Secondary Bile Acid Biosynthesis Research Articles

A Membrane-free Liver-Gut-on-Chip Platform for the Assessment on Dysregulated Mechanisms of Cholesterol and Bile Acid Metabolism Induced by PM2.5.

Fine particulate matter (PM2.5)-induced metabolic diseases have attracted a great deal of attention recently. However, the relevant metabolic mechanisms of PM2.5 in vivo have not yet been fully described due to the lack of reliable platforms. Herein, a membrane-free liver-gut-on-chip (L-GOC) platform was developed to investigate metabolism dysregulation induced by PM2.5. A multiple organ system with a liver-gut structure and two circulation paths (L-G and G-L circulation paths) was created, and then cells were exposed to PM2.5 on this platform. Secreted high-density lipoprotein (HDL) levels were detected, which demonstrates that this multiple organ system functioned with normal physiological metabolism at the organ level. Untargeted metabolomic analysis showed that there were 364 metabolites of LO2 cells dysregulated after exposure to PM2.5 at a concentration of 200 μg/mL. Moreover, cholesterol and bile acid metabolism were significantly dysregulated. Further immunofluorescence and ELISA assays confirmed that signal transduction pathways related to cholesterol metabolism (LCAT-CE, PON1-HDL, and SRB1-HDL metabolic pathways) and bile acid metabolism (CYP7A1-CA/CDCA/DCA metabolic pathways) were disturbed. These results indicate that PM2.5 primarily disturbed cholesterol metabolism of the liver and then disrupted bile acid metabolism of the liver (primary bile acid biosynthesis) and gut (secondary bile acid biosynthesis) via related metabolic pathways. These findings may partially explain the metabolic mechanisms of cells triggered by PM2.5 exposure.

Gut microbiome alterations and its link to corticosteroid resistance in immune thrombocytopenia

Quantitative metagenomic studies have linked the gut microbiota to autoimmune disorders. Here, we performed deep shotgun metagenomic sequencing of fecal samples from 99 immune thrombocytopenia (ITP) patients and 52 healthy controls. Dysbiosis in the gut microbiome of ITP was detected phylogenetically and functionally, and classifier based on species markers distinguished individuals with ITP from healthy controls. In particular, the abundance of Ruminococcus gnavus, Bifidobacterium longum and Akkermansia muciniphila was markedly increased in treatment-naïve ITP patients, and the alterations of microbial species were correlated with clinical indices. Functionally, the secondary bile acid biosynthesis and flagellar assembly were depleted in the gut microbiota of ITP, which may contribute to the onset of ITP by affecting the immune system. Furthermore, we found that corticosteroid treatment affected the gut microbiome of ITP. Compared with corticosteroid-sensitive ITP patients, we identified that the corticosteroid-resistant ITP patients displayed a distinct gut microbiome, which was different from that of the treatment-naïve ITP patients. Together, we provided support for the critical role of gut microbiota in the development of ITP and established a foundation for further research characterizing gut microbiota in relation to corticosteroid resistance of ITP.

Alterations of gut microbiota and serum bile acids are associated with parenteral nutrition-associated liver disease

BackgroundParenteral nutrition-associated liver disease (PNALD) is a major complication of long-term parenteral nutrition (PN). The pathogenesis of PNALD remains unclear. We investigated the changes in taxonomic and functional composition of gut microbiota and serum bile acid levels in a rat model of PNALD. MethodsMale 4-week-old Sprague Dawley rats received either total parenteral nutrition or standard chow with 0.9% saline for 7 days. The taxonomic composition of cecal microbiota and its functional composition associated with bile acid metabolism were measured. ResultsThere were differences in taxonomic composition between the two groups. The abundance of the secondary bile acid biosynthesis pathway was higher in the TPN group (p < 0.05) with an increase in the percentage of bacteria expressing 7-alpha-hydroxysteroid dehydrogenase (p < 0.05). The abundance of enzymes associated with bile salt hydrolase was also higher (p < 0.05) in the TPN group. The TPN group showed a distinct bile acid profile characterized by a higher ratio of secondary bile acids to primary bile acids. ConclusionsThe alteration of bile acid-associated microbiota may lead to increased secondary bile acid production in a rat model of PNALD.

