Isolation and characterization of a novel human intestinal Enterococcus faecium FUA027 capable of producing urolithin A from ellagic acid

Appeal of Urolithins from Synthesis to Biological Activities

Urolithins (Uros), a series of natural polyphenols derived from ellagic acid through gut bacteria metabolism, have gathered significant attention due to their diverse bioactivities such as maintaining mitochondrial health and anti-inflammatory and antioxidative effects. However, the ability to metabolize Uros varies among individuals. This Review provides a comprehensive insight into the synthesis, encapsulation and bioactivities of Uros, focusing on their biotransformation in vivo. We highlight the critical role of gut microbiota in the biotransformation of urolithins, including primary bacterial species such as Gordonibacter urolithinfaciens, Enterocloster bolteae and Enterococcus faecium. Furthermore, the therapeutic potential of Uros in alleviating neurodegenerative diseases, cancer, and Duchenne muscular dystrophy is discussed. Finally, several encapsulation strategies for enhancing the solubility and bioavailability of Uros are summarized. Future research direction includes identifying key genes involved in Uros biotransformation, elucidating the bioactive mechanisms of Uros, and improving their bioavailability. In conclusion, we synthesized biosynthetic pathways and bioactive properties of Uros for better utilization in health management.

Ellagic Acid and Gut Microbiota: Interactions, and Implications for Health

Ellagic acid (EA), a widely distributed natural polyphenolic acid existing in many kinds of plant-based foods, undergoes complex physical and chemical transformations during digestion and biotransformation. Particularly, EA is metabolized by gut microbiota and transformed into urolithins in the colon. These metabolites exhibit enhanced bioavailability and bioactivity. This review explores the intricate interactions between EA and gut microbiota, emphasizing their implications for human health. We discuss the role of gut microbiota in EA metabolism, resulting in distinct metabolic phenotypes associated with varying urolithin production profiles. EA and its gut-derived metabolites, urolithins, have been reported to have the potential to modulate the microbial community composition and function of gut microbiota, promoting beneficial bacteria while reducing harmful ones. Furthermore, EA and urolithins exhibit a spectrum of beneficial biological activities, including antioxidant, anti-inflammatory, and anticancer properties, along with enhancements to intestinal barrier function and modulatory effects on metabolic and cardiovascular systems, through molecular mechanisms such as activating Nrf2 and inhibiting NF-κB pathways. The review highlights and compares the potential of EA and its gut microbial metabolites in the prevention and treatment of various diseases. However, further studies are required to elucidate the underlying mechanisms of the interactions between EA and gut microbiota and their health benefits. Continued investigation into EA and its metabolites is essential for advancing our understanding of their role in promoting human health and developing novel therapeutic applications.

Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species

Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.

Berberine Degradation Characteristics and its Degradation Pathway by a Newly Isolated Berberine-Utilizing Agrobacterium

Berberine (BBR) is widely used as a botanical pesticide due to its broad-spectrum antibacterial and antifungal activities. However, BBR degradation pathway in soil microorganisms, which determines its impact on soil environment, remains poorly understood. Herein, a novel BBR-degrading bacterium Agrobacterium sp. V1 was isolated and characterized. Agrobacterium sp. V1 was able to utilize BBR as the sole carbon source for cell growth, and 50 μg/mL of BBR was completely degraded within 48 h. To reveal the possible BBR degradation pathway, whole genome sequencing of Agrobacterium sp. V1 was conducted, and proteins in Agrobacterium sp. V1 were aligned with enzymes involved in BBR biosynthesis in Rhizoma Coptidis. The results indicated that more than 60% of enzymes in BBR biosynthesis pathway had orthologs in Agrobacterium sp. V1. Combined with the primary mass spectra of BBR metabolites, a novel BBR degradation pathway in this bacterium was proposed. In summary, the proposed BBR degradation pathway offered new insights into the impact of BBR to the environment and also provided a reference for studying BBR metabolism in microorganisms.

(Poly)phenol-related gut metabotypes and human health: an update

Dietary (poly)phenols have received great interest due to their potential role in the prevention and management of non-communicable diseases. In recent years, a high inter-individual variability in the biological response to (poly)phenols has been demonstrated, which could be related to the high variability in (poly)phenol gut microbial metabolism existing within individuals. An interplay between (poly)phenols and the gut microbiota exists, with (poly)phenols being metabolised by the gut microbiota and their metabolites modulating gut microbiota diversity and composition. A number of (poly)phenol metabolising phenotypes or metabotypes have been proposed, however, potential metabotypes for most (poly)phenols have not been investigated, and the relationship between metabotypes and human health remains ambiguous. This review presents updated knowledge on the reciprocal interaction between (poly)phenols and the gut microbiome, associated gut metabotypes, and subsequent impact on human health.

