Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria

Discovery of an ene-reductase initiating resveratrol catabolism in gut microbiota and its application in disease treatment

Resveratrol (RSV) is a plant-derived natural compound with multiple biological activities. Upon entering the intestine, RSV undergoes rapid metabolism and transformation by the gut microbiota. In this study, we isolated a bacterium capable of efficiently metabolizing RSV, Eggerthella lenta J01. Through induced enrichment transcriptomics and bioinformatic analyses, we identified an RSV reductase (RER) from E. lenta J01. Using RER structure simulation, site-directed mutagenesis, and biochemical assays, we further determined the key amino acids in RER associated with RSV catalytic activity. Studies in animal models demonstrated that RER enhances RSV's ability to alleviate inflammatory bowel disease. Additionally, bioinformatics analysis revealed that the abundance of the rer gene in the gut microbiota of healthy individuals was higher than in patients with enteritis. Collectively, these findings suggest that the activity of natural products may be modulated by the gut microbiota through metabolic transformations.

Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism

Microbiota-mediated drug metabolism can affect pharmacological efficacy. Here we conducted a systematic comparative metabolomics investigation of drug metabolism modes by evaluating the impacts of human gut commensal bacteria on 127 G-protein-coupled receptor (GPCR)-targeted drugs. For the most extensively metabolized drugs in our screen, we elucidated both conventional and unconventional drug transformations and the corresponding activities of generated metabolites. Comparisons of drug metabolism by a gut microbial community versus individual species revealed both taxon intrinsic and collaborative processes that influenced the activity of the metabolized drugs against target GPCRs. We also observed iloperidone inactivation by generating unconventional metabolites. The human gut commensal bacteria mixture incorporated sulfur in the form of a thiophene motif, whereas Morganella morganii used a cascade reaction to incorporate amino-acid-derived tricyclic systems into the drug metabolites. Our results reveal a broad impact of human gut commensal bacteria on GPCR-targeted drug structures and activities through diverse microbiota-mediated biotransformations.

Catalytic Mechanism of Gut Benzyl Ether Reductase for Efficient Bioconversion of Furofuran Lignans into Enterolignan Precursors

Enterolignan is a vital anticancer compound, and benzyl ether reductase (BER) plays a key role in its biosynthesis by facilitating lignan biotransformation. Using virtual alanine scanning and site-directed mutagenesis, we identified critical residues influencing BER activity in DSM 2243T. Mutations Y214A, K383A, and K395A led to a near-complete loss of enzymatic activity, highlighting their essential roles. Conversely, the E332Y, G393V, and L515A variants demonstrated over a 2-fold increase in catalytic efficiency compared to the wild-type BER. Molecular docking and dynamics simulations revealed that Y214 and K383 are involved in substrate recognition and binding, while K395, functioning as a catalytic base, forms a critical η3 loop (residues 389-396) that regulates the catalytic pocket's size and spatial resistance. In the wild-type BER, this loop moves inward by 5 Å upon substrate binding. However, in the E332Y, G393V, and L515A mutants, the loop shifts outward by 4.8, 6.1, and 5.6 Å, respectively, likely enhancing substrate accommodation and catalytic efficiency. This η3 loop movement also appears to influence hydride transfer from cofactors to pinoresinol, which is a crucial step in the catalytic mechanism. These findings offer valuable insights into BER's catalytic mechanism and lay a foundation for enzyme engineering to optimize enterolignan biomanufacturing.

Enantiocomplementary Gut Bacterial Enzymes Metabolize Dietary Polyphenols

Molybdenum-dependent catechol dehydroxylases in gut Actinobacteria catalyze the removal of para-hydroxyl groups from catechols, a central reaction in the microbial metabolism of polyphenol compounds. However, the substrates of most putative catechol dehydroxylases remain unidentified due to the challenges of obtaining these enzymes from standard heterologous expression systems. In this work, we establish Gordonibacter urolithinfaciens as a versatile bacterial host to express active catechol dehydroxylases. Using this system, we rapidly deorphanize eight previously uncharacterized gut bacterial catechol dehydroxylases that selectively dehydroxylate intermediates in the gut bacterial metabolism of plant-derived catechins and lignans. Unexpectedly, we discover multiple instances of distinct catechol dehydroxylases that have evolved to selectively metabolize individual substrate enantiomers, setting the stage for future efforts to elucidate their mechanisms and evolution. Altogether, these findings greatly increase our knowledge of these metalloenzymes, illustrating the power of bacterial genetics to accelerate enzyme discovery and providing a more complete understanding of transformations relevant to the health benefits of phytochemicals.

Trends in extraction and purification methods of Lignans in plant-derived foods

Lignans are widely used as dietary supplements within health foods. However, excess addition of lignans can induce adverse reactions, therefore, it is necessary to develop rapid, effective, economical, and environmentally friendly extraction and purification methods to enhance lignan extraction efficiency. Recently, the advancement of sample pretreatment has been primarily directed towards the application of novel extraction solvents (e.g., supramolecular solvents) in dispersive liquid-liquid microextraction, the miniaturization of solid-phase extraction, the utilization of innovative adsorbent materials in dispersive solid-phase microextraction and matrix-assisted solid-phase extraction, and the employment of subcritical water extraction technology. Up to now, no systematic review has encompassed these advancements. Consequently, this review provides a comprehensive overview of the extraction and purification methods of lignans from plant-derived foods since 2017, with a particular focus on the application of microextraction technologies and new materials. It also analyzes the advantages and disadvantages of these methods and discusses their future developing trends.