The Gut Microbiome Modifies the Protective Effects of a Mediterranean Diet Against Cardiometabolic Disease Risk

Abstract Objectives We aim to test whether the effects of different diets on an individual's cardiometabolic disease risk could be modified by the personalized nature of the gut microbiome. Methods We analyzed 925 shotgun metagenomes and 340 metatranscriptomes, dietary information longitudinally collected by food frequency questionnaires during nearly three decades, and biomarkers of glucose homeostasis, lipid metabolism, and inflammation measured on blood samples in a cohort of 307 men. A Mediterranean diet (MedDiet) index was applied to quantify each participant's adherence to a Mediterranean dietary pattern. To evaluate each participant's cardiometabolic disease risk, we derived a composite score that summarized levels of biomarkers. Results We demonstrate that the MedDiet was associated with the abundances of phylogenetically diverse gut microbes, including both prevalent broadly anaerobic fermenters and more niche- and subject-specific biochemical specialists. A higher adherence to the MedDiet was positively associated with the abundances of major dietary fiber metabolizers, such as Faecalibacterium prausnitzii, Eubacterium eligens, and Bacteroides cellulosilyticus, but inversely associated with abundances of Ruminococcus torques, Clostridium leptum and Collinsella aerofaciens. The gut microbiomes of participants with greater MedDiet adherence were enriched for bacterial metabolism including plant-derived polysaccharide degradation, short-chain fatty acid production, and secondary bile acid biosynthesis. Furthermore, the MedDiet index was positively associated with the transcription of several microbial enzymes involved in the degradation of pectin. Notably, our study, for the first time, identified a significant interaction between a healthy dietary pattern and the gut microbiome in relation to the cardiometabolic disease risk (P-value for interaction = 0.02). We found that better adherence to a MedDiet was specifically associated with lower cardiometabolic disease risk among participants with greater abundance of Prevotella copri. Conclusions Our findings have the potential to inform more effective and precise dietary approaches for the prevention of diabetes and cardiovascular disease. Funding Sources National Institutes of Health and STARR Cancer Consortium.

Compositional and Functional Changes in the Gut Microbiota in Irritable Bowel Syndrome Patients.

Background/AimsThis study aimed to characterize the changes in the gut microbiota of irritable bowel syndrome (IBS) patients and to investigate the consequent alterations in bacterial functions.MethodsWe performed 16S rRNA metagenomic sequencing and a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analyses using fecal samples from control (n=12) and diarrhea-dominant IBS patients (n=7).ResultsThe samples were clustered by the principal coordinates analysis depending on the presence of IBS (p=0.003). In the IBS patients, the abundances of Acidaminococcaceae, Sutterellaceae, and Desulfovibrionaceae were significantly increased, while those of Enterococcaceae, Leuconostocaceae, Clostridiaceae, Peptostreptococcaceae, and Lachnospiraceae were significantly decreased. The PICRUSt results indicated that two orthologues involved in secondary bile acid biosynthesis were significantly decreased in IBS patients. Modules involved in multidrug resistance, lipopolysaccharide biosynthesis, the reductive citrate cycle, and the citrate cycle were significantly increased in the IBS patients. In contrast, modules involved in cationic antimicrobial peptide resistance, and some transport systems were more abundant in controls than in IBS patients.ConclusionsChanges in the gut microbiota composition in IBS patients lead to alterations in bacterial functions, such as bile acid transformation and the induction of inflammation, which is a known pathophysiological mechanism of IBS.

