subjects – A Metabolomics Study

Intervention studies with active B vitamin supplementation in cognitively impaired individuals have yielded varying results in randomized controlled trials. In addition, a negative interaction of active B vitamin supplementation with aspirin usage on cognitive outcome was noted, but the molecular basis of the interaction has largely remained unknown. To investigate the metabolic basis of cognitive improvement brought about by active B vitamin supplementation, we conducted an extensive metabolomics analysis covering 302 identified metabolites on the baseline and 24-month serum samples from a cohort of 137 subjects randomly assigned to active supplementation or placebo. Pathway analysis uncovered enhanced gluconeogenesis and War-burg effects underlying cognitive improvement in non-aspirin users supplemented with active B vitamins. In addition, metabolomics revealed that aspirin usage may interact with B vitamin supplementation by altering gut microbial metabolism, particularly in terms of propionate production. Lastly, our omics data suggest that varying capacities to assimilate B vitamins at baseline, possibly mediated by differences in gut microbial composition, may underlie variations in inter-individual responses to active B vitamin supplementation.

Pharmacokinetic, Metabolism, and Metabolomic Strategies Provide Deep Insight Into the Underlying Mechanism of Ginkgo biloba Flavonoids in the Treatment of Cardiovascular Disease.

Ginkgo biloba, known as the “living fossil,” has a long history of being used as botanical drug for treating cardiovascular diseases and the content of flavonoids as high as 24%. More than 110 different kinds of flavonoids and their derivatives have been separated from G. biloba, including flavones, flavonols, biflavonoids, catechins, and their glycosides, etc., all of which display the ability to dilate blood vessels, regulate blood lipids, and antagonize platelet activating factor, and protect against ischemic damage. At present, many types of preparations based on G. biloba extract or the bioactive flavonoids of it have been developed, which are mostly used for the treatment of cardiovascular diseases. We herein review recent progress in understanding the metabolic regulatory processes and gene regulation of cellular metabolism in cardiovascular diseases of G. biloba flavonoids. First, we present the cardioprotective flavonoids of G. biloba and their possible pharmacological mechanism. Then, it is the pharmacokinetic and liver and gut microbial metabolism pathways that enable the flavonoids to reach the target organ to exert effect that is analyzed. In the end, we review the possible endogenous pathways toward restoring lipid metabolism and energy metabolism as well as detail novel metabolomic methods for probing the cardioprotective effect of flavonoids of G. biloba.

Intestinal microbiota-mediated biotransformations alter the pharmacokinetics of the major metabolites of azathioprine in rats after oral administration

Adverse reactions to azathioprine (AZA) vary greatly among individuals, which is associated with the variable levels of its major metabolites 6-thioguanine nucleotides (6-TGN) and 6-methylmercaptopurine (6-MMP). The intestinal microbiota has been proven to contain AZA-metabolizing enzymes, although the explicit role of the intestinal microbiota in AZA metabolism in vivo remains poorly comprehended. In this study, the pharmacokinetic behaviours of 6-TGN and 6-MMP were assessed in the pseudo germ-free (PGF) group and control group following oral administration of AZA. The AUC0-t and Cmax of 6-TGN in the PGF group were significantly decreased by 34.0% and 35.0% (P < 0.05) compared with those in the control group. Additionally, the AUC0-t and Cmax of 6-MMP were reduced by 27.9% and 34.2% in the PGF group, although the differences were not significant. The TPMT and NUDT15 genotypes of rats in the two groups were genetically identical. The expression levels of key AZA-metabolizing enzymes in liver were not different between two groups. Furthermore, the major metabolites of AZA in the incubation system with intestinal microbial enzymes were identified. In summary, shifts in the composition of the intestinal microbiota may regulate the exposure of 6-TGN in vivo by altering the gut microbial metabolism of AZA.

Effects of an SGLT Inhibitor on the Production, Toxicity, and Elimination of Gut-Derived Uremic Toxins: A Call for Additional Evidence.