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.

Polyphenol-Derived Microbiota Metabolites and Cardiovascular Health: A Concise Review of Human Studies

Polyphenols, plant-derived secondary metabolites, play crucial roles in plant stress responses, growth regulation, and environmental interactions. In humans, polyphenols are associated with various health benefits, particularly in cardiometabolic health. Despite growing evidence of polyphenols' health-promoting effects, their mechanisms remain poorly understood due to high interindividual variability in bioavailability and metabolism. Recent research highlights the bidirectional relationship between dietary polyphenols and the gut microbiota, which can influence polyphenol metabolism and, conversely, be modulated by polyphenol intake. In this concise review, we summarized recent advances in this area, with a special focus on isoflavones and ellagitannins and their corresponding metabotypes, and their effect on cardiovascular health. Human observational studies published in the past 10 years provide evidence for a consistent association of isoflavones and ellagitannins and their metabotypes with better cardiovascular risk factors. However, interventional studies with dietary polyphenols or isolated microbial metabolites indicate that the polyphenol-gut microbiota interrelationship is complex and not yet fully elucidated. Finally, we highlighted various pending research questions that will help identify effective targets for intervention with precision nutrition, thus maximizing individual responses to dietary and lifestyle interventions and improving human health.

Study of Microbiota Associated to Early Tumors Can Shed Light on Colon Carcinogenesis

An increasingly important role for gut microbiota in the initiation and progression of colorectal cancer (CRC) has been described. Even in the early stages of transformation, i.e., colorectal adenomas, changes in gut microbiota composition have been observed, and several bacterial species, such as pks+Escherichia coli and enterotoxigenic Bacteroides fragilis, have been proposed to drive colon tumorigenesis. In recent years, several strategies have been developed to study mucosa-associated microbiota (MAM), which is more closely associated with CRC development than lumen-associated microbiota (LAM) derived from fecal samples. This review summarizes the state of the art about the oncogenic actions of gut bacteria and compares the different sampling strategies to collect intestinal microbiota (feces, biopsies, swabs, brushes, and washing aspirates). In particular, this article recapitulates the current knowledge on MAM in colorectal adenomas and serrated polyps, since studying the intestinal microbiota associated with early-stage tumors can elucidate the molecular mechanisms underpinning CRC carcinogenesis.

A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children

To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.

Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme

Gut microbial catechol dehydroxylases are a largely uncharacterized family of metalloenzymes that potentially impact human health by metabolizing dietary polyphenols. Here, we use metatranscriptomics (MTX) to identify highly transcribed catechol-dehydroxylase-encoding genes in human gut microbiomes. We discover a prevalent, previously uncharacterized catechol dehydroxylase (Gp Hcdh) from Gordonibacter pamelaeae that dehydroxylates hydrocaffeic acid (HCA), an anti-inflammatory gut microbial metabolite derived from plant-based foods. Further analyses suggest that the activity of Gp Hcdh may reduce anti-inflammatory benefits of polyphenol-rich foods. Together, these results show the utility of combining MTX analysis and biochemical characterization for gut microbial enzyme discovery and reveal a potential link between host inflammation and a specific polyphenol-metabolizing gut microbial enzyme.

Iron-sulfur cluster-dependent enzymes and molybdenum-dependent reductases in the anaerobic metabolism of human gut microbes

Metalloenzymes play central roles in the anaerobic metabolism of human gut microbes. They facilitate redox and radical-based chemistry that enables microbial degradation and modification of various endogenous, dietary, and xenobiotic nutrients in the anoxic gut environment. In this review, we highlight major families of iron-sulfur (Fe-S) cluster-dependent enzymes and molybdenum cofactor-containing enzymes used by human gut microbes. We describe the metabolic functions of 2-hydroxyacyl-CoA dehydratases, glycyl radical enzyme activating enzymes, Fe-S cluster-dependent flavoenzymes, U32 oxidases, and molybdenum-dependent reductases and catechol dehydroxylases in the human gut microbiota. We demonstrate the widespread distribution and prevalence of these metalloenzyme families across 5000 human gut microbial genomes. Lastly, we discuss opportunities for metalloenzyme discovery in the human gut microbiota to reveal new chemistry and biology in this important community.

Microbial transformation of dietary xenobiotics shapes gut microbiome composition

Diet is a major determinant of gut microbiome composition, and variation in diet-microbiome interactions may contribute to variation in their health consequences. To mechanistically understand these relationships, here we map interactions between ∼150 small-molecule dietary xenobiotics and the gut microbiome, including the impacts of these compounds on community composition, the metabolic activities of human gut microbes on dietary xenobiotics, and interindividual variation in these traits. Microbial metabolism can toxify and detoxify these compounds, producing emergent interactions that explain community-specific remodeling by dietary xenobiotics. We identify the gene and enzyme responsible for detoxification of one such dietary xenobiotic, resveratrol, and demonstrate that this enzyme contributes to interindividual variation in community remodeling by resveratrol. Together, these results systematically map interactions between dietary xenobiotics and the gut microbiome and connect toxification and detoxification to interpersonal differences in microbiome response to diet.

