Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria

Construction and Optimization of Engineered Saccharomyces cerevisiae for De Novo Synthesis of Phloretin and Its Derivatives

Phloretin and its derivatives are dihydrochalcone compounds with diverse pharmacological properties and biological activities, offering significant potential for applications in the food and pharmaceutical industries. Due to their structural similarity to flavonoids, their extraction and isolation were highly challenging. Although the biosynthesis of phloretin via three distinct pathways has been reported, a systematic comparison within the same host has yet to be conducted. In this study, we employed rational design and synthetic biology approaches to engineer Saccharomyces cerevisiae for de novo synthesis of phloretin and its derivatives. We constructed and evaluated three biosynthetic pathways for phloretin in S. cerevisiae, demonstrating that effective phloretin synthesis is achievable only via the p-coumaryl-CoA pathway. Additionally, by optimizing enzyme screening, strain engineering, and coordinating heterologous pathways with endogenous metabolism, we achieved the highest reported de novo titer of 287.2 mg/L for phloretin, 184.6 mg/L for phlorizin, 103.1 mg/L for trilobatin, and 164.5 mg/L for nothofagin and the first-time synthesis of 4-methylphloretin and hesperetin dihydrochalcone. This study was committed to addressing the growing demand for dihydrochalcones while laying the foundation for the biosynthesis of more complex derivatives.

Combining vitamin E metabolite 13'-carboxychromanol and a lactic acid bacterium synergistically mitigates colitis and colitis-associated dysbiosis in mice

Synbiotics may be useful to mitigate intestinal diseases such as ulcerative colitis. Here we show that combining 13'-carboxychromanol (δT3-13'), a metabolite of vitamin E δ-tocotrienol (δT3) via omega-oxidation, and Lactococcus lactis subsp. cremori (L. cremoris), but neither agent alone, significantly attenuated dextran sulfate sodium (DSS)-induced fecal bleeding and diarrhea, histologic colitis and interleukin 1β in mice. The combination of δT3-13'+L. cremoris also synergistically prevented DSS-caused compositional changes in gut microbiota and enriched beneficial bacteria including Lactococcus and Butyricicoccus. Interestingly, the anti-colitis effect correlated with the concentrations of δT3-13'-hydrogenated metabolite that contains 2 double bonds on the side chain (δT2-13'), instead of δT3-13' itself. Moreover, in contrast to δT3-13', combining δT3 and L. cremoris showed modest anti-colitis effects and did not prevent colitis-associated dysbiosis. In addition, ex vivo anaerobic incubation studies revealed that gut microbes selected by δT3-13' in the animal study could metabolize this compound to δT2-13' via hydrogenation, which appeared to be enhanced by L. cremoris. Overall, our study demonstrates that combining δT3-13' and L. cremoris can synergically prevent dysbiosis, and may be a novel synbiotic against colitis potentially via promoting δT3-13' metabolizers, which in turn contributes to superior beneficial effects of the combination.

Microbial metabolism of host-derived antioxidants

Humans are exposed to a wide variety of small molecules with antioxidant properties that are poorly metabolized by mammalian cells. However, gastrointestinal microbes encode enzymes that convert these redox-active molecules into nutrient sources and electron acceptors to support bacterial growth in the gut. Here, we describe recent studies highlighting how microbial metabolism of host-derived antioxidants modulates interspecies interactions and provide an overview of the interdisciplinary approaches being used to map these metabolic pathways in vivo. Uncovering microbe-driven biotransformations of redox-active small molecules could create new opportunities to improve human health by modulating redox reactions at the host-microbe interface.

Biochemical characterization of HcrF from Limosilactobacillus fermentum, a NADH-dependent 2-ene reductase with activity on hydroxycinnamic acids

In fermented plant foods, phenolic compounds are metabolized by 2-ene reductases, which reduce double bonds adjacent to an aromatic rings in phytochemicals, including hydroxycinnamic acids, isoflavones, and flavones. Only few 2-ene reductases of lactic acid bacteria were characterized, including the hydrocinnamic reductases HcrB and Par1, and the daidzein reductase of Lactococcus lactis. This study aimed to characterize HcrF, a homologue of HcrB, in Limosilactobacillus fermentum. HcrF was purified after cloning in Escherichia coli and purification by affinity chromatography. HcrF was optimally active at 30°C-40°C and pH 7.0 and required both flavin mononucleotide and nicotinamide adenine dinucleotide as co-factors. Ferulic, caffeic, p-coumaric, and sinapic acids but not trans-cinnamic acids were reduced to dihydro derivatives. The maximum reaction velocity Vmax of HcrF was highest for ferulic acid. On a phylogenetic tree of 2-ene reductases, HcrF clustered most closely with the hydroxycinnamic acid reductase HcrB of Lactiplantibacillus plantarum. The hydroxycinnamic acid reductase Par1 of Furfurilactobacillus milii and flavone or isoflavone reductases were only distantly related to HcrF. In summary, current knowledge does not allow to predict the substrate specificity of 2-ene reductases on the basis of the protein sequence; this study adds HcrF to the short list of enzymes with known substrate specificity.

Akkermansia muciniphila Growth Promoted by Lychee Major Flavonoid through Bacteroides uniformis Metabolism

Akkermansia muciniphila (A. muciniphila) possesses health-promoting properties. Nevertheless, A. muciniphila enrichment remains a challenging endeavor. Quercetin-3-O-rutinose-7-O-α-l-rhamnoside (QRR), a flavonoid found in lychee pulp, has a unique double-substituted glycosylated structure, requiring a specific intestinal microbiota for effective metabolism. Here, QRR was fermented using a coculture of Bacteroides uniformis and A. muciniphila, and the interactions between the two were elucidated in terms of QRR regulation of microbial growth changes and metabolic properties. The results demonstrated that QRR effectively promoted the proliferation of A. muciniphila based on the metabolic action of B. uniformis in vitro, which was evidenced by a notable increase in the number of viable bacteria. Furthermore, the coculture sample exhibited a significant increase in SCFAs. Qualitative analysis of metabolites by UPLC-ESI-Triple-TOF-MS/MS showed that B. uniformis could release sugars on QRR to produce quercetin-3-O-glucoside-7-O-α-rhamnoside and further quercetin. In the coculture and B. uniformis culture, quercetin was converted to taxifolin, which was identified as a crucial intermediate in the metabolism of QRR. Notably, the metabolite kaempferol was only detected in the coculture. The present study reveals the interaction between QRR and the coculture of A. muciniphila and B. uniformis, providing a practical basis for the potential prebiotic value of QRR.

