Optimization of an in vitro gut microbiome biotransformation platform with chlorogenic acid as model compound: From fecal sample to biotransformation product identification

Integrating HPLC-Q-TOF-MS/MS, network pharmacology and experimental validation to decipher the chemical substances and mechanism of modified Gui-shao-liu-jun-zi decoction against gastric cancer

Background and aim

Gastric cancer (GC) is a common malignant tumor worldwide. Modified Gui-shao-liu-jun-zi decoction (mGSLJZ) is a clinically effective traditional Chinese medicine (TCM) compound in GC treatment. This study aimed to analyze main chemical substances of mGSLJZ and investigate active ingredients and molecular mechanism of mGSLJZ against GC.

Experimental procedure

HPLC-Q-TOF-MS/MS was used to analyze chemical substances of mGSLJZ, and potential active ingredients were screened from TCMSP. The target set of mGSLJZ for GC was obtained based on SwissTargetPrediction. The PPI network was constructed to screen out core targets. GO and KEGG enrichment analyses were conducted to identify BPs, CCs, MFs and pathways. The "active ingredient-core target-pathway" regulatory network was constructed to obtain core substances. Subsequently, Oncomine, Proteinatlas and molecular docking were performed to validate these findings. The cell experiments were conducted to confirm the anti-GC effects of mGLSJZ.

Results and conclusion

Forty-one potential active ingredients were filtered out from 120 chemical substances in mGSLJZ, including various organic acids and flavonoids. The top 10 key targets, 20 related pathways and 6 core medicinal substances were obtained based on network pharmacology analysis. Molecular docking results indicated that the core substances and key targets had good binding activities. The cell experiments validated that mGSLJZ and the core substances inhibited the proliferation in multiple GC cells and that mGLSJZ restrained the migration of GC. Meanwhile, the top 5 targets and top 2 pathways were verified. The rescue experiments demonstrated that mGSLJZ suppressed the proliferation and migration of GC through the PI3K/AKT/HIF-1 pathway.

Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases

The human gut microbiota and its associated perturbations are implicated in a variety of cardiovascular diseases (CVDs). There is evidence that the structure and metabolic composition of the gut microbiome and some of its metabolites have mechanistic associations with several CVDs. Nevertheless, there is a need to unravel metabolic behavior and underlying mechanisms of microbiome-host interactions. This need is even more highlighted when considering that microbiome-secreted metabolites contributing to CVDs are the subject of intensive research to develop new prevention and therapeutic techniques. In addition to the application of high-throughput data used in microbiome-related studies, advanced computational tools enable us to integrate omics into different mathematical models, including constraint-based models, dynamic models, agent-based models, and machine learning tools, to build a holistic picture of metabolic pathological mechanisms. In this article, we aim to review and introduce state-of-the-art mathematical models and computational approaches addressing the link between the microbiome and CVDs.

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods

Riboflavin-producing lactic acid bacteria represent a promising and cost-effective strategy for food biofortification, but production levels are typically insufficient to support daily human requirements. In this study, we describe the novel human isolate Limosilactobacillus reuteri AMBV339 as a strong food biofortification candidate. This strain shows a high natural riboflavin (vitamin B2) overproduction of 18.36 μg/ml, biomass production up to 6 × 10¹⁰ colony-forming units/ml (in the typical range of model lactobacilli), and pH-lowering capacities to a pH as low as 4.03 in common plant-based (coconut, soy, and oat) and cow milk beverages when cultured up to 72 h at 37°C. These properties were especially pronounced in coconut beverage and butter milk fermentations, and were sustained in co-culture with the model starter Streptococcus thermophilus. Furthermore, L. reuteri AMBV339 grown in laboratory media or in a coconut beverage survived in gastric juice and in a simulated gastrointestinal dialysis model with colon phase (GIDM-colon system) inoculated with fecal material from a healthy volunteer. Passive transport of L. reuteri AMBV339-produced riboflavin occurred in the small intestinal and colon stage of the GIDM system, and active transport via intestinal epithelial Caco-2 monolayers was also demonstrated. L. reuteri AMBV339 did not cause fecal microbiome perturbations in the GIDM-colon system and inhibited enteric bacterial pathogens in vitro. Taken together, our data suggests that L. reuteri AMBV339 represents a promising candidate to provide riboflavin fortification of plant-based and dairy foods, and has a high application potential in the human gastrointestinal tract.