Bacterial interactions on nutrient-rich surfaces in the gut lumen

The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.

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.

A comparative study on flaxseed lignan biotransformation through resting cell catalysis and microbial fermentation by β-glucosidase production Lactiplantibacillus plantarum

BACKGROUND

Flax lignan has attracted much attention because of its potential bioactivities. However, the bioavailability of secoisolariciresinol diglucoside (SDG), the main lignan in flaxseed, depends on the bioconversion by the colon bacteria. Lactic acid bacteria (LAB) with β-glucosidase activity has found wide application in preparing bioactive aglycone.

RESULTS

LAB strains with good β-glucosidase activity were isolated from fermented tofu. Their bioconversion of flax lignan extract was investigated by resting cell catalysis and microbial fermentation, and the metabolism of SDG by Lactiplantibacillus plantarum C5 following fermentation was characterized by widely targeted metabolomics. Five L. plantarum strains producing β-glucosidase with broad substrate specificity were isolated and identified, and they all can transform SDG into secoisolariciresinol (SECO). L. plantarum C5 resting cell reached a maximum SDG conversion of 49.19 ± 3.75%, and SECO generation of 21.49 ± 1.32% (0.215 ± 0.013 mm) at an SDG substrate concentration of 1 mM and 0.477 ± 0.003 mm SECO was produced at 4 mm within 24 h. Although sixteen flax lignan metabolites were identified following the fermentation of SDG extract by L. plantarum C5, among them, four were produced following the fermentation: SECO, demethyl-SECO, demethyl-dehydroxy-SECO and isolariciresinol. Moreover, seven lignans increased significantly.

CONCLUSION

Fermentation significantly increased the profile and level of flax lignan metabolites, and the resting cell catalysis benefits from higher bioconversion efficiency and more straightforward product separation. Resting cell catalysis and microbial fermentation of flax lignan extract by the isolated β-glucosidase production L. plantarum could be potentially applied in preparing flax lignan ingredients and fermented flaxseed. © 2024 Society of Chemical Industry.

Rodents consuming the same toxic diet harbor a unique functional core microbiome

Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.S. desert southwest from 20 populations (~ 150 individuals) with differential ingestion of creosote bush and analyzed three gut regions (foregut, cecum, hindgut) using16S sequencing and shotgun metagenomics. In each gut region sampled, we found a distinctive set of microbes in individuals feeding on creosote bush that were more abundant than other ASVs, enriched in creosote feeding woodrats, and occurred more frequently than would be predicted by chance. Creosote core members were from microbial families e.g., Eggerthellaceae, known to metabolize plant secondary compounds and three of the identified core KEGG orthologs (4-hydroxybenzoate decarboxylase, benzoyl-CoA reductase subunit B, and 2-pyrone-4, 6-dicarboxylate lactonase) coded for enzymes that play important roles in metabolism of plant secondary compounds. The results support the hypothesis that the ingestion of creosote bush sculpts the microbiome across all major gut regions to select for functional characteristics associated with the degradation of the PSCs in this unique diet.

Digesting the complex metabolic effects of diet on the host and microbiome

The past 50 years of interdisciplinary research in humans and model organisms has delivered unprecedented insights into the mechanisms through which diet affects energy balance. However, translating these results to prevent and treat obesity and its associated diseases remains challenging. Given the vast scope of this literature, we focus this Review on recent conceptual advances in molecular nutrition targeting the management of energy balance, including emerging dietary and pharmaceutical interventions and their interactions with the human gut microbiome. Notably, multiple current dietary patterns of interest embrace moderate-to-high fat intake or prioritize the timing of eating over macronutrient intake. Furthermore, the rapid expansion of microbiome research findings has complicated multiple longstanding tenets of nutrition while also providing new opportunities for intervention. Continued progress promises more precise and reliable dietary recommendations that leverage our growing knowledge of the microbiome, the changing landscape of clinical interventions, and our molecular understanding of human biology.

Urinary enterolignans and enterolignan-predicting microbial species are favourably associated with liver fat and other obesity markers

Aims: Plant-derived lignans may protect against obesity, while their bioactivity needs gut microbial conversion to enterolignans. We used repeated measures to identify enterolignan-predicting microbial species and investigate whether enterolignans and enterolignan-predicting microbial species are associated with obesity. Methods: Urinary enterolignans, fecal microbiota, body weight, height, and circumferences of the waist (WC) and hips (HC) were repeatedly measured at the baseline and after 1 year in 305 community-dwelling adults in Huoshan, China. Body composition and liver fat [indicated by the controlled attenuation parameter (CAP)] were measured after 1 year. Multivariate-adjusted linear models and linear mixed-effects models were used to analyze single and repeated measurements, respectively. Results: Enterolactone and enterodiol levels were both inversely associated with the waist-to-hip ratio, body fat mass (BFM), visceral fat level (VFL), and liver fat accumulation (all P < 0.05). Enterolactone levels were also associated with lower WC (β = -0.0035 and P = 0.013) and HC (β = -0.0028 and P = 0.044). We identified multiple bacterial genera whose relative abundance was positively associated with the levels of enterolactone (26 genera) and enterodiol (22 genera, all P false discovery rate < 0.05), and constructed the enterolactone-predicting microbial score and enterodiol-predicting microbial score to reflect the overall enterolignan-producing potential of the host gut microbiota. Both these scores were associated with lower body weight and CAP (all P < 0.05). The enterolactone-predicting microbial score was also inversely associated with the BFM (β = -0.1128 and P = 0.027) and VFL (β = -0.1265 and P = 0.044). Conclusion: Our findings support that modulating the host gut microbiome could be a potential strategy to prevent obesity by enhancing the production of enterolignans.