Unveiling biotransformation of free flavonoids into phenolic acids and Chromones alongside dynamic migration of bound Phenolics in Lactobacillus-fermented lychee pulp

Lactobacillus strains have emerged as promising probiotics for enhancing the bioactivities of plant-based foods associated with flavonoid biotransformation. Employing microbial fermentation and mass spectrometry, we explored flavonoid metabolism in lychee pulp fermented separately by Lactiplantibacillus plantarum and Limosilactobacillus fermentum. Two novel metabolites, 3,5,7-trihydroxychromone and catechol, were exclusively identified in L. plantarum-fermented pulp. Concomitant with consumption of catechin and quercetin glycosides, dihydroquercetin glycosides, 2,4-dihydroxybenzoic acid and p-hydroxyphenyllactic acid were synthesized by two strains through hydrogenation and fission of C-ring. Quantitative analysis revealed that bound phenolics were primarily located in water-insoluble polysaccharides in lychee pulp. Quercetin 3-O-rutinoside was partially liberated from water-insoluble polysaccharides and migrated to water-soluble polysaccharides during fermentation. Meanwhile, substantial accumulations in short-chain fatty acids (increased 1.45 to 3.08-fold) and viable strains (increased by 1.97 to 2.00 Log10 CFU/mL) were observed in fermentative pulp. These findings provide broader insight into microbial biotransformation of phenolics and possible guidance for personalized nutrition.

Perspective on the Coevolutionary Role of Host and Gut Microbiota in Polyphenol Health Effects: Metabotypes and Precision Health

"Personalized nutrition" aims to establish nutritional strategies to improve health outcomes for non-responders. However, it is utopian since most people share similar nutritional requirements. "Precision health," encompassing lifestyles, may be more fitting. Dietary (poly)phenols are "healthy" but non-nutritional molecules (thus, we can live without them). The gut microbiota influences (poly)phenol effects, producing metabolites with different activity than their precursors. Furthermore, producing distinctive metabolites, like urolithins, lunularin, and equol, leads to the term "polyphenol-related gut microbiota metabotypes," grouping individuals based on a genuine microbial metabolism of ellagic acid, resveratrol, and isoflavones, respectively. Additionally, (poly)phenols exert prebiotic-like effects through their antimicrobial activities, typically reducing microbial diversity and modulating microbiota functionality by impacting its composition and transcriptomics. Since the gut microbiota perceives (poly)phenols as a threat, (poly)phenol effects are mostly a consequence of microbiota adaptation through differential (poly)phenol metabolism (e.g., distinctive reductions, dehydroxylations, etc.). This viewpoint is less prosaic than considering (poly)phenols as essential nutritional players in human health, yet underscores their health significance in a coevolutionary partnership with the gut microbiota. In the perspective on the gut microbiota and (poly)phenols interplay, microbiota metabotypes could arbiter health effects. An innovative aspect is also emphasized: modulating the interacting microbial networks without altering the composition.

The dynamic crosslinking between gut microbiota and inflammation during aging: reviewing the nutritional and hormetic approaches against dysbiosis and inflammaging

The early-life gut microbiota (GM) is increasingly recognized for its contributions to human health and disease over time. Microbiota composition, influenced by factors like race, geography, lifestyle, and individual differences, is subject to change. The GM serves dual roles, defending against pathogens and shaping the host immune system. Disruptions in microbial composition can lead to immune dysregulation, impacting defense mechanisms. Additionally, GM aids digestion, releasing nutrients and influencing physiological systems like the liver, brain, and endocrine system through microbial metabolites. Dysbiosis disrupts intestinal homeostasis, contributing to age-related diseases. Recent studies are elucidating the bacterial species that characterize a healthy microbiota, defining what constitutes a 'healthy' colonic microbiota. The present review article focuses on the importance of microbiome composition for the development of homeostasis and the roles of GM during aging and the age-related diseases caused by the alteration in gut microbial communities. This article might also help the readers to find treatments targeting GM for the prevention of various diseases linked to it effectively.

Lacticaseibacillus casei- and Bifidobacterium breve-fermented red pitaya promotes beneficial microbial proliferation in the colon

Red pitaya has been demonstrated to strongly inhibit α-glucosidase activity; however, the impact of red pitaya fermentation by probiotic bacteria on α-glucosidase inhibition remains unclear. In this study, six strains of lactic acid bacteria (Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, Lactobacillus bulgaricus, Lacticaseibacillus casei, Lactobacillus acidophilus and Streptococcus thermophilus) and one strain of Bifidobacterium breve were utilized for the fermentation of red pitaya pulp. The α-glucosidase and α-amylase inhibition rates of red pitaya pulp were significantly greater after fermentation by Bifidobacterium breve and Lacticaseibacillus casei than by the other abovementioned strains. The LC group exhibited an α-glucosidase inhibition rate of 99%, with an α-amylase inhibition rate of 89.91%. In contrast, the BB group exhibited an α-glucosidase inhibition rate of 95.28%, accompanied by an α-amylase inhibition rate of 95.28%. Moreover, red pitaya pulp fermented with Bifidobacterium breve and Lacticaseibacillus casei produced a notable quantity of oligosaccharides, which was more than three times greater than that in the other groups. Furthermore, 16S rRNA high-throughput sequencing analysis was conducted to assess alterations in the composition of the gut microbiota. This revealed an increase in the abundance of Lactobacillus and Faecalibacterium in the pulp fermented by Bifidobacterium breve and Lacticaseibacillus casei, whereas the abundance of Sutterella decreased. Further analysis at the species level revealed that Bifidobacterium longum, Faecalibacterium prausnitzii, and Lactobacillus zeae were the dominant strains present during colonic fermentation. These results indicate a beneficial health trend associated with probiotic bacterial fermentation of red pitaya pulp, which is highly important for the development of functional products.

Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites

Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.

The adhesin RadD enhances Fusobacterium nucleatum tumour colonization and colorectal carcinogenesis

Fusobacterium nucleatum can bind to host cells and potentiate intestinal tumorigenesis. Here we used a genome-wide screen to identify an adhesin, RadD, which facilitates the attachment of F. nucleatum to colorectal cancer (CRC) cells in vitro. RadD directly binds to CD147, a receptor overexpressed on CRC cell surfaces, which initiated a PI3K-AKT-NF-κB-MMP9 cascade, subsequently enhancing tumorigenesis in mice. Clinical specimen analysis showed that elevated radD gene levels in CRC tissues correlated positively with activated oncogenic signalling and poor patient outcomes. Finally, blockade of the interaction between RadD and CD147 in mice effectively impaired F. nucleatum attachment and attenuated F. nucleatum-induced oncogenic response. Together, our study provides insights into an oncogenic mechanism driven by F. nucleatum RadD and suggests that the RadD-CD147 interaction could be a potential therapeutic target for CRC.

An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085

Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn2+-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP+-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome.IMPORTANCEPhloroglucinol is an important intermediate in the bacterial degradation of polyphenols, a highly abundant class of plant natural products. Recent research has identified key enzymes of the phloroglucinol degradation pathway in butyrate-producing anaerobic bacteria, which involves cleavage of a linear triketide intermediate by a beta ketoacid cleavage enzyme, requiring acetyl-CoA as a co-substrate. This paper reports a variant of the pathway in the lactic acid bacterium Collinsella sp. zg1085, which involves cleavage of the triketide intermediate by a homolog of deoxyribose-5-phosphate aldolase, highlighting the variety of mechanisms for phloroglucinol degradation by different anaerobic bacterial taxa.