Sodium–glucose cotransporter (SGLT) inhibitors are a class of oral hypoglycemic agents, which, in recent years, have been shown to improve renal and cardiovascular outcomes in patients with diabetic and non-diabetic chronic kidney disease. There remains considerable debate regarding the potential glucose-independent mechanisms by which these benefits are conferred. SGLT inhibitors, to a variable extent, impair small intestinal glucose absorption, facilitating the delivery of glucose into the colon. This suppresses protein fermentation, and thus the generation of uremic toxins such as phenols and indoles. It is acknowledged that such a shift in gut microbial metabolism yields health benefits for the host. SGLT inhibition, in addition, may be hypothesized to foster the renal clearance of protein-bound uremic toxins. Altered generation and elimination of uremic toxins may be in the causal pathway between SGLT inhibition and improved cardiometabolic health. Present review calls for additional research.

Recruitment and Retention of Healthy, Postmenopausal Women of African and European Ancestry: Results from a Dietary Intervention with Repeated Biospecimen Collections

ABSTRACTRecruitment of minority participants to clinical trials, especially studies without therapeutic intent, has been historically challenging. This study describes barriers to and successes of recruitment and retention strategies to dietary studies. A flaxseed study was conducted in healthy, postmenopausal women of African ancestry (AA) and European ancestry (EA) to assess associations between gut microbial community composition and host metabolism (NCT01698294). To ensure equitable participation by AA and EA women, multiple forms of recruitment were utilized, including advertisements, posters, e-mail, word of mouth, and community outreach. Successful recruitment and retention of AA women to the intervention depended upon the specific methods used. AA women compared with EA women were more likely to respond to direct recruitment and community-based methods, rather than general advertisements. However, once women expressed interest, similar rates of consent were observed for AA and EA women (AA and EA: 51.6% vs. 55.7%, respectively; P > 0.05), supporting the willingness of minority populations to participate in clinical research. Retention, however, was lower among AA compared with EA women (AA and EA: 57.6% vs. 80.9%, respectively; P < 0.01), which may be related to multiple factors, including health reasons, intolerance to flaxseed, noncompliance with study requirements, time constraints, and nonspecified personal reasons. This study confirms the utility of direct community-based strategies for recruitment of diverse populations into nontherapeutic dietary intervention studies. The methods used successfully identified eligible women who expressed willingness to consent to the trial and were able to achieve >70% of recruitment goals for AA women. Future efforts are warranted to improve retention to complex studies. This trial was registered at www.clinicaltrials.gov as NCT01698294.

Dietary licorice enhances in vivo cadmium detoxification and modulates gut microbial metabolism in mice.

Mass cadmium (Cd) poisoning is a serious health problem in many parts of the world. We propose that dietary intervention can be a practical solution to this problem. This study aimed to identify effective dietary products from traditional Chinese herbs that can detoxify Cd. Five candidate herbal foods with detoxifying potential were selected and subjected to mouse toxicological tests. The chemical composition and dose-response effects of licorice on mouse hepatocytes were determined. Licorice was selected for further tests to examine its effects on growth, tissue Cd accumulation, and gut and liver fitness of mice. The expression of hepatic metallothionein (Mt) genes was quantified in vitro in hepatocytes and in vivo in liver tissues of mice. The results showed that licorice dietary intervention was effective in reducing blood Cd by >50% within 1 month. Cd was also substantially reduced in the heart and lung tissues, but increased 2.1-fold in the liver. The liver of Cd poisoned mice improved with licorice intervention. Licorice treatment significantly induced Cd accumulation and expression of the Mt1 gene in hepatic cells both in vitro and in vivo. Licorice intake substantially altered gut microbial structure and enriched Parabacteroides distasonis. Omics results showed that licorice improved gut metabolism, particularly the metabolic pathways for glycyrrhizin, bile acids, and amino acids. Dietary licorice effectively reduced mouse blood Cd and had a profound impact on liver and gut fitness. We conclude that herbal licorice can be used as a dietary intervention for mass Cd poisoning.