Emerging tools and best practices for studying gut microbial community metabolism

The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.

Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors

Drug efflux transporters are a major determinant of drug efficacy and toxicity. A canonical example is P-glycoprotein (P-gp), an efflux transporter that controls the intestinal absorption of diverse compounds. Despite a rich literature on the dietary and pharmaceutical compounds that impact P-gp activity, its sensitivity to gut microbial metabolites remains an open question. Surprisingly, we found that the cardiac drug-metabolizing gut Actinobacterium Eggerthella lenta increases drug absorption in mice. Experiments in cell culture revealed that E. lenta produces a soluble factor that post-translationally inhibits P-gp ATPase efflux activity. P-gp inhibition is conserved in the Eggerthellaceae family but absent in other Actinobacteria. Comparative genomics identified genes associated with P-gp inhibition. Finally, activity-guided biochemical fractionation coupled to metabolomics implicated a group of small polar metabolites with P-gp inhibitory activity. These results highlight the importance of considering the broader relevance of the gut microbiome for drug disposition beyond first-pass metabolism.

Availability of dietary secoisolariciresinol diglucoside on borderline blood cholesterol level in men: a randomized, parallel, controlled, double-blinded clinical trial

Borderline low-density lipoprotein cholesterol levels (120-139 mg/dl) increase the risk of cardiovascular disease. Therefore, the use of functional dietary nutrients is expected to control blood low-density lipoprotein cholesterol levels. This study aimed to evaluate the effect of dietary secoisolariciresinol diglucoside on blood cholesterol in healthy adults with borderline low-density lipoprotein cholesterol levels. A randomized, parallel, controlled, double-blinded clinical trial was performed for participants with borderline low-density lipoprotein cholesterol levels, for 12 weeks with secoisolariciresinol diglucoside (60 mg/day) or placebo. Lipid profile [low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol/high-density lipoprotein cholesterol ratio, total cholesterol, and triglycerides] and liver disease risk markers were measured at weeks 0, 4, 8, and 12. Analyzing 36 participants in each group revealed a significant interaction between treatment and time, indicating reduced low-density lipoprotein cholesterol (p = 0.049) and total cholesterol (p = 0.020) levels in secoisolariciresinol diglucoside-receiving men but not women. However, no significant differences were observed in other markers regardless of gender. The results suggest that a daily intake of 60 mg of secoisolariciresinol diglucoside lowers low-density lipoprotein cholesterol and total cholesterol levels in men with borderline low-density lipoprotein cholesterol, proposing secoisolariciresinol diglucoside potential as a functional dietary nutrient for cardiovascular disease prevention. This study was registered in the UMIN-CTR database (UMIN000046202).

(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.

The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice

The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis, but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.

Microbial metabolites as modulators of host physiology

The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration

Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.

Exploring the Evolvability of Plant Specialized Metabolism: Uniqueness Out Of Uniformity and Uniqueness Behind Uniformity

The huge structural diversity exhibited by plant specialized metabolites has primarily been considered to result from the catalytic specificity of their biosynthetic enzymes. Accordingly, enzyme gene multiplication and functional differentiation through spontaneous mutations have been established as the molecular mechanisms that drive metabolic evolution. Nevertheless, how plants have assembled and maintained such metabolic enzyme genes and the typical clusters that are observed in plant genomes, as well as why identical specialized metabolites often exist in phylogenetically remote lineages, is currently only poorly explained by a concept known as convergent evolution. Here, we compile recent knowledge on the co-presence of metabolic modules that are common in the plant kingdom but have evolved under specific historical and contextual constraints defined by the physicochemical properties of each plant specialized metabolite and the genetic presets of the biosynthetic genes. Furthermore, we discuss a common manner to generate uncommon metabolites (uniqueness out of uniformity) and an uncommon manner to generate common metabolites (uniqueness behind uniformity). This review describes the emerging aspects of the evolvability of plant specialized metabolism that underlie the vast structural diversity of plant specialized metabolites in nature.

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics

BACKGROUND

Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the backbone of treatment of pouchitis; however, antibiotic-resistant pouchitis develops in 5-10% of those patients. It has been shown that fecal microbiota transplantation (FMT) is an effective treatment for UC, but results for FMT antibiotic-resistant pouchitis are inconsistent.

METHODS

To uncover which metabolic activities were transferred to the recipients during FMT and helped the remission, we performed a longitudinal case study of the gut metatranscriptomes from three patients and their donors. The patients were treated by two to three FMTs, and stool samples were analyzed for up to 140 days.