A comparative metabolomics analysis of phytochemcials and antioxidant activity between broccoli floret and by-products (leaves and stalks)

Leaves and stalks, which account for about 45% and 25% of broccoli biomass, respectively, are usually discarded during broccoli production, leading to the waste of green resources. In this study, the phytochemical composition and antioxidant capacity of broccoli florets and their by-products (leaves and stalks) were comprehensively analyzed. The metabolomics identified several unique metabolites (e.g., scopoletin, Harpagoside, and sinalbin) in the leaves and stalks compared to florets. Notably, the leaves were found to be a rich source of flavonoids and coumarins, with superior antioxidant capacity. The random forest model and correlation analysis indicated that flavonoids, coumarin, and indole compounds were the important factors contributing to the antioxidant activity. Moreover, the stalks contained higher levels of carbohydrates and exhibited better antioxidant enzyme activity. Together, these results provided valuable data to support the comprehensive utilization of broccoli waste, the development of new products, and the expansion of the broccoli industry chain.

Inflammatory macrophage reprogramming strategy of fucoidan microneedles-mediated ROS-responsive polymers for rheumatoid arthritis

During the pathogenesis of rheumatoid arthritis, inflammatory cells usually infiltrate synovial tissues, notably, M1-type macrophages, whose redox imbalance leads to the degradation of joint structures and deterioration of function. Natural active products play a vital role in immune modulation and antioxidants. In this study, we constructed a ROS-responsive nanoparticle called FTL@SIN, which consists of fucoidan (Fuc) and luteolin (Lut) connected by a ROS-responsive bond, Thioketal (TK), and encapsulated with an anti-rheumatic drug, Sinomenine (SIN), for synergistic anti-inflammatory effects. The FTL@SIN is then dispersed in high molecular weight Fuc-fabricated dissolvable microneedles (FTL@SIN MNs) for local administration. Therapy of FTL@SIN MNs afforded a significant decrease in macrophage inflammation while decreasing key pro-inflammatory cytokines and repolarizing M1 type to M2 type, thereby ameliorating synovial inflammation, and promoting cartilage repair. Additionally, our investigations have revealed that Fucoidan (Fuc) demonstrates synergistic effects, exhibiting superior mechanical strength and enhanced physical stability when compared to microneedles formulated solely with hyaluronic acid. This study combines nanomedicine with traditional Chinese medicine, a novel drug delivery strategy that presents a promising avenue for therapeutic intervention in rheumatoid arthritis.

Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts

Eco-friendly reagents derived from plants represent a promising strategy to mitigate the occurrence of toxic cyanobacterial blooms. The use of an amentoflavone-containing Selaginella tamariscina extract (STE) markedly decreased the number of Microcystis aeruginosa cells, thus demonstrating significant anti-cyanobacterial activity. In particular, the Microcystis-killing fraction obtained from pulverized S. tamariscina using hot-water-based extraction at temperatures of 40 °C induced cell disruption in both axenic and xenic M. aeruginosa. Liquid chromatographic analysis was also conducted to measure the concentration of amentoflavone in the STE, thus supporting the potential M. aeruginosa-specific killing effects of STE. Bacterial community analysis revealed that STE treatment led to a reduction in the relative abundance of Microcystis species while also increasing the 16S rRNA gene copy number in both xenic M. aeruginosa NIBR18 and cyanobacterial bloom samples isolated from a freshwater environment. Subsequent testing on bacteria, cyanobacteria, and algae isolated from freshwater revealed that STE was not toxic for other taxa. Furthermore, ecotoxicology assessment involving Aliivibrio fischeri, Daphnia magna, and Danio rerio found that high STE doses immobilized D. magna but did not impact the other organisms, while there was no change in the water quality. Overall, due to its effective Microcystis-killing capability and low ecotoxicity, aqueous STE represents a promising practical alternative for the management of Microcystis blooms.

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.

Probiotic cocktails accelerate baicalin metabolism in the ileum to modulate intestinal health in broiler chickens

BACKGROUND

Baicalin and probiotic cocktails are promising feed additives with broad application prospects. While probiotic cocktails are known to enhance intestinal health, the potential synergistic impact of combining baicalin with probiotic cocktails on the gut health of broiler chickens remains largely unexplored. Therefore, this study aims to investigate the influence of the combined administration of baicalin and probiotic cocktails on the composition of ileal and cecal microbiota in broiler chickens to elucidate the underlying mechanisms responsible for the health-promoting effects.

RESULTS

A total of 320 1-day-old male Arbor Acres broilers were divided into 4 groups, each with 8 replicates of 10 chicks per replicate. Over a period of 42 d, the birds were fed a basal diet or the same diet supplemented with 37.5 g/t baicalin (BC), 1,000 g/t probiotic cocktails (PC), or a combination of both BC (37.5 g/t) and PC (1,000 g/t). The results demonstrated that BC + PC exhibited positive synergistic effects, enhancing intestinal morphology, immune function, and barrier function. This was evidenced by increased VH/CD ratio, sIgA levels, and upregulated expression of occludin and claudin-1 (P < 0.05). 16S rRNA analysis indicated that PC potentiated the effects of BC, particularly in the ileum, where BC + PC significantly increased the α-diversity of the ileal microbiota, altered its β-diversity, and increased the relative abundance of Flavonifractor (P < 0.05), a flavonoid-metabolizing bacterium. Furthermore, Flavonifractor positively correlated with chicken ileum crypt depth (P < 0.05). While BC + PC had a limited effect on cecal microbiota structure, the PC group had a very similar microbial composition to BC + PC, suggesting that the effect of PC at the distal end of the gut overshadowed those of BC.

CONCLUSIONS

We demonstrated the synergistic enhancement of gut health regulation in broiler chickens by combining baicalin and probiotic cocktails. Probiotic cocktails enhanced the effects of baicalin and accelerated its metabolism in the ileum, thereby influencing the ileal microbiota structure. This study elucidates the interaction mechanism between probiotic cocktails and plant extract additives within the host microbiota. These findings provide compelling evidence for the future development of feed additive combinations.

High-throughput prediction of enzyme promiscuity based on substrate-product pairs

The screening of enzymes for catalyzing specific substrate-product pairs is often constrained in the realms of metabolic engineering and synthetic biology. Existing tools based on substrate and reaction similarity predominantly rely on prior knowledge, demonstrating limited extrapolative capabilities and an inability to incorporate custom candidate-enzyme libraries. Addressing these limitations, we have developed the Substrate-product Pair-based Enzyme Promiscuity Prediction (SPEPP) model. This innovative approach utilizes transfer learning and transformer architecture to predict enzyme promiscuity, thereby elucidating the intricate interplay between enzymes and substrate-product pairs. SPEPP exhibited robust predictive ability, eliminating the need for prior knowledge of reactions and allowing users to define their own candidate-enzyme libraries. It can be seamlessly integrated into various applications, including metabolic engineering, de novo pathway design, and hazardous material degradation. To better assist metabolic engineers in designing and refining biochemical pathways, particularly those without programming skills, we also designed EnzyPick, an easy-to-use web server for enzyme screening based on SPEPP. EnzyPick is accessible at http://www.biosynther.com/enzypick/.