In vitro conversion of ellagic acid to urolithin A by different gut microbiota of urolithin metabotype A

The metabolite urolithin A, a metabolite of the dietary polyphenol ellagic acid (EA), has significant health benefits for humans. However, studies on the gut microbiota involved in ellagic acid metabolism are limited. In this study, we conducted in vitro fermentation of EA using human intestinal microbiome combined with antibiotics (vancomycin, polymyxin B sulfate, and amphotericin B). Liquid chromatography-mass spectrometry (LC-MS/MS) analysis demonstrated that the production capacity of urolithin A by gut microbiota co-treated with polymyxin B sulfate and amphotericin B (22.39 µM) was similar to that of untreated gut microbiota (24.26 µM). Macrogenomics (high-throughput sequencing) was used to analyze the composition and structure of the gut microbiota. The results showed that the abundance of Bifidobacterium longum, Bifidobacterium adolescentis, and Bifidobacterium bifidum in the gut microbiota without antibiotic treatment or co-treated with polymyxin B sulfate and amphotericin B during EA fermentation was higher than that in other antibiotic treatment gut microbiota. Therefore, B. longum, B. adolescentis, and B. bifidum may be new genera involved in the conversion of EA to urolithin A. In conclusion, the study revealed unique interactions between polyphenols and gut microbiota, deepening our understanding of the relationship between phenolic compounds like EA and the gut microbiota. These findings may contribute to the development of gut bacteria as potential probiotics for further development. KEY POINTS: • Intestinal microbiome involved in ellagic acid metabolism. • Gram-positive bacteria in the intestinal microbiome are crucial for ellagic acid metabolism. • Bifidobacterium longum, Bifidobacterium adolescentis, and Bifidobacterium bifidum participate in ellagic acid metabolism.

Improvement of Urolithin A Yield by In Vitro Cofermentation of Streptococcus thermophilus FUA329 with Human Gut Microbiota from Different Urolithin Metabotypes

Streptococcus thermophilus FUA329 converts ellagic acid (EA) to urolithin A (Uro-A), which is not autonomously converted by the gut microbiota to produce highly bioavailable and multibiologically active Uro-A in urolithin metabotype 0 (UM-0) populations. We consider that Streptococcus thermophilus FUA329 has the potential to be developed as a probiotic. Therefore, we utilized S. thermophilus FUA329 for in vitro cofermentation with gut microbiota. The results revealed that strain FUA329 increased the production of EA-converted Uro-A during in vitro cofermentation with the human gut microbiota of different urolithin metabotypes (UMs), with a significant increase in the production of Uro-A in the experimental group of UM-0. In addition, changes in the in vitro cofermentation microbial community were determined using high-throughput sequencing. Strain FUA329 modulated the structure and composition of the gut microbiota in different UMs, thereby significantly increasing the abundance of beneficial microbiota in the gut microbiota while decreasing the abundance of harmful microbiota. Of greatest interest was the significant increase in the abundance of Actinobacteria phylum after the cofermentation of strain FUA329 with UM-0 gut microbiota, which might be related to the significant increase in the production of Uro-A.

Genomic and phenotypic-based safety assessment and probiotic properties of Streptococcus thermophilus FUA329, a urolithin A-producing bacterium of human milk origin

Streptococcus thermophilus FUA329, a urolithin A-producing bacterium, is isolated from human breast milk. The complete genome sequence of FUA329 did not contain any plasmids and at least 20 proteins were related to extreme environment resistance. Phenotypic assay results demonstrated that FUA329 was susceptible to 12 kinds of antibiotics and did not exhibit any hemolytic or nitrate reductase activity. Three free radical scavenging assays revealed that FUA329 have high antioxidant capability. FUA329 exhibited a cell surface hydrophobicity of 52.58 ± 1.17% and an auto-aggregation rate of 18.69 ± 2.48%. Moreover, FUA329 demonstrated a survival rate of over 60% in strong acid and bile salt environments, indicating that FUA329 may be stable colonization in the gastrointestinal tract. Additionally, we firstly found 3 potential proteins and 11 potential genes of transforming ellagic acid to urolithins in FUA329 genome. The above results indicate that FUA329 has credible safety and probiotic properties, as well as the potential to be developed as a new generation of urolithin A-producing probiotics.

Pharmacological Effects of Urolithin A and Its Role in Muscle Health and Performance: Current Knowledge and Prospects

Urolithin A (UA) is a naturally occurring compound derived from the metabolism of gut microbiota, which has attracted considerable research attention due to its pharmacological effects and potential implications in muscle health and performance. Recent studies have demonstrated that Urolithin A exhibits diverse biological activities, encompassing anti-inflammatory, antioxidant, anti-tumor, and anti-aging properties. In terms of muscle health, accumulating evidence suggests that Urolithin A may promote muscle protein synthesis and muscle growth through various pathways, offering promise in mitigating muscle atrophy. Moreover, Urolithin A exhibits the potential to enhance muscle health and performance by improving mitochondrial function and regulating autophagy. Nonetheless, further comprehensive investigations are still warranted to elucidate the underlying mechanisms of Urolithin A and to assess its feasibility and safety in human subjects, thereby advancing its potential applications in the realms of muscle health and performance.