An insight into an intriguing oxidative biotransformation pathway of 5-O-caffeoylquinic acid by a gut bacterium

Microbiota is known to play a pivotal role in generating bioavailable and bioactive low-molecular-weight metabolites from dietary polyphenols. 5-O-caffeoylquinic acid (5-CQA), one of the main polyphenols found in human diet, was submitted to a resting cell biotransformation study using three gut bacteria species Lactobacillus reuteri, Bacteroides fragilis and Bifidobacterium longum. These bacteria were selected according to their belonging to the main phyla found in human gut microbiota. Our study highlighted the ability of only one of the strains studied, L. reuteri, to bioconverse 5-CQA into various metabolites due to the expression of the cinnamoyl esterase enzyme as the first step. Interestingly, one known natural compound, esculetin, was described for the first time as a 5-CQA-derived metabolite after conversion by a gut bacterium, the other metabolites had already been reported. This evidence highlighted an interesting oxidative pathway occurring in vivo by intestinal microbiota leading to esculetin. This molecule was also identified after electrochemical and enzymatic oxidations of caffeic acid. The oxidation capacity of L. reuteri led to less diverse metabolites in comparison to those obtained either electrochemically and enzymatically where dimers and trimers were reported. Thus, esculetin may have interesting and benefical biological effects on gut microbiota, which should be further evaluated. Novel synbiotics could be formulated from the association of L. reuteri with 5-CQA.

Antiplasmodial activity of constituents and their metabolites after in vitro gastrointestinal biotransformation of a Nauclea pobeguinii extract

Nauclea pobeguinii is traditionally used for treatment of malaria. Previous studies on the plant extract and strictosamide, the putative active constituent, showed a profound in vivo activity of the extract but no in vitro activity of strictosamide. This might indicate that one or more compounds present in the extract, most likely alkaloids, act as prodrugs undergoing biotransformation after oral administration resulting in the active compounds. The phytochemical composition of a N. pobeguinii extract was characterized using UHPLC-UV-HRMS (Ultrahigh-Performance Liquid Chromatography-Ultraviolet-High Resolution Mass Spectrometry) data. An in vitro gastrointestinal model was used to simulate biotransformation of the extract allowing monitoring of the relative abundances of individual constituents over time on one hand, while antiplasmodial activity and cytotoxicity of the biotransformed extract could be evaluated on the other hand. A diversity of compounds was (tentatively) identified in the extract, mainly saponins and alkaloids, including 32 compounds that have not been reported before in N. pobeguinii. The automated data analysis workflow used for unbiased screening for metabolites showed that glycosylated compounds decreased in intensity over time. Alkaloids containing no sugar moieties, including angustine-type alkaloids, showed no gastrointestinal biotransformation. In vitro gastrointestinal biotransformation of strictosamide did not result in a major metabolite. Moreover, multivariate data analysis using Orthogonal Partial Least Square-Discriminant Analysis (OPLS-DA) showed no in vitro activity of strictosamide or its metabolites suggesting that other compounds or metabolites present in the extract are responsible for the antiplasmodial effect of the N. pobeguinii extract. The OPLS-DA proposes alkaloids with a β-carboline moiety as active principles, suggesting that antiplasmodial activity of N. pobeguinii derives from an additive or synergistic effect of multiple minor alkaloids and their metabolites present in the bark extract of N. pobeguinii.

Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation

Cardiovascular disease (CVD) is strongly associated with the gut microbiota and its metabolites, including trimethylamine-N-oxide (TMAO), formed from metaorganismal metabolism of ʟ-carnitine. Raw garlic juice, with allicin as its primary compound, exhibits considerable effects on the gut microbiota. This study validated the benefits of raw garlic juice against CVD risk via modulation of the gut microbiota and its metabolites. Allicin supplementation significantly decreased serum TMAO in ʟ-carnitine-fed C57BL/6 J mice, reduced aortic lesions, and altered the fecal microbiota in carnitine-induced, atherosclerosis-prone, apolipoprotein E-deficient (ApoE-/-) mice. In human subjects exhibiting high-TMAO production, raw garlic juice intake for a week reduced TMAO formation, improved gut microbial diversity, and increased the relative abundances of beneficial bacteria. In in vitro and ex vivo studies, raw garlic juice and allicin inhibited γ-butyrobetaine (γBB) and trimethylamine production by the gut microbiota. Thus, raw garlic juice and allicin can potentially prevent cardiovascular disease by decreasing TMAO production via gut microbiota modulation.