Mechanisms of gut bacterial metabolism of dietary polyphenols into bioactive compounds

The fruits and vegetables we consume as part of our diet are rich in bioactive metabolites that can prevent and ameliorate cardiometabolic diseases, cancers, and neurological conditions. Polyphenols are a major metabolite family that has been intensively investigated in this context. However, for these compounds to exert their optimal bioactivity, they rely on the enzymatic capacity of an individual's gut microbiota. Indeed, for most polyphenols, the human host is restricted to more basic metabolism such as deglycosylation and hepatic conjugation. In this review, we discuss the mechanisms by which gut bacteria metabolize the core scaffold of polyphenol substrates, and how their conversion into bioactive small molecules impacts host health.

Divergent metabolism of two lychee (Litchi chinensis Sonn.) pulp flavonols and their modulatory effects on gut microbiota: Discovery of hydroxyethylation in vitro colonic fermentation

Quercetin 3-O-rutinose-7-O-α-l-rhamnoside (QRR), a characteristic lychee pulp flavonoid, has been linked to diverse bioactivities involving microbial metabolism. By integrating colonic fermentation and mass spectrometry, the catabolites including 7-O-hydroxyethyl-isorhamnetin and 3'-amino-4'-O-methyl-7-O-hydroxyethyl-isorhamnetin were unprecedently identified and unique to QRR metabolism, relative to the structural analog quercetin 3-O-rutinoside (QR) metabolism. These above-described metabolites highlighted a special biotransformation hydroxyethylation in QRR catabolism. QRR was partially deglycosylated into quercetin 3-O-glucoside-7-O-α-l-rhamnoside potentially catalyzed by Bacteroides. QR was more directly degradable to aglycone during colonic fermentation than are QRR. Unlike with QR fermentation, equivalent QRR effectively upregulated concentrations of propionic and butyric acids that were highly relevant with Faecalibacterium and Coprococcus. After fermentation, the relative abundances of Bacteroides uniformis (0.03%) and Akkermansia muciniphila (0.13%) were only upregulated by QRR among all fermentation groups, leading to the enrichments of the corresponding genera. These results further reveal the relationship between flavonoid structures and metabolic characteristics.

Molecular basis of phytochemical-gut microbiota interactions

Dysbiosis-associated molecular pathology is significantly involved in developing and perpetuating metabolic disorders, disrupting host energy regulation, and triggering inflammatory signaling cascades, insulin resistance, and metabolic dysfunction. Concurrently, numerous phytoconstituents are able to interact with the gut microbiota and produce bioactive metabolites that influence host cellular pathways, inflammation, and metabolic processes. These effects include improved insulin sensitivity, lipid metabolism regulation, and suppression of chronic inflammation, highlighting the therapeutic potential of phytoconstituents against metabolic abnormalities. Understanding this symbiotic relationship and the underlying molecular cascades offers innovative strategies for tailored interventions and promising therapeutic approaches to address the growing burden of metabolic disease.

Structural and Anticancer Studies of Methoxyflavone Derivative from Strychnos pseudoquina A.St.-Hil. (Loganiaceae) from Brazilian Cerrado

The Cerrado biome is the world's largest and most diversified tropical savanna. Despite its diversity, there remains a paucity of scientific discussion and evidence about the medicinal use of Cerrado plants. One of the greatest challenges is the complexity of secondary metabolites, such as flavonoids, present in those plants and their extraction, purification, and characterization, which involves a wide range of approaches, tools, and techniques. Notwithstanding these difficulties, the search for accurately proven medicinal plants against cancer, a leading cause of death worldwide, has contributed to this growing area of research. This study set out to extract, purify, and characterize 3-O-methylquercetin isolated from the plant Strychnos pseudoquina A.St.-Hil. (Loganiaceae) and to test it for antiproliferative activity and selectivity against different tumor and nontumor human cell lines. A combined-method approach was employed using 1H and 13C nuclear magnetic resonance, thermogravimetric analysis, differential scanning calorimetry, single-crystal X-ray diffraction, Hirshfeld surface analysis, and theoretical calculations to extensively characterize this bioflavonoid. 3-O-methylquercetin melts around 275 °C and crystallizes in a nonplanar conformation with an angle of 18.02° between the pyran ring (C) and the phenyl ring (B), unlike quercetin and luteolin, which are planar. Finally, the in vitro cytotoxicity of 3-O-methylquercetin was compared with data from quercetin, luteolin, and cisplatin, showing that structural differences influenced the antiproliferative activity and the selectivity against different tumor cell lines.

Anaerobic phloroglucinol degradation by Clostridium scatologenes

Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O2 requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium Clostridium scatologenes for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as (S)-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health.

Targeting gut-brain axis by dietary flavonoids ameliorate aging-related cognition decline: Evidences and mechanisms

Aging-related cognitive impairment, mainly Alzheimer's disease (AD), has been widely studied. However, effective prevention and treatment methods are still lacking. In recent years, researchers have observed beneficial effects of plant-based supplements, such as flavonoids, on cognitive protection. This provides a new clue for the prevention of cognitive dysfunction. Studies have shown that dietary flavonoids have neuroprotective effects, but the mechanism is not clear. In this review, we systematically reviewed the research progress on the effects of dietary flavonoids on gut microbes and their metabolites, and concluded that flavonoids could improve cognitive function through the gut-brain axis. Flavonoids can be absorbed through the intestine, cross the blood-brain barrier, and enter the brain tissue. Flavonoids can inhibit the expression and secretion of inflammatory factors in brain tissue, reduce the damage caused by oxidative stress, clear neural damage proteins and inhibit neuronal apoptosis, thereby ameliorating age-related cognitive disorders. Future work will continue to explore the gut-brain axis and target genes regulated by flavonoids. In addition, clinical research and its mechanisms need to be further explored to provide solutions or advise for patients with cognitive impairment.

Metabolic Engineering of Escherichia coli for the Biosynthesis of 3-Phenylpropionic Acid and 3-Phenylpropyl Acetate

3-Phenylpropionic acid (3PPA) and its derivative 3-phenylpropyl acetate (3PPAAc) are important aromatic compounds with broad applications in the cosmetics and food industries. In this study, we constructed a plasmid-free 3PPA-producing Escherichia coli strain and designed a novel 3PPAAc biosynthetic pathway. A module containing tyrosine ammonia lyase and enoate reductase, evaluated under the control of different promoters, was combined with phenylalanine-overproducing strain E. coli ATCC31884, enabling the plasmid-free de novo production of 218.16 ± 43.62 mg L^-1 3PPA. The feasibility of the pathway was proved by screening four heterologous alcohol acetyltransferases, which catalyzed the transformation of 3-phenylpropyl alcohol into 3PPAAc. Afterward, 94.59 ± 16.25 mg L^-1 3PPAAc was achieved in the engineered E. coli strain. Overall, we have not only demonstrated the potential of de novo synthesis of 3PPAAc in microbes for the first time but also provided a platform for the future of biosynthesis of other aromatic compounds.