Akkermansia muciniphila Ameliorates Acetaminophen-Induced Liver Injury by Regulating Gut Microbial Composition and Metabolism.

ABSTRACTThe gut microbiota drives individual sensitivity to excess acetaminophen (APAP)-mediated hepatotoxicity. It has been reported that the bacterium Akkermansia muciniphila protects hosts against liver disease via the liver-gut axis, but its therapeutic potential for drug-induced liver injury remains unclear. In this study, we aimed to investigate the effect of A. muciniphila on APAP-induced liver injury and the underlying mechanism. Administration of A. muciniphila efficiently alleviated APAP-induced hepatotoxicity and reduced the levels of serum alanine aminotransferase (ALT) and aspartate transaminase (AST). A. muciniphila significantly attenuated APAP-induced oxidative stress and the inflammatory response, as evidenced by restoration of the reduced glutathione/oxidized glutathione (GSH/GSSG) balance, enhanced superoxide dismutase (SOD) activity, reduced proinflammatory cytokine production, and alleviation of macrophage and neutrophil infiltration. Moreover, A. muciniphila maintained gut barrier function, reshaped the perturbed microbial community and promoted short-chain fatty acid (SCFA) secretion. The beneficial effects of A. muciniphila were accompanied by alterations in hepatic gene expression at the transcriptional level and activation of the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway. Our results suggested that A. muciniphila could be a potential pretreatment for APAP-induced liver injury.IMPORTANCE Our work revealed that A. muciniphila attenuated APAP-induced liver injury by alleviating oxidative stress and inflammation in the liver, and its hepatoprotective effect was accompanied by activation of the PI3K/Akt pathway and mediated by regulation of the composition and metabolic function of the intestinal microbiota. This finding suggested that the microbial community is a non-negligible impact on drug metabolism and probiotic administration could be a potential therapy for drug-induced liver injury.

Dynamic Alterations of the Gut Microbial Pyrimidine and Purine Metabolism in the Development of Liver Cirrhosis.

Background: Liver cirrhosis is the common end-stage of liver disease which lacks effective treatment, thus studies to determine prevention targets are an urgent need. The intestinal microbiota (IM) play important roles in modulating liver diseases which are mediated by microbial metabolites. Despite decades of growing microbial studies, whether IM contribute to the development of cirrhosis and the intimate metabolic link remain obscure. Here, we aimed to reveal the dynamic alterations of microbial composition and metabolic signatures in carbon tetrachloride (CCl4)-induced liver cirrhosis mice. Methods: CCl4-treated mice or normal control (NC) were sacrificed (n = 10 per group) after 5 and 15 weeks of intervention. The disease severity was confirmed by Masson’s trichrome or Sirius red staining. Metagenomics sequencing and fecal untargeted metabolomics were performed to evaluate the composition and metabolic function of IM in parallel with the development of cirrhosis. Results: The CCl4-treated mice presented liver fibrosis at 5 weeks and liver cirrhosis at 15 weeks indicated by collagen deposition and pseudo-lobule formation, respectively. Mice with liver cirrhosis showed distinct microbial composition from NC, even in the earlier fibrosis stage. Importantly, both of the liver fibrosis and cirrhosis mice were characterized with the depletion of Deltaproteobacteria (p < 0.05) and enrichment of Akkermansia (p < 0.05). Furthermore, fecal metabolomics revealed distinguished metabolomics profiles of mice with liver fibrosis and cirrhosis from the NC. Notably, pathway enrichment analysis pointed to remarkable disturbance of purine (p < 0.001 at 5 weeks, p = 0.034 at 15 weeks) and pyrimidine metabolic pathways (p = 0.005 at 5 weeks, p = 0.006 at 15 weeks) during the development of liver cirrhosis. Interestingly, the disorders of pyrimidine and purine metabolites like the known microbial metabolites thymidine and 2′-deoxyuridine had already occurred in liver fibrosis and continued in cirrhosis. Conclusion: These novel findings indicated the crucial role of IM-modulated pyrimidine and purine metabolites in the development of liver cirrhosis, which provides microbial targets for disease prevention.