RESULTS

Reduced expression in pouchitis patients compared to healthy donors was observed for genes involved in biosynthesis of amino acids, cofactors, and B vitamins. An independent metatranscriptome dataset of UC patients showed a similar result. Other functions including biosynthesis of butyrate, metabolism of bile acids, and tryptophan were also much lower expressed in pouchitis. After FMT, these activities transiently increased, and the overall metatranscriptome profiles closely mirrored those of the respective donors with notable fluctuations during the subsequent weeks. The levels of the clinical marker fecal calprotectin were concordant with the metatranscriptome data. Faecalibacterium prausnitzii represented the most active species contributing to butyrate synthesis via the acetyl-CoA pathway. Remission occurred after the last FMT in all patients and was characterized by a microbiota activity profile distinct from donors in two of the patients.

CONCLUSIONS

Our study demonstrates the clear but short-lived activity engraftment of donor microbiota, particularly the butyrate biosynthesis after each FMT. The data suggest that FMT triggers shifts in the activity of patient microbiota towards health which need to be repeated to reach critical thresholds. As a case study, these insights warrant cautious interpretation, and validation in larger cohorts is necessary for generalized applications. In the long run, probiotics with high taxonomic diversity consisting of well characterized strains could replace FMT to avoid the costly screening of donors and the risk of transferring unwanted genetic material. Video Abstract.

Comparative Study on the Absorption and Metabolism of Pinoresinol and Pinoresinol-4-O-β-D-Glucopyranoside in Mice

SCOPE

Lignans are a group of phenolic compounds commonly found in plants, often in the form of glycosides. This study investigates the differences in the digestion, absorption, and metabolism of lignans and their glucosides using pinoresinol (PIN) and pinoresinol-4-O-β-D-glucopyranoside (PMG).

METHODS AND RESULTS

After oral administration mice PIN and PMG with a dose of 0.1 µmol kg-1 . The results showed that the stomach and small intestine rapidly absorbe PIN and PMG in their prototype form. After oral administration of 0.25 h, serum levels of PIN and PMG reach peak values of 61.14 and 52.97 ng mL-1 , respectively. This indicates a faster PIN absorption rate than PMG, likely due to the glycosides attach to the parent compound, with concentrations of 1574.14 and 876.75 ng g-1 , respectively. Pharmacokinetic analysis reveals that PIN has a greater area under the curve and a longer half-life than PMG in serum and liver. Moreover, mice in the PIN group exhibit higher metabolite levels in the serum and liver compared to those in the PMG group.

CONCLUSION

The deglycosylation process that occurs during the pickling of white radish facilitates the absorption and metabolism of the lignans fraction in the body.

The What and Who of Dietary Lignans in Human Health: Special Attention to Estrogen Effects and Safety Evaluation

Lignans are a group of phenolic compounds found in plant-based diets. The human body can obtain lignans through diet, which are then metabolized into enterolignans. The enterolignans have been linked to several health benefits, including anticancer, anti-inflammatory, antioxidant effects, and estrogen effects. This review explores the relationship between the estrogenic effects of lignans and health. This review not only considers the estrogen-like activity of lignans but also discusses the safe dosage of lignans at different life stages. In addition, this review also identified other types of bioactive compounds that can act synergistically with lignans to promote health. Studies have shown that lignan administration during pregnancy and lactation reduces the risk of breast cancer in offspring. Further studies are needed to investigate the estrogenic safety effects of lignan on pregnant women and children. Whether lignans combine with other nutrients in complex food substrates to produce synergistic effects remains to be investigated. This review provides a basis for future studies on the safe dose of lignan and recommended dietary intake of lignan. We believe that the acquired as discussed here has implications for developing dietary therapies that can promote host nutrition and modulate estrogenic diseases.

Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors

BACKGROUND

Adherence to the American Cancer Society (ACS) guidelines of avoiding obesity, maintaining physical activity, and consuming a diet rich in fruits, vegetables, and whole grains is associated with longer survival in colorectal cancer (CRC) survivors. Dietary components of the ACS guidelines may act in part by changing the microbiome, which is implicated in CRC outcomes.

OBJECTIVES

We conducted a pilot cross-sectional study to explore associations between ACS guidelines and the gut microbiome.

METHODS

Stool samples and questionnaires were collected from 28 CRC survivors at the University of California, San Francisco from 2019 to 2020. ACS scores were calculated based on validated questionnaires. Gut microbial community structure from 16S amplicons and gene/pathway abundances from metagenomics were tested for associations with the ACS score and its components using ANOVA and general linear models.

RESULTS

The overall ACS score was not significantly associated with variations in the fecal microbiota. However, fruit and vegetable intake and alcohol intake accounted for 19% (P = 0.005) and 13% (P = 0.01) of variation in the microbiota, respectively. Fruit/vegetable consumption was associated with increased microbial diversity, increased Firmicutes, decreased Bacteroidota, and changes to multiple genes and metabolic pathways, including enriched pathways for amino acid and short-chain fatty acid biosynthesis and plant-associated sugar degradation. In contrast, alcohol consumption was positively associated with overall microbial diversity, negatively associated with Bacteroidota abundance, and associated with changes to multiple genes and metabolic pathways. The other components of the ACS score were not statistically significantly associated with the fecal microbiota in our sample.