Metabolites analysis of plantamajoside based on gut microbiota-drug interaction

BACKGROUND

Plantaginis Herba (Plantago asiatica L.) has the effects of clearing heat and diuresis, oozing wet and drenching. As the main active components of Plantaginis Herba (Plantago asiatica L.), plantamajoside have a wide range of antitumor activities but very low bioavailability. The process of interacting between plantamajoside and gut microbiota remains unclear.

PURPOSE

To illustrate the process of interacting between plantamajoside and gut microbiota based on high-resolution mass spectrometry and targeted metabolomics methods.

STUDY DESIGN AND METHODS

This experiment was divided into two parts. First, metabolites produced from plantamajoside by gut microbiota were identified and quantified based on high-resolution mass spectrometry and LC-MS/MS. Additionally, stimulation of plantamajoside on gut microbiota-derived metabolites was determined by targeted metabolomics and gas chromatography.

RESULTS

We first found that plantamajoside was rapidly metabolized by gut microbiota. Then, we identified metabolites of plantamajoside by high-resolution mass spectrometry and speculated that plantamajoside was metabolized into five metabolites including calceolarioside A, dopaol glucoside, hydroxytyrosol, 3-(3-hydroxyphenyl) propionic acid (3-HPP) and caffeic acid. Among them, we quantitatively analyzed four possible metabolites based on LC‒MS/MS and found that hydroxytyrosol and 3-HPP were final products by the gut microbiota. In addition, we studied whether plantamajoside could affect the short-chain fatty acid (SCFA) and amino acid metabolites. We found that plantamajoside could inhibit the acetic acid, kynurenic acid (KYNA) and kynurenine (KN) produced by intestinal bacteria and promote the indole propionic acid (IPA) and indole formaldehyde (IALD) produced by intestinal bacteria.

CONCLUSION

An interaction between plantamajoside and gut microbiota was revealed in this study. Unlike the traditional metabolic system, the special metabolic characteristics of plantamajoside in gut microbiota was found. Plantamajoside was metabolized into the following active metabolites: calceolarioside A, dopaol glucoside, hydroxytyrosol, caffeic acid and 3-HPP. Besides, plantamajoside could affect SCFA and tryptophan metabolism by gut microbiota. Especially, the exogenous metabolites hydroxytyrosol, caffeic acid and endogenous metabolites IPA may have potential association with the antitumor activity of plantamajoside.

Purification and biochemical characterization of a novel ene- reductase from Kazachstania exigua HSC6 for dihydro-β-ionone from β-ionone

PURPOSE

We purified and characterized a novel ene-reductase (KaDBR1) from Kazachstania exigua HSC6 for the synthesis of dihydro-β-ionone from β-ionone.

METHODS

KaDBR1 was purified to homogeneity by ammonium sulfate precipitation and phenyl-Sepharose Fast Flow and Q-Sepharose chromatography. The purified enzyme was characterized by measuring the amount of dihydro-β-ionone from β-ionone with LC-MS analysis method.

RESULTS

The molecular mass of KaDBR1 was estimated to be 45 kDa by SDS-PAGE. The purified KaDBR1 enzyme had optimal activity at 60 °C and pH 6.0. The addition of 5 mM Mg²⁺, Ca²⁺, Al³⁺, Na⁺, and dithiothreitol increased the activity of KaDBR1 by 25%, 18%, 34%, 20%, and 23%, respectively. KaDBR1 favored NADH over NADPH as a cofactor, and its catalytic efficiency (kcat/Km) toward β-ionone using NADH was 8.1-fold greater than when using NADPH.

CONCLUSION

Owing to its unique properties, KaDBR1 is a potential candidate for the enzymatic biotransformation of β-ionone to dihydro-β-ionone in biotechnology applications.

Discovery of a Unique Flavonoid Biosynthesis Mechanism in Fungi by Genome Mining

Flavonoids are important plant natural products with variable structures and bioactivities. All known plant flavonoids are generated under the catalysis of a type III polyketide synthase (PKS) followed by a chalcone isomerase (CHI) and a flavone synthase (FNS). In this study, the biosynthetic gene cluster of chlorflavonin, a fungal flavonoid with acetolactate synthase inhibitory activity, was discovered using a self-resistance-gene-directed strategy. A novel flavonoid biosynthetic pathway in fungi was revealed. A core nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) is responsible for the generation of the key precursor chalcone. Then, a new type of CHI catalyzes the conversion of a chalcone into a flavanone by a histidine-mediated oxa-Michael addition mechanism. Finally, the desaturation of flavanone to flavone is catalyzed by a new type of FNS, a flavin mononucleotide (FMN)-dependent oxidoreductase.

Glucose oxidase as an alternative to antibiotic growth promoters improves the immunity function, antioxidative status, and cecal microbiota environment in white-feathered broilers

This study aimed to demonstrate the effects of glucose oxidase (GOD) on broilers as a potential antibiotic substitute. A total of four hundred twenty 1-day-old male Cobb500 broilers were randomly assigned into five dietary treatments, each with six replicates (12 chicks per replicate). The treatments included two control groups (a basal diet and a basal diet with 50 mg/kg aureomycin) and three GOD-additive groups involving three different concentrations of GOD. Analysis after the t-test showed that, on day 21, the feed:gain ratio significantly decreased in the 1,200 U/kg GOD-supplied group (GOD1200) compared to the antibiotic group (Ant). The same effect was also observed in GOD1200 during days 22-42 and in the 600 U/kg GOD-supplied group (GOD600) when compared to the control group (Ctr). The serum tests indicated that, on day 21, the TGF-β cytokine was significantly decreased in both GOD600 and GOD1200 when compared with Ctr. A decrease in malondialdehyde and an increase in superoxide dismutase in GOD1200 were observed, which is similar to the effects seen in Ant. On day 42, the D-lactate and glutathione peroxidase activity changed remarkably in GOD1200 and surpassed Ant. Furthermore, GOD upregulated the expression of the jejunal barrier genes (MUC-2 and ZO-1) in two phases relative to Ctr. In the aureomycin-supplied group, the secretory immunoglobulin A significantly decreased in the jejunum at 42 days. Changes in microbial genera were also discovered in the cecum by sequencing 16S rRNA genes at 42 days. The biomarkers for GOD supplementation were identified as Colidextribacter, Oscillibacter, Flavonifractor, Oscillospira, and Shuttleworthia. Except for Shuttleworthia, all the abovementioned genera were n-butyrate producers known for imparting their various benefits to broilers. The PICRUSt prediction of microbial communities revealed 11 pathways that were enriched in both the control and GOD-supplied groups. GOD1200 accounted for an increased number of metabolic pathways, demonstrating their potential in aiding nutrient absorption and digestion. In conclusion, a diet containing GOD can be beneficial to broiler health, particularly at a GOD concentration of 1,200 U/kg. The improved feed conversion ratio, immunity, antioxidative capacity, and intestinal condition demonstrated that GOD could be a valuable alternative to antibiotics in broiler breeding.