Danggui Buxue Tang restores antibiotic-induced metabolic disorders by remodeling the gut microbiota

Ethnopharmacological relevanceDanggui Buxue Tang (DBT) has been used to promote hematopoiesis and relieve myelosuppression in China. Antibiotics can cause myelosuppression through gut microbiota disorders.Aim of the study: This study aims to explore the way of DBT to alleviate the metabolic disorder caused by antibiotics. Materials and methodsIn this study, 16S rRNA sequencing was used to detect the change of gut microbiota, metabolomics to analyze the change of metabolites. Correlation analysis was used to establishment the correlation between gut microbiota and metabolites. PICRUST 2 was used to predict the function of gut microbiota. ResultsResults showed that eighty-two genera of gut microbiota were affected by antibiotic, while twelve were significantly restored after DBT. Seventy-four potential metabolites were significantly different from the antibiotics and DBT. We found significant recovery by the Bacteroides and Rikenellaceae RC9 after DBT. The metabolic pathways influenced by the antibiotic treatment included primary and secondary bile biosynthesis, etc. The metabolic pathways that could be restored after DBT included the primary and secondary bile acid biosynthesis pathway, etc. Through correlation analysis, we found a correlation between the Bacteroides, Rikenellaceae_RC9_gut_group and other potential differential metabolisms such as those of taurodeoxycholic acid, N-phenylacetyl glycine, etc. The functional prediction showed that the biosynthesis of primary bile acid, secondary bile acid was significantly affected. ConclusionsDBT can restore the gut and reverse the metabolic disorder caused by antibiotics through Bacteroides, and it provides a new medical idea regarding the gut microbiota balance.

Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease.

Chronic kidney disease (CKD) is a serious healthcare dilemma, associated with specific changes in gut microbiota and circulating metabolome. Yet, the functional capacity of CKD microbiome and its intricate relationship with the host metabolism at different stages of disease are less understood. Methods: Here, shotgun sequencing of fecal samples and targeted metabolomics profiling of serum bile acids, short- and medium-chain fatty acids, and uremic solutes were performed in a cohort of CKD patients with different severities and non-CKD controls. Results: We identified that levels of 13 microbial species and 6 circulating metabolites were significantly altered across early to advanced stages or only in particular stage(s). Among these, Prevotella sp. 885 (decreased) was associated with urea excretion, while caproic acid (decreased) and p-cresyl sulfate (elevated) were positively and negatively correlated with the glomerular filtration rate, respectively. In addition, we identified gut microbial species linked to changes in circulating metabolites. Microbial genes related to secondary bile acid biosynthesis were differentially abundant at the early stage, while pathway modules related to lipid metabolism and lipopolysaccharide biosynthesis were enriched in the CKD microbiome at the advanced stage, suggesting that changes in microbial metabolism and host inflammation may contribute to renal health. Further, we identified metagenomic and metabolomic markers to discriminate cases of different severities from the controls, among which Bacteroides eggerthii individually was of particular value in early diagnosis. Conclusions: Our dual-omics data reveal the connections between intestinal microbes and circulating metabolites perturbed in CKD, which may be of etiological and diagnostic importance.

Gut Microbiota and Risk of Persistent Nonalcoholic Fatty Liver Diseases.

Gut dysbiosis is regarded as a pathogenetic factor of nonalcoholic fatty liver disease (NAFLD), but its role in NAFLD persistence is unknown. We investigated the influence of the gut microbiota on persistent NAFLD. This cohort study included 766 subjects with 16S ribosomal RNA (rRNA) gene sequencing data from fecal samples at baseline who underwent repeated health check-up examinations. Fatty liver was determined using ultrasound at baseline and follow-up. Participants were categorized into four groups: none (control), developed, regressed, or persistent NAFLD. The persistent NAFLD group had lower richness compared with the control group. Significant differences were also found in both non-phylogenic and phylogenic beta diversity measures according to NAFLD persistence. Pairwise comparisons indicated that taxa abundance mainly differed between the control and persistent NAFLD groups. A relative high abundance of Fusobacteria and low abundance of genera Oscillospira and Ruminococcus of the family Ruminococcaceae and genus Coprococcus of the family Lachnospiraceae were found in the persistent NAFLD group. Based on the functional predictions, pathways related to primary and secondary bile acid biosynthesis were highly detected in the persistent NAFLD group compared with the control group. These findings support that the composition of the gut microbiome associated with dysregulation of bile acid biosynthetic pathways may contribute to the persistence of NAFLD. This is the first cohort study to demonstrate the influence of microbiota on persistent NAFLD. Our findings may help identify potential targets for therapeutic intervention in NAFLD.