Simulated Gastrointestinal Biotransformation of Chlorogenic Acid, Flavonoids, Flavonolignans and Triterpenoid Saponins in Cecropia obtusifolia Leaf Extract

It is well known that biotransformation processes in the human body are crucial to form potentially bioactive metabolites from particular classes of natural products. However, little research has been conducted concerning the bioavailability of polyphenols, especially in the colon. The gastrointestinal stability and colonic biotransformation of the crude extract of the leaves of Cecropia obtusifolia, rich in flavone C-glycosides, was investigated under in vitro conditions, and the processing and interpretation of results were facilitated by using an automated machine learning model. This investigation revealed that flavone C-glycosides and flavonolignans from C. obtusifolia were stable throughout their passage in the simulated gastrointestinal tract including the colon phase. On the other hand, the colon bacteria extensively metabolized chlorogenic acid, flavonol, and triterpenoid O-glycosides. This investigation revealed that the colonic microbiota has an important role in the biotransformation of some chemical constituents of this extract.

Demonstrating the involvement of an active efflux mechanism in the intestinal absorption of chlorogenic acid and quinic acid using a Caco-2 bidirectional permeability assay

SCOPE

Chlorogenic acid (5-caffeoylquinic acid), the most prominent polyphenolic compound in coffee, has been attributed multiple health-promoting effects such as anti-inflammatory, antidiabetic and antioxidative effects. These effects are dependent on the bioavailability of chlorogenic acid, which is determined by the pharmacokinetic properties: absorption, distribution, metabolism and excretion (ADME). In order to have a better understanding of the biological properties of chlorogenic acid and to optimize formulation and dosing of chlorogenic acid-containing food supplements, information on the absorption of chlorogenic acid and its microbial biotransformation products is of essence.

METHODS AND RESULTS

In the present work, the intestinal absorption of chlorogenic acid and quinic acid, one of its most prominent intestinal biotransformation products, was studied by an in vitro permeability assay using a human Caco-2 cell line model. For both chlorogenic acid and quinic acid, the involvement of an active efflux mechanism was demonstrated, suggesting an overall low intestinal absorption.

CONCLUSIONS

An overall low intestinal absorption for chlorogenic acid and quinic acid was reported given the involvement of an active efflux mechanism. These findings could aid in the development of optimal formulation and dosing strategies of chlorogenic acid in food supplements in order to obtain beneficial health effects.

Compound Characterization and Metabolic Profile Elucidation after In Vitro Gastrointestinal and Hepatic Biotransformation of an Herniaria hirsuta Extract Using Unbiased Dynamic Metabolomic Data Analysis

Herniaria hirsuta L. (Caryophyllaceae) is used for treatment of urinary stones and as a diuretic. Little is known about the active compounds and the mechanism of action. The phytochemical composition of H. hirsuta was comprehensively characterized using UHPLC-UV-HRMS (Ultrahigh-Performance Liquid Chromatography-Ultraviolet-High Resolution Mass Spectrometry) data. An in vitro gastrointestinal model was used to simulate biotransformation, which allowed the monitoring of the relative abundances of individual compounds over time. To analyze the longitudinal multiclass LC-MS data, XCMS, a platform that enables online metabolomics data processing and interpretation, and EDGE, a statistical method for time series data, were used to extract significant differential profiles from the raw data. An interactive Shiny app in R was used to rate the quality of the resulting features. These ratings were used to train a random forest model. The most abundant aglycone after gastrointestinal biotransformation was subjected to hepatic biotransformation using human S9 fractions. A diversity of compounds was detected, mainly saponins and flavonoids. Besides the known saponins, 15 new saponins were tentatively identified as glycosides of medicagenic acid, acetylated medicagenic acid and zanhic acid. It is suggested that metabolites of phytochemicals present in H. hirsuta, most likely saponins, are responsible for the pharmaceutical effects. It was observed that the relative abundance of saponin aglycones increased, indicating loss of sugar moieties during colonic biotransformation, with medicagenic acid as the most abundant aglycone. Hepatic biotransformation of this aglycone resulted in different metabolites formed by phase I and II reactions.