Expanding the viewpoint: Leveraging sequence information in enzymology

The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and phylogenetic analyses has allowed the identification of new substrates and metabolites, novel pathways, and unexpected reaction mechanisms. The holistic examination of superfamilies can yield insight into the origins and paths of evolution of enzymes and the range of their substrates and mechanisms. Herein, we highlight advances in the use of genomic enzymology to address problems which the in-depth analyses of a single enzyme alone could not enable.

Biohydrogenation of 1,3-Butadiene to 1-Butene under Acetogenic Conditions by Acetobacterium wieringae

The environmental fate and transformation mechanism(s) of 1,3-butadiene (BD) under anoxic conditions remain largely unexplored. Anaerobic consortia that can biohydrogenate BD to stoichiometric amounts of 1-butene at a maximum rate of 205.7 ± 38.6 μM day^-1 were derived from freshwater river sediment. The formation of 1-butene occurred only in the presence of both H₂ and CO₂ with concomitant acetate production, suggesting the dependence of BD biohydrogenation on acetogenesis. The 16S rRNA gene-targeted amplicon sequencing revealed the enrichment and dominance of a novel Acetobacterium wieringae population, designated as strain N, in the BD-biohydrogenating community. Multiple genes encoding putative ene-reductases, candidate catalysts for the hydrogenation of the C═C bond in diene compounds, were annotated on the metagenome-assembled genome of strain N, and thus attributed the BD biohydrogenation activity to strain N. Our findings emphasize an essential but overlooked role of certain Acetobacterium members (e.g., strain N) contributing to the natural attenuation of BD in contaminated subsurface environments (e.g., sediment and groundwater). Future efforts to identify and characterize the ene-reductase(s) responsible for BD biohydrogenation in strain N hold promise for the development of industrial biocatalysts capable of stereoselective conversion of BD to 1-butene.

Dietary flavonoids: a novel strategy for the amelioration of cognitive impairment through intestinal microbiota

The chances of people suffering from cognitive impairments increase gradually with age. Diet and lifestyle are closely related to the occurrence and development of cognitive function. Dietary flavonoid supplementation has been shown to be one of the protective factors against cognitive decline. Flavonoids belong to a class of polyphenols that have been proposed for the treatment of cognitive decline. Recent evidence has shown that intestinal flora in the human body can interact with flavonoids. Intestinal microbiota can modify the chemical structure of flavonoids, producing new metabolites, the pharmacological activities of which may be different from those of the parent; meanwhile, flavonoids and their metabolites can, in turn, regulate the composition and structure of intestinal flora. Notably, intestinal flora affect host nervous system activity through the gut-brain axis, ultimately causing changes in cognitive function. This review therefore summarizes the interaction of dietary flavonoids and intestinal flora, and their protective effect against cognitive decline through the gut-brain axis, indicating that dietary flavonoids may ameliorate cognitive impairment through their interaction with intestinal microbiota. © 2022 Society of Chemical Industry.

Plant-Derived Xanthones against Clostridial Enteric Infections

Intestinal bacterial infections are a major threat to human and animal health. In this study, we found plant-derived antibacterial xanthones, particularly α-mangostin (AMG) from the mangosteen peel, exhibiting extraordinary activities against Clostridium perfringens. Structure-activity relationship analysis showed that prenylation modulated the activity of xanthones. The efficacy of AMG (4, 8, 20 mg/kg body weight) was also demonstrated in the broiler chicken necrotic enteritis model infected with Clostridium perfringens. In the models (n = 6 per group), feed supplementation of AMG maintained the homeostasis of the gut microbiome by reducing the colonization of clostridia and promoting the integrity of intestinal barriers via the upregulation of mucin expression. These results suggest that plant-derived xanthones may be a potential alternative to antibiotics for treating clostridial enteric infections in the clinic.

Flavonifractor plautii Protects Against Elevated Arterial Stiffness

BACKGROUND

Dysbiosis of gut microbiota plays a pivotal role in vascular dysfunction and microbial diversity was reported to be inversely correlated with arterial stiffness. However, the causal role of gut microbiota in the progression of arterial stiffness and the specific species along with the molecular mechanisms underlying this change remain largely unknown.

METHODS

Participants with elevated arterial stiffness and normal controls free of medication were matched for age and sex. The microbial composition and metabolic capacities between the 2 groups were compared with the integration of metagenomics and metabolomics. Subsequently, Ang II (angiotensin II)-induced and humanized mouse model were employed to evaluate the protective effect of Flavonifractor plautii (F plautii) and its main effector cis-aconitic acid.

RESULTS

Human fecal metagenomic sequencing revealed a significantly high abundance and centrality of F plautii in normal controls, which was absent in the microbial community of subjects with elevated arterial stiffness. Moreover, blood pressure only mediated part of the effect of F plautii on lower arterial stiffness. The microbiome of normal controls exhibited an enhanced capacity for glycolysis and polysaccharide degradation, whereas, those of subjects with increased arterial stiffness were characterized by increased biosynthesis of fatty acids and aromatic amino acids. Integrative analysis with metabolomics profiling further suggested that increased cis-aconitic acid served as the main effector for the protective effect of F plautii against arterial stiffness. Replenishment with F plautii and cis-aconitic acid improved elastic fiber network and reversed increased pulse wave velocity through the suppression of MMP-2 (matrix metalloproteinase-2) and inhibition of MCP-1 (monocyte chemoattractant protein-1) and NF-κB (nuclear factor kappa-B) activation in both Ang II-induced and humanized model of arterial stiffness.

CONCLUSIONS

Our translational study identifies a novel link between F plautii and arterial function and raises the possibility of sustaining vascular health by targeting gut microbiota.

Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes

In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.

High Titer of (S)-Equol Synthesis from Daidzein in Escherichia coli

(S)-Equol is the terminal metabolite of daidzein and plays important roles in human health. However, due to anaerobic inefficiency, limited productivity in (S)-equol-producing strains often hinders (S)-equol mass production. Here, a multi-enzyme cascade system was designed to generate a higher (S)-equol titer. First, full reversibility of the (S)-equol synthesis pathway was found and a blocking reverse conversion strategy was established. As biosynthetic genes are present in the microbial genome, an effective daidzein reductase was chosen using evolutionary principles. And our analyses showed that NADPH was crucial for the pathway. In response to this, a novel NADPH pool was redesigned after analyzing a cofactor metabolism model. By adjusting synthesis pathway genes at the right expression level, the entire synthesis pathway can take place smoothly. Thus, the cascade system was optimized by regulating the gene expression intensity. Finally, after optimizing fermentation conditions, a 5 L bioreactor was used to generate a high (S)-equol production titer (3418.5 mg/L), with a conversion rate of approximately 85.9%. This study shows a feasible green process route for the production of (S)-equol.