CONCLUSIONS

These results guide future studies examining the impact of changes in the intake of fruits, vegetables, and alcoholic drinks on the gut microbiome of CRC survivors.

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. Our culture media formulations, atlas of metabolomics data, and genome-scale metabolic reconstructions form a freely available collection of resources to support further study of the biology of this prevalent gut bacterium.

Decipher enzymes from human microbiota for drug discovery and development

The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.

Challenges and opportunities of strain diversity in gut microbiome research

Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.

Anti-allergic property of dietary phytoestrogen secoisolariciresinol diglucoside through microbial and β-glucuronidase-mediated metabolism

Phytoestrogens play pivotal roles in controlling not only the endocrine system but also inflammatory metabolic disorders. However, the effects of dietary phytoestrogens on allergic diseases and underlying mechanisms remain unclear. In this study, we revealed the unique metabolic conversion of phytoestrogen to exert anti-allergic properties, using an ovalbumin-induced allergic rhinitis mouse model. We found that dietary secoisolariciresinol diglucoside (SDG), a phytoestrogen abundantly present in flaxseed, alleviated allergic rhinitis by the microbial conversion to enterodiol (ED). We also found that ED circulated mainly in the glucuronide form (EDGlu) in blood, and deconjugation of EDGlu to ED aglycone occurred in the nasal passage; this activity was enhanced after the induction of allergic rhinitis, which was mediated by β-glucuronidase. We further found that IgE-mediated degranulation was inhibited by ED aglycone, but not by EDGlu, in a G protein-coupled receptor 30 (GPR30)-dependent manner. These results provide new insights into the anti-allergic properties of phytoestrogens and their metabolism in vivo for the development of novel therapeutic strategies against allergic rhinitis.

Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators

Eggerthella lenta is a prevalent human gut Actinobacterium implicated in drug, dietary phytochemical, and bile acid metabolism and associated with multiple human diseases. No genetic tools are currently available for the direct manipulation of E. lenta. Here, we construct shuttle vectors and develop methods to transform E. lenta and other Coriobacteriia. With these tools, we characterize endogenous E. lenta constitutive and inducible promoters using a reporter system and construct inducible expression systems, enabling tunable gene regulation. We also achieve genome editing by harnessing an endogenous type I-C CRISPR-Cas system. Using these tools to perform genetic knockout and complementation, we dissect the functions of regulatory proteins and enzymes involved in catechol metabolism, revealing a previously unappreciated family of membrane-spanning LuxR-type transcriptional regulators. Finally, we employ our genetic toolbox to study the effects of E. lenta genes on mammalian host biology. By greatly expanding our ability to study and engineer gut Coriobacteriia, these tools will reveal mechanistic details of host-microbe interactions and provide a roadmap for genetic manipulation of other understudied human gut bacteria.

Identification of Human Gut Microbiome Associated with Enterolignan Production

Dietary plant lignans are converted inside the gut to enterolignans enterodiol (ED) and enterolactone (EL), which have several biological functions, and health benefits. In this study, we characterized the gut microbiome composition associated with enterolignan production using data from a cross-sectional study in the Japanese population. We identified enterolignan producers by measuring ED and EL levels in subject's serum using liquid chromatography-tandem mass spectrometry. Enterolignan producers show more abundant proportion of Ruminococcaceae and Lachnospiraceae than non-enterolignan producers. In particular, subjects with EL in their serum had a highly diverse gut microbiome that was rich in Ruminococcaceae and Rikenellaceae. Moreover, we built a random forest classification model to classify subjects to either EL producers or not using three characteristic bacteria. In conclusion, our analysis revealed the composition of gut microbiome that is associated with lignan metabolism. We also confirmed that it can be used to classify the microbiome ability to metabolize lignan using machine learning approach.

Ethanol Extract of Licorice Alleviates HFD-Induced Liver Fat Accumulation in Association with Modulation of Gut Microbiota and Intestinal Metabolites in Obesity Mice

As a traditional Chinese medicine, licorice is often used in functional foods for its health benefits. However, the role of gut microbiota in the efficacy of licorice has not yet been fully elucidated. We hypothesized that the involvement of intestinal flora may be a key link in licorice ethanol extract (LEE)-induced health benefits. The aim of this study was to investigate whether LEE improves hepatic lipid accumulation in obese mice fed a high-fat diet (HFD) and whether the gut microbiota plays a key role in LEE treatment. Male C57BL/6J mice were fed HFD for liver fat accumulation and then treated with LEE. The same experiments were later performed using pseudo-sterile mice to verify the importance of gut flora. Supplementation with LEE improved the obesity profile, lipid profile and liver fat accumulation in HFD mice. In addition, LEE treatment improved intestinal flora dysbiosis caused by HFD in mice, as evidenced by a decrease in the percentage of Firmicutes/Bacteroidetes and an increase in the abundance of known anti-obesity-related bacteria. However, LEE failed to exhibit a therapeutic effect in pseudo-sterile mice. The results of the cellular assay showed that glycyrrhetic acid (GA), the main conversion product of glycyrrhizin (GL), was more effective in reducing fat accumulation and intracellular TG content in hepatocytes compared to GL. In conclusion, our data suggest that LEE attenuates obesity and hepatic fat accumulation in HFD mice, which may be associated with modulating the composition of gut microbiota and the conversion of LLE by the intestinal flora.