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity.

The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.

Fecal Metabolomics of Type 2 Diabetic Rats and Treatment with Gardenia jasminoides Ellis Based on Mass Spectrometry Technique

Modern studies have indicated Gardenia jasminoides Ellis (G. jasminoides) showed positive effect in treating type 2 diabetes mellitus (T2DM). In this study, 60 streptozotocin-induced T2DM rats were divided into four groups: type 2 diabetes control group, geniposide-treated group, total iridoid glycosides-treated group, and crude extraction of gardenlae fructus-treated group. The other ten healthy rats were the healthy control group. During 12 weeks of treatment, rat's feces samples were collected for the metabolomics study based on mass spectrometry technique. On the basis of the fecal metabolomics method, 19 potential biomarkers were screened and their relative intensities in each group were compared. The results revealed G. jasminoides mainly regulated dysfunctions in phenylalanine metabolism, tryptophan metabolism, and secondary bile acid biosynthesis pathways induced by diabetes. The current study provides new insight for metabonomics methodology toward T2DM, and the results show that feces can preferably reflect the liver and intestines disorders.

In vivo therapeutic effect of combination treatment with metformin and Scutellaria baicalensis on maintaining bile acid homeostasis.

The radix of Scutellaria baicalensis (SB) is a herb widely used in traditional Chinese medicine to treat metabolic diseases. Several main components, including baicalin and wogonoside, possess anti-dyslipidemia, anti-obesity and anti-diabetic effects. We hypothesized that co-administration of SB extract and metformin exerts a better effect on obesity-induced insulin resistance and lipid metabolism than treatment with metformin alone. We compared the effect of metformin (100 mg/10 mL/kg/day) alone with co-administration of metformin (100 mg/5 mL/kg/day) and SB extract (200 mg/5 mL/kg/day) on Otsuka Long Evans Tokushima Fatty rats, a useful model of type II diabetes with obesity, and used Long-Evans Tokushima Otsuka rats as a control. Weight, fasting glucose, oral glucose tolerance test, intraperitoneal insulin tolerance test, and serum total cholesterol were measured after 12 weeks of drug administration. We observed a synergetic effect of metformin and SB on lowering cholesterol level by excretion of bile acid through feces. We found that this accompanied activation of FXR, CYP7A1 and LDLR genes and repression of HMGCR in the liver. Although there were no significant changes in BSH-active gut microbiota due to high variability, functional prediction with 16S sequences showed increased primary and secondary bile acid biosynthesis in the combination treatment group. Further study is needed to find the specific strains of bacteria which contribute to FXR-related cholesterol and bile acid regulations.

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet

In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.

Clostridium difficile Infection.

Clostridium difficile Infection.

Urinary metabolic profiling identifies a key role for glycocholic acid in human liver cancer by ultra-performance liquid-chromatography coupled with high-definition mass spectrometry

BackgroundMetabolomics has been proposed to be a hallmark of cancer, yet a systematic characterization of a metabolite and metabolic pathways in human hepatocarcinoma (HCC) remains a challenge. MethodsUsing ultra-performance liquid-chromatography/quadrupole-time-of-flight coupled with high-definition mass spectrometry (UPLC–Q-TOF–HDMS) in conjunction with multivariate data analysis methods, we identified and measured the metabolite profile of glycocholic acid from urine samples obtained from patients with HCC diseases. Bioinformatic tools were used to construct the metabolite network that can identify a key role for glycocholic acid in HCC. ResultsBiochemical analyses revealed that glycocholic acid expression was up-regulated in urine samples associated with HCC. Its pathway analysis suggested the modulation of multiple vital physiological pathways, including primary bile acid biosynthesis, secondary bile acid biosynthesis, metabolic pathways, and bile secretion. The network generation clearly enhances the interpretation and understanding of mechanisms for glycocholic acid. ConclusionsMetabolomics can contribute to evaluating the potential of metabolites in HCC patients and may provide new insight into pathophysiologic mechanisms.