Multifaceted roles of flavonoids mediating plant-microbe interactions

Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are-to a large extent-mediated by specialized host-derived secondary metabolites. Flavonoids are one of the most studied classes of such metabolites, regulating both plant development and the interaction with commensal microbes. Here, we provide a comprehensive review of the multiple roles of flavonoids in mediating plant-microbe interactions. First, we briefly summarize the general aspects of flavonoid synthesis, transport, and exudation in plants. Then, we review the importance of flavonoids regulating plant-microbe interactions and dynamically influencing the overall community assembly of plant-root microbiomes. Last, we highlight potential knowledge gaps in our understanding of how flavonoids determine the interactions between plants and commensal microbes. Collectively, we advocate the importance of advancing research in this area toward innovative strategies to effectively manipulate plant-microbiome composition, in this case, via flavonoid production and exudation in plant roots. Video Abstract.

A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis

The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption hinge, in part, on gut microbial metabolism. Specifically, we show that a single gut microbial flavonoid catabolite, 4-hydroxyphenylacetic acid (4-HPAA), is sufficient to reduce diet-induced cardiometabolic disease (CMD) burden in mice. The addition of flavonoids to a high fat diet heightened the levels of 4-HPAA within the portal plasma and attenuated obesity, and continuous delivery of 4-HPAA was sufficient to reverse hepatic steatosis. The antisteatotic effect was shown to be associated with the activation of AMP-activated protein kinase α (AMPKα). In a large survey of healthy human gut metagenomes, just over one percent contained homologs of all four characterized bacterial genes required to catabolize flavonols into 4-HPAA. Our results demonstrate the gut microbial contribution to the metabolic benefits associated with flavonoid consumption and underscore the rarity of this process in human gut microbial communities.

Potential roles of gut microbes in biotransformation of natural products: An overview

Natural products have been extensively applied in clinical practice, characterized by multi-component and multi-target, many pharmacodynamic substances, complex action mechanisms, and various physiological activities. For the oral administration of natural products, the gut microbiota and clinical efficacy are closely related, but this relationship remains unclear. Gut microbes play an important role in the transformation and utilization of natural products caused by the diversity of enzyme systems. Effective components such as flavonoids, alkaloids, lignans, and phenols cannot be metabolized directly through human digestive enzymes but can be transformed by enzymes produced by gut microorganisms and then utilized. Therefore, the focus is paid to the metabolism of natural products through the gut microbiota. In the present study, we systematically reviewed the studies about gut microbiota and their effect on the biotransformation of various components of natural products and highlighted the involved common bacteria, reaction types, pharmacological actions, and research methods. This study aims to provide theoretical support for the clinical application in the prevention and treatment of diseases and provide new ideas for studying natural products based on gut biotransformation.

Asymmetric synthesis of (+)-teratosphaerone B, its non-natural analogue and (+)-xylarenone using an ene- and naphthol reductase cascade

Herein, a one-pot bienzymatic cascade containing an ene and a naphthol reductase is developed. It is applied for the synthesis of (+)-(3R,4R)-teratosphaerone B, its non-natural regioisomer in both cis- and trans-forms and (+)-xylarenone by the reduction of chemically synthesized naphthoquinone precursors in high yields (76-92%) and excellent ee (>99%). This work implies similar biosynthetic steps in the formation of the synthesized natural products.

Recent insights into oxidative metabolism of quercetin: catabolic profiles, degradation pathways, catalyzing metalloenzymes and molecular mechanisms

Quercetin is the most abundant polyphenolic flavonoid (flavonol subclass) in vegetal foods and medicinal plants. This dietary chemopreventive agent has drawn significant interest for its multiple beneficial health effects ("polypharmacology") largely associated with the well-documented antioxidant properties. However, controversies exist in the literature due to its dual anti-/pro-oxidant character, poor stability/bioavailability but multifaceted bioactivities, leaving much confusion as to its exact roles in vivo. Increasing evidence indicates that a prior oxidation of quercetin to generate an array of chemical diverse products with redox-active/electrophilic moieties is emerging as a new linkage to its versatile actions. The present review aims to provide a comprehensive overview of the oxidative conversion of quercetin by systematically analyzing the current quercetin-related knowledge, with a particular focus on the complete spectrum of metabolite products, the enzymes involved in the catabolism and the underlying molecular mechanisms. Herein we review and compare the oxidation pathways, protein structures and catalytic patterns of the related metalloenzymes (phenol oxidases, heme enzymes and specially quercetinases), aiming for a deeper mechanistic understanding of the unusual biotransformation behaviors of quercetin and its seemingly controversial biological functions.

Metabolites Analysis of Anti-Myocardial Ischemia Active Components of Saussurea involucrata Based on Gut Microbiota-Drug Interaction

Saussurea involucrata has been reported to have potential therapeutic effects against myocardial ischemia. The pharmacological effects of oral natural medicines may be influenced by the participation of gut microbiota. In this study, we aimed to investigate the bidirectional regulation of gut microbiota and the main components of Saussurea involucrata. We first established a quantitative method for the four main components (chlorogenic acid, syringin, acanthoside B, rutin) which were chosen by fingerprint using liquid chromatography tandem mass spectrometry (LC-MS/MS), and found that gut microbiota has a strong metabolic effect on them. Meanwhile, we identified five major rat gut microbiota metabolites (M1-M5) using liquid chromatography tandem time-of-flight mass spectrometry (LC/MSn-IT-TOF). The metabolic properties of metabolites in vitro were preliminarily elucidated by LC-MS/MS for the first time. These five metabolites of Saussurea involucrata may all have potential contributions to the treatment of myocardial ischemia. Furthermore, the four main components (10 μg/mL) can significantly stimulate intestinal bacteria to produce short chain fatty acids in vitro, respectively, which can further contribute to the effect in myocardial ischemia. In this study, the therapeutic effect against myocardial ischemia of Saussurea involucrata was first reported to be related to the intestinal flora, which can be useful in understanding the effective substances of Saussurea involucrata.

Polyphenol and Tannin Nutraceuticals and Their Metabolites: How the Human Gut Microbiota Influences Their Properties

Nutraceuticals have been receiving increasing attention in the last few years due to their potential role as adjuvants against non-communicable chronic diseases (cardiovascular disease, diabetes, cancer, etc.). However, a limited number of studies have been performed to evaluate the bioavailability of such compounds, and it is generally reported that a substantial elevation of their plasma concentration can only be achieved when they are consumed at pharmacological levels. Even so, positive effects have been reported associated with an average dietary consumption of several nutraceutical classes, meaning that the primary compound might not be solely responsible for all the biological effects. The in vivo activities of such biomolecules might be carried out by metabolites derived from gut microbiota fermentative transformation. This review discusses the structure and properties of phenolic nutraceuticals (i.e., polyphenols and tannins) and the putative role of the human gut microbiota in influencing the beneficial effects of such compounds.