A Review of Gut Microbiota-Derived Metabolites in Tumor Progression and Cancer Therapy

Gut microbiota-derived metabolites are key hubs connecting the gut microbiome and cancer progression, primarily by remodeling the tumor microenvironment and regulating key signaling pathways in cancer cells and multiple immune cells. The use of microbial metabolites in radiotherapy and chemotherapy mitigates the severe side effects from treatment and improves the efficacy of treatment. Immunotherapy combined with microbial metabolites effectively activates the immune system to kill tumors and overcomes drug resistance. Consequently, various novel strategies have been developed to modulate microbial metabolites. Manipulation of genes involved in microbial metabolism using synthetic biology approaches directly affects levels of microbial metabolites, while fecal microbial transplantation and phage strategies affect levels of microbial metabolites by altering the composition of the microbiome. However, some microbial metabolites harbor paradoxical functions depending on the context (e.g., type of cancer). Furthermore, the metabolic effects of microorganisms on certain anticancer drugs such as irinotecan and gemcitabine, render the drugs ineffective or exacerbate their adverse effects. Therefore, a personalized and comprehensive consideration of the patient's condition is required when employing microbial metabolites to treat cancer. The purpose of this review is to summarize the correlation between gut microbiota-derived metabolites and cancer, and to provide fresh ideas for future scientific research.

Genetic and Probiotic Characteristics of Urolithin A Producing Enterococcus faecium FUA027

Enterococcus faecium FUA027 transforms ellagic acid (EA) to urolithin A (UA), which makes it a potential application in the preparation of UA by industrial fermentation. Here, the genetic and probiotic characteristics of E. faecium FUA027 were evaluated through whole-genome sequence analysis and phenotypic assays. The chromosome size of this strain was 2,718,096 bp, with a GC content of 38.27%. The whole-genome analysis revealed that the genome contained 18 antibiotic resistance genes and seven putative virulence factor genes. E. faecium FUA027 does not contain plasmids and mobile genetic elements (MGEs), and so the transmissibility of antibiotic resistance genes or putative virulence factors should not occur. Phenotypic testing further indicated that E. faecium FUA027 is sensitive to clinically relevant antibiotics. In addition, this bacterium exhibited no hemolytic activity, no biogenic amine production, and could significantly inhibit the growth of the quality control strain. In vitro viability was >60% in all simulated gastrointestinal environments, with good antioxidant activity. The study results suggest that E. faecium FUA027 has the potential to be used in industrial fermentation for the production of urolithin A.

Effect of urolithin A on the improvement of vascular endothelial function depends on the gut microbiota

Background

Urolithin A (UA) is a metabolite produced by gut microbiota from ingested ellagic acid. Although the effect of ellagic acid intake on vascular endothelial function (VEF) improvement has been reported, the effect of UA intake on VEF improvement remains obscure. In addition, UA has been reported to improve the intestinal barrier function, and UA may have improved VEF by gut microbiome alteration.

Objective

In this study, we conducted a clinical trial to explore and analyze the effects of UA intake on vascular endothelial function (VEF) and characteristics of the intestinal environment, such as gut microbiome profiling and organic acid composition.

Methods

A placebo-controlled, randomized, double-blinded, parallel group trial was conducted on participants who could metabolize small amounts of UA from ellagic acid (non-UA producers) and had relatively poor VEF. VEF was assessed using the flow-mediated vasodilatation (FMD) score. Participants were administered placebo, UA 10 mg/day, or UA 50 mg/day for 12 weeks. FMD was measured and fecal samples were collected at 0, 4, 8, and 12 weeks of treatment. Gut microbiome analysis and organic acid level measurements were performed to evaluate the effects of UA intake on the intestinal environment. This clinical trial is publicly registered at the UMIN-CTR, trial number: UMIN000042014.

Results

The gut microbiota of the UA 50 mg/day group showed a significant increase in alpha diversity (Faith's phylogenetic diversity). Four and nine microbial genera were significantly altered in the UA 10 mg/day and UA 50 mg/day groups, respectively (p < 0.05, not corrected). Participants whose FMD scores improved with UA intake had poor baseline FMD values as well as a low Bacillota/Bacteroidota ratio.

Conclusion

Urolithin A intake alters the gut microbiota and improves their alpha diversity. In addition, the effect of UA on VEF correlated with the individual gut microbiota. Our results have practical implications for a new approach to providing healthcare that focuses on intestinal environment-based diet therapy.