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.

Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps

Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 10–15% of the variation observed in the microbiome. Multiple mucosal brushings were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Mucosal aspirate sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 1–4% of the variance in the microbiome. Microbiome composition also enabled the accurate prediction of subject polyp types using Random Forest, which produced an area under curve values of 0.87–0.99. By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, our study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method’s practicality and effect on microbial community composition.

Alternative pathway for dopamine production by acetogenic gut bacteria that O-Demethylate 3-Methoxytyramine, a metabolite of catechol O-Methyltransferase

AIMS

The gut microbiota modulates dopamine levels in vivo, but the bacteria and biochemical processes responsible remain incompletely characterized. A potential precursor of bacterial dopamine production is 3-methoxytyramine (3MT); 3MT is produced when dopamine is O-methylated by host catechol O-methyltransferase (COMT), thereby attenuating dopamine levels. This study aimed to identify whether gut bacteria are capable of reverting 3MT to dopamine.

METHODS AND RESULTS

Human faecal bacterial communities O-demethylated 3MT and yielded dopamine. Gut bacteria that mediate this transformation were identified as acetogens Eubacterium limosum and Blautia producta. Upon exposing these acetogens to propyl iodide, a known inhibitor of cobalamin-dependent O-demethylases, 3MT O-demethylation was inhibited. Culturing E. limosum and B. producta with 3MT afforded increased acetate levels as compared with vehicle controls.

CONCLUSIONS

Gut bacterial acetogens E. limosum and B. producta synthesized dopamine from 3MT. This O-demethylation of 3MT was likely performed by cobalamin-dependent O-demethylases implicated in reductive acetogenesis.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report that gut bacteria can synthesize dopamine by O-demethylation of 3MT. Owing to 3MT being the product of host COMT attenuating dopamine levels, gut bacteria that reverse this transformation-converting 3MT to dopamine-may act as a counterbalance for dopamine regulation by COMT.

Identification and Antibiotic Susceptibility of Eggerthella lenta in Bloodstream Infections

The identification and antibiotic susceptibility of two clinical isolates of Eggerthella lenta from bloodstream infections were determined. This microorganism is rarely pathogenic, and the findings are presented here to promote the detection and awareness of this infection. The bacteria were obtained from one patient with pressure sores and another with a malignant gastric tumor. Smears were prepared, stained, and examined by microscopy. Single colonies were analyzed by Gram staining, MALDI-TOF MS, and the 16S rRNA gene sequencing. Antibiotic sensitivity was assessed by the agar dilution method. The bacilli were found to be Gram-positive, and the MS results showed 99.8% homology with E. lenta. It was confirmed by gene sequencing. Antibiotic susceptibility tests demonstrated that E. lenta was sensitive to piperacillin-tazobactam, ampicillin-sulbactam, imipenem, meropenem, metronidazole, clindamycin, and vancomycin. This study could increase awareness of this rare infection.

Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome

BACKGROUND

The conversion of plant lignans to bioactive enterolignans in the gastrointestinal tract is mediated through microbial processing. The goal of this study was to examine the relationships between lignan intake, plasma enterolactone concentrations, gut microbiome composition, and metabolic risk in free-living male adults.

RESULTS

In 303 men participating in the Men's Lifestyle Validation Study (MLVS), lignan intake was assessed using two sets of 7-day diet records, and gut microbiome was profiled through shotgun sequencing of up to 2 pairs of fecal samples (n = 911). A score was calculated to summarize the abundance of bacteria species that were significantly associated with plasma enterolactone levels. Of the 138 filtered species, plasma enterolactone levels were significantly associated with the relative abundances of 18 species at FDR < 0.05 level. Per SD increment of lignan intake was associated with 20.7 nM (SEM: 2.3 nM) higher enterolactone concentrations among participants with a higher species score, whereas the corresponding estimate was 4.0 nM (SEM: 1.7 nM) among participants with a lower species score (P for interaction < 0.001). A total of 12 plasma metabolites were also significantly associated with these enterolactone-predicting species. Of the association between lignan intake and metabolic risk, 19.8% (95%CI: 7.3%-43.6%) was explained by the species score alone, 54.5% (95%CI: 21.8%-83.7%) by both species score and enterolactone levels, and 79.8% (95%CI: 17.7%-98.6%) by further considering the 12 plasma metabolites.

CONCLUSION

We identified multiple gut bacteria species that were enriched or depleted at higher plasma levels of enterolactone in men. These species jointly modified the associations of lignan intake with plasma enterolactone levels and explained the majority of association between lignan intake and metabolic risk along with enterolactone levels and certain plasma metabolites.

Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity

Eggerthella lenta is an anaerobic, high GC, Gram-positive bacillus commonly found in the human digestive tract that belongs to the class Coriobacteriia of the phylum Actinobacteria. This species has been of increasing interest as an important player in the metabolism of xenobiotics and dietary compounds. However, little is known regarding its susceptibility to bacteriophage predation and how this may influence its fitness. Here, we report the isolation of seven novel E. lenta strains using cefotaxime and ceftriaxone as selective agents. We conducted comparative and pangenome analyses of these strains and those publicly available to investigate the diversity of prophages associated with this species. Prophage gene products represent a minimum of 5.8% of the E. lenta pangenome, comprising at least ten distantly related prophage clades that display limited homology to currently known bacteriophages. All clades possess genes implicated in virion structure, lysis, lysogeny and, to a limited extent, DNA replication. Some prophages utilise tyrosine recombinases and diversity generating retroelements to generate phase variation among targeted genes. The prophages have differing levels of sensitivity to the CRISPR/cas systems of their hosts, with spacers from 44 E. lenta isolates found to target only five out of the ten identified prophage clades. Furthermore, using a PCR-based approach targeting the prophage attP site, we were able to determine that several of these elements can excise from the host chromosome, thus supporting the notion that these are active prophages. The findings of this study provide further insights into the diversity of prophages infecting species of the phylum Actinobacteria.

The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2

Coronavirus disease 2019 (COVID-19) continues to exact a devastating global toll. Ascertaining the factors underlying differential susceptibility and prognosis following viral exposure is critical to improving public health responses. We propose that gut microbes may contribute to variation in COVID-19 outcomes. We synthesise evidence for gut microbial contributions to immunity and inflammation, and associations with demographic factors affecting disease severity. We suggest mechanisms potentially underlying microbially mediated differential susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These include gut microbiome-mediated priming of host inflammatory responses and regulation of endocrine signalling, with consequences for the cellular features exploited by SARS-CoV-2 virions. We argue that considering gut microbiome-mediated mechanisms may offer a lens for appreciating differential susceptibility to SARS-CoV-2, potentially contributing to clinical and epidemiological approaches to understanding and managing COVID-19.

Gut microbiota response to antibiotics is personalized and depends on baseline microbiota

BACKGROUND

The magnitude of microbiota perturbations after exposure to antibiotics varies among individuals. It has been suggested that the composition of pre-treatment microbiota underpins personalized responses to antibiotics. However, this hypothesis has not been directly tested in humans. In this high-throughput amplicon study, we analyzed 16S ribosomal RNA gene sequences of 260 stool samples collected twice weekly from 39 patients with acute leukemia during their ~ 4 weeks of hospitalization for chemotherapy while they received multiple antibiotics.

RESULTS

Despite heavy and sustained antibiotic pressure, microbial communities in samples from the same patient remained more similar to one another than to those from other patients. Principal component mixed effect regression using microbiota and granular antibiotic exposure data showed that microbiota departures from baseline depend on the composition of the pre-treatment microbiota. Penalized generalized estimating equations identified 6 taxa within pre-treatment microbiota that predicted the extent of antibiotic-induced perturbations.

CONCLUSIONS

Our results indicate that specific species in pre-treatment microbiota determine personalized microbiota responses to antibiotics in humans. Thus, precision interventions targeting pre-treatment microbiota may prevent antibiotic-induced dysbiosis and its adverse clinical consequences. Video abstract.

Small Molecule Metabolites at the Host-Microbiota Interface

The trillions of bacteria that constitutively colonize the human gut collectively generate thousands of unique small molecules. These microbial metabolites can accumulate both locally and systemically and potentially influence nearly all aspects of mammalian biology, including immunity, metabolism, and even mood and behavior. In this review, we briefly summarize recent work identifying bioactive microbiota metabolites, the means through which they are synthesized, and their effects on host physiology. Rather than offering an exhaustive list of all known bioactive microbial small molecules, we select a few examples from each key class of metabolites to illustrate the diverse impacts of microbiota-derived compounds on the host. In addition, we attempt to address the microbial logic behind specific biotransformations. Finally, we outline current and emerging strategies for identifying previously undiscovered bioactive microbiota metabolites that may shape human health and disease.

Strategies to achieve significant physiological concentrations of bioactive phytoestrogens in plasma

The benefits to health attributed to the intake of phytoestrogens (PEs) have been demonstrated in previous studies with significant physiological concentrations of bioactive PEs, such as genistein, equol, enterolignans and urolithins in plasma. However, the achievement of high bioactive PE levels in plasma is restricted to a select population group, mainly due to the low intake of plant PEs and/or the absence, or inhibition, of the microbiota capable of producing these bioactive forms. In this study, the intake of plant PEs, the concentration of bioactive PEs in plasma, the ability of the intestinal microbiota to produce bioactive PEs, as well as the different mechanisms used by GRAS bacteria to increase the level of bioactive PEs were evaluated concluding that the use of GRAS bacteria bioactive PE producers and the development of fermented foods enriched in bioactive PEs in addition to a high intake of plant PEs and taking care of the intestinal microbiota, are some of the different strategies to achieve significant physiological concentrations of bioactive PEs in the intestine and, subsequently, in plasma and targets organs which are essential to improve menopausal symptoms or reduce the risk of some pathologies such as breast and colon cancer, or cardiovascular disease.