Biotransformation of Liquiritigenin into Characteristic Metabolites by the Gut Microbiota

The bioavailability of flavonoids is generally low after oral administration. The metabolic transformation of flavonoids by the gut microbiota may be one of the main reasons for this, although these metabolites have potential pharmacological activities. Liquiritigenin is an important dihydroflavonoid compound found in Glycyrrhiza uralensis that has a wide range of pharmacological properties, such as antitumor, antiulcer, anti-inflammatory, and anti-AIDS effects, but its mechanism of action remains unclear. This study explored the metabolites of liquiritigenin by examining gut microbiota metabolism and hepatic metabolism in vitro. Using LC-MS/MS and LC/MSⁿ-IT-TOF techniques, three possible metabolites of liquiritigenin metabolized by the gut microbiota were identified: phloretic acid (M3), resorcinol (M4), and M5. M5 is speculated to be davidigenin, which has antitumor activity. By comparing these two metabolic pathways of liquiritigenin (the gut microbiota and liver microsomes), this study revealed that there are three main metabolites of liquiritigenin generated by intestinal bacteria, which provides a theoretical basis for the study of pharmacologically active substances in vivo.

Ene-Reductase: A Multifaceted Biocatalyst in Organic Synthesis

Biocatalysis integrate microbiologists, enzymologists, and organic chemists to access the repertoire of pharmaceutical and agrochemicals with high chemoselectivity, regioselectivity, and enantioselectivity. The saturation of carbon-carbon double bonds by biocatalysts challenges the conventional chemical methodology as it bypasses the use of precious metals (in combination with chiral ligands and molecular hydrogen) or organocatalysts. In this line, Ene-reductases (ERs) from the Old Yellow Enzymes (OYEs) family are found to be a prominent asymmetric biocatalyst that is increasingly used in academia and industries towards unparalleled stereoselective trans-hydrogenations of activated C=C bonds. ERs gained prominence as they were used as individual catalysts, multi-enzyme cascades, and in conjugation with chemical reagents (chemoenzymatic approach). Besides, ERs' participation in the photoelectrochemical and radical-mediated process helps to unlock many scopes outside traditional biocatalysis. These up-and-coming methodologies entice the enzymologists and chemists to explore, expand and harness the chemistries displayed by ERs for industrial settings. Herein, we reviewed the last five year's exploration of organic transformations using ERs.

Novel Catabolic Pathway of Quercetin-3-O-Rutinose-7-O-α-L-Rhamnoside by Lactobacillus plantarum GDMCC 1.140: The Direct Fission of C-Ring

Lychee pulp phenolics (LPP) is mainly catabolized in the host colon, increasing the abundances of Bacteroides and Lactobacillus. Herein, five selected gut microbial strains (Bacteroides uniformis, B. thetaiotaomicron, Lactobacillus rhamnosus, L. plantarum, and L. acidophilus) were separately incubated with LPP to ascertain the specific strains participating in phenolic metabolism and the corresponding metabolites. The results indicated that B. uniformis, L. rhamnosus, and L. plantarum were involved in LPP utilization, contributing to 52.37, 28.33, and 45.11% of LPP degradation after 48 h fermentation, respectively. Unprecedentedly, the metabolic pathway of the major phenolic compound quercetin-3-O-rutinose-7-O-α-L-rhamnoside by L. plantarum, appeared to be the direct fission of C-ring at C2–O1 and C3–C4 bonds, which was proved from the occurrence of two substances with the deprotonated molecule [M–H]⁻ ion at m/z 299 and 459, respectively. Meanwhile, it was fully confirmed that B. uniformis participated in the catabolism of isorhamnetin glycoside and procyanidin B2. In the B. uniformis culture, kaempferol was synthesized through dehydroxylation of quercetin which could be catabolized into alphitonin by L. rhamnosus. Furthermore, LPP metabolites exerted higher antioxidant activity than their precursors and gave clues to understand the interindividual differences for phenolic metabolism by gut microbiota.

Platanus hybrida’s Phenolic Profile, Antioxidant Power, and Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus (MRSA)

Methicillin-resistant S. aureus (MRSA) are a threat to public health as they frequently reveal a multidrug-resistant pattern. Researchers all over the world are on an urgent hunt for new treatments to help fight infections before antibiotics become obsolete, and some natural alternatives, such as polyphenols, have already exhibited therapeutic properties. Therefore, this study aimed to determine the phenolic profile, antioxidant capacity, and antimicrobial activity against MRSA of the leaf, fruit, and stem bark extracts of Platanus hybrida. The polyphenols were extracted with a water/ethanol (20:80) mixture and the methodology included HPLC-DAD, DPPH, FRAP, and CuPRAC. To address this issue from a One Health perspective, the Kirby–Bauer disc diffusion method was performed against nine MRSA strains from three different sources (livestock, wild animals, and humans). Fourteen phenolics were identified and the leaf extract showed the highest phenolic content, followed by the fruit extract. The leaf extract also showed the highest antioxidant capacity while the fruit extract had the lowest antioxidant capacity. Both leaf and fruit extracts inhibited the growth of strains from all sources, while the stem bark extract did not inhibit the growth of human strains. This work highlights the complex chemical composition and the antioxidative and antimicrobial potential of extracts derived from P. hydrida.

New Insights into the Efficacy of Aspalathin and Other Related Phytochemicals in Type 2 Diabetes-A Review

In the pursuit of bioactive phytochemicals as a therapeutic strategy to manage metabolic risk factors for type 2 diabetes (T2D), aspalathin, C-glucosyl dihydrochalcone from rooibos (Aspalathus linearis), has received much attention, along with its C-glucosyl flavone derivatives and phlorizin, the apple O-glucosyl dihydrochalcone well-known for its antidiabetic properties. We provided context for dietary exposure by highlighting dietary sources, compound stability during processing, bioavailability and microbial biotransformation. The review covered the role of these compounds in attenuating insulin resistance and enhancing glucose metabolism, alleviating gut dysbiosis and associated oxidative stress and inflammation, and hyperuricemia associated with T2D, focusing largely on the literature of the past 5 years. A key focus of this review was on emerging targets in the management of T2D, as highlighted in the recent literature, including enhancing of the insulin receptor and insulin receptor substrate 1 signaling via protein tyrosine phosphatase inhibition, increasing glycolysis with suppression of gluconeogenesis by sirtuin modulation, and reducing renal glucose reabsorption via sodium-glucose co-transporter 2. We conclude that biotransformation in the gut is most likely responsible for enhancing therapeutic effects observed for the C-glycosyl parent compounds, including aspalathin, and that these compounds and their derivatives have the potential to regulate multiple factors associated with the development and progression of T2D.

Dysbiosis of human gut microbiome in young-onset colorectal cancer

The incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 310 samples is used to validate the results. Furthermore, species-level and functional analysis are performed by metagenome sequencing using 200 samples. Gut microbial diversity is increased in yCRC. Flavonifractor plautii is an important bacterial species in yCRC, while genus Streptococcus contains the key phylotype in the old-onset colorectal cancer. Functional analysis reveals that yCRC has unique characteristics of bacterial metabolism characterized by the dominance of DNA binding and RNA-dependent DNA biosynthetic process. The random forest classifier model achieves a powerful classification potential. This study highlights the potential of the gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with yCRC.