Gut microbial trimethylamine is elevated in alcohol-associated hepatitis and contributes to ethanol-induced liver injury in mice.

There is mounting evidence that microbes residing in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcohol-associated hepatitis (AH). However, mechanisms by which gut microbes synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. We used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, finding elevated levels of the microbial metabolite trimethylamine (TMA) in AH. In subsequent studies, we treated mice with non-lethal bacterial choline TMA lyase (CutC/D) inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. We show the gut microbial choline metabolite TMA is elevated in AH patients and correlates with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial CutC/D activity protects mice from ethanol-induced liver injury. CutC/D inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome and host liver transcriptome. The microbial metabolite TMA is elevated in patients with AH, and inhibition of TMA production from gut microbes can protect mice from ethanol-induced liver injury.

Interplays between drugs and the gut microbiome.

The gut microbiota is considered a key ‘metabolic organ’. Its metabolic activities play essential roles complementary to the host metabolic functions. The interplays between gut microbes and commonly used non-antibiotic drugs have garnered substantial attention over the years. Drugs can reshape the gut microorganism communities and, vice versa, the diverse gut microbes can affect drug efficacy by altering the bioavailability and bioactivity of drugs. The metabolism of drugs by gut microbial action or by microbiota–host cometabolism can transform the drugs into various metabolites. Secondary metabolites produced from the gut microbial metabolism of drugs contribute to both the therapeutic benefits and the side effects. In view of the significant effect of the gut microbiota on drug efficiency and clinical outcomes, it is pivotal to explore the interactions between drugs and gut microbiota underlying medical treatments. In this review, we describe and summarize the complex bidirectional interplays between gut microbes and drugs. We also illustrate the gut-microbiota profile altered by non-antibiotic drugs, the impacts and consequences of microbial alteration, and the biochemical mechanism of microbes impacting drug effectiveness. Understanding how the gut microbes interact with drugs and influence the therapeutic efficacy will help in discovering diverse novel avenues of regulating the gut microbes to improve the therapeutic effects and clinical outcomes of a drug in precision.

Metabolic modeling of host\u2013microbe interactions for therapeutics in colorectal cancer

The onset of colorectal cancer (CRC) is often attributed to gut bacterial dysbiosis, and thus gut microbiota are highly relevant in devising treatment strategies. Certain gut microbes, like Enterococcus spp., exhibit remarkable anti-neoplastic and probiotic properties, which can aid in silver nanoparticle (AgNPs) induced reactive oxygen species (ROS)-based CRC treatment. However, the effects of AgNPs on gut microbial metabolism have not been reported thus far. In this study, a detailed systems-level understanding of ROS metabolism in Enterococcus durans (E. durans), a representative gut microbe, was gained using constraint-based modeling, wherein, the critical association between ROS and folate metabolism was established. Experimental studies involving low AgNP concentration treatment of E. durans cultures confirmed these modeling predictions (an increased extracellular folate concentration by 52%, at the 9th h of microbial growth, was observed). Besides, the computational studies established various metabolic pathways involving amino acids, energy metabolites, nucleotides, and SCFAs as the key players in elevating folate levels on ROS exposure. The anti-cancer potential of E. durans was also studied through MTT analysis of HCT 116 cells treated with microbial culture (AgNP treated) supernatant. A decrease in cell viability by 19% implicated the role of microbial metabolites (primarily folate) in causing cell death. The genome-scale modeling approach was then extended to extensively model CRC metabolism, as well as CRC–E. durans interactions in the context of CRC treatment, using tissue-specific metabolic models of CRC and healthy colon. These findings on further validation can facilitate the development of robust and effective cancer therapy.