Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis.

Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.

Ruminococcoides bili gen. nov., sp. nov., a bile-resistant bacterium from human bile with autolytic behavior.

A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002T, belonging to the family Ruminococcaceae, was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002T, though with average nucleotide identity values below 90 %. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002T is phylogenetically distinct from other species within the genus Ruminococcus. Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002T strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae. Strain IPLA60002T (=DSM 110008T=LMG 31505T) is proposed as the type strain of Ruminococcoides bili.

Interaction of Intestinal Bacteria with Human Rotavirus during Infection in Children.

The gut microbiota has emerged as a key factor in the pathogenesis of intestinal viruses, including enteroviruses, noroviruses and rotaviruses (RVs), where stimulatory and inhibitory effects on infectivity have been reported. With the aim of determining whether members of the microbiota interact with RVs during infection, a combination of anti-RV antibody labeling, fluorescence-activated cell sorting and 16S rRNA amplicon sequencing was used to characterize the interaction between specific bacteria and RV in stool samples of children suffering from diarrhea produced by G1P[8] RV. The genera Ruminococcus and Oxalobacter were identified as RV binders in stools, displaying enrichments between 4.8- and 5.4-fold compared to samples nonlabeled with anti-RV antibodies. In vitro binding of the G1P[8] Wa human RV strain to two Ruminococcus gauvreauii human isolates was confirmed by fluorescence microscopy. Analysis in R. gauvreauii with antibodies directed to several histo-blood group antigens (HBGAs) indicated that these bacteria express HBGA-like substances on their surfaces, which can be the target for RV binding. Furthermore, in vitro infection of the Wa strain in differentiated Caco-2 cells was significantly reduced by incubation with R. gauvreauii. These data, together with previous findings showing a negative correlation between Ruminococcus levels and antibody titers to RV in healthy individuals, suggest a pivotal interaction between this bacterial group and human RV. These results reveal likely mechanisms of how specific bacterial taxa of the intestinal microbiota could negatively affect RV infection and open new possibilities for antiviral strategies.

The gut microbiota, a key to understanding the health implications of micro(nano)plastics and their biodegradation.

The effects of plastic debris on the environment and plant, animal, and human health are a global challenge, with micro(nano)plastics (MNPs) being the main focus. MNPs are found so often in the food chain that they are provoking an increase in human intake. They have been detected in most categories of consumed foods, drinking water, and even human feces. Therefore, oral ingestion becomes the main source of exposure to MNPs, and the gastrointestinal tract, primarily the gut, constantly interacts with these small particles. The consequences of human exposure to MNPs remain unclear. However, current in vivo studies and in vitro gastrointestinal tract models have shown that MNPs of several types and sizes impact gut intestinal bacteria, affecting gut homeostasis. The typical microbiome signature of MNP ingestion is often associated with dysbiosis and loss of resilience, leads to frequent pathogen outbreaks, and local and systemic metabolic disorders. Moreover, the small micro- and nano-plastic particles found in animal tissues with accumulated evidence of microbial degradation of plastics/MNPs by bacteria and insect gut microbiota raise the issue of whether human gut bacteria make key contributions to the bio-transformation of ingested MNPs. Here, we discuss these issues and unveil the complex interplay between MNPs and the human gut microbiome. Therefore, the elucidation of the biological consequences of this interaction on both host and microbiota is undoubtedly challenging. It is expected that microbial biotechnology and microbiome research could help decipher the extent to which gut microorganisms diversify and MNP-determinant species, mechanisms, and enzymatic systems, as well as become important to understand our response to MNP exposure and provide background information to inspire future holistic studies.

Gut Microbiota, an Additional Hallmark of Human Aging and Neurodegeneration.

Gut microbiota represents a diverse and dynamic population of microorganisms harbouring the gastrointestinal tract, which influences host health and disease. Bacterial colonization of the gastrointestinal tract begins at birth and changes throughout life, with age being one of the conditioning factors for its vitality. Aging is also a primary risk factor for most neurodegenerative diseases. Among them, Alzheimers disease (AD) is probably the one where its association with a state of dysbiosis of the gut microbiota has been most studied. In particular, intestinal microbial-derived metabolites have been associated with ß-amyloid formation and brain amyloid deposition, tau phosphorylation, as well as neuroinflammation in AD patients. Moreover, it has been suggested that some oral bacteria increase the risk of developing AD. However, the causal connections among microbiome, amyloid-tau interaction, and neurodegeneration need to be addressed. This paper summarizes the emerging evidence in the literature regarding the link between the oral and gut microbiome and neurodegeneration with a focus on AD. Taxonomic features of bacteria as well as microbial functional alterations associated with AD biomarkers are the main points reviewed. Data from clinical studies as well as the link between microbiome and clinical determinants of AD are particularly emphasized. Further, relationships between gut microbiota and age-dependent epigenetic changes and other neurological disorders are also described. Together, all this evidence suggests that, in some sense, gut microbiota can be seen as an additional hallmark of human aging and neurodegeneration.

Deciphering the interactions between lipids and red wine polyphenols through the gastrointestinal tract.

This paper investigates the mutual interactions between lipids and red wine polyphenols at different stages of the gastrointestinal tract by using the simgi® dynamic simulator. Three food models were tested: a Wine model, a Lipid model (olive oil + cholesterol) and a Wine + Lipid model (red wine + olive oil + cholesterol). With regard to wine polyphenols, results showed that co-digestion with lipids slightly affected the phenolic profile after gastrointestinal digestion. In relation to lipid bioaccessibility, the co-digestion with red wine tended to increase the percentage of bioaccessible monoglycerides, although significant differences were not found (p > 0.05). Furthermore, co-digestion with red wine tended to reduce cholesterol bioaccessibility (from 80 to 49 %), which could be related to the decrease in bile salt content observed in the micellar phase. For free fatty acids, almost no changes were observed. At the colonic level, the co-digestion of red wine and lipids conditioned the composition and metabolism of colonic microbiota. For instance, the growth [log (ufc/mL)] of lactic acid bacteria (6.9 ± 0.2) and bifidobacteria (6.8 ± 0.1) populations were significantly higher for the Wine + Lipid food model respect to the control colonic fermentation (5.2 ± 0.1 and 5.3 ± 0.2, respectively). Besides, the production of total SCFAs was greater for the Wine + Lipid food model. Also, the cytotoxicity of the colonic-digested samples towards human colon adenocarcinoma cells (HCT-116 and HT-29) was found to be significantly lower for the Wine and Wine + Lipid models than for the Lipid model and the control (no food addition). Overall, the results obtained using the simgi® model were consistent with those reported in vivo in the literature. In particular, they suggest that red wine may favourably modulate lipid bioaccessibility - a fact that could explain the hypocholesterolemic effects of red wine and red wine polyphenols observed in humans.

Simulated gastrointestinal digestion of beer using the simgi® model. Investigation of colonic phenolic metabolism and impact on human gut microbiota.

Beer is a source of bioactive compounds, mainly polyphenols, which can reach the large intestine and interact with colonic microbiota. However, the effects of beer consumption in the gastrointestinal function have scarcely been studied. This paper reports, for the first time, the in vitro digestion of beer and its impact on intestinal microbiota metabolism. Three commercial beers of different styles were subjected to gastrointestinal digestion using the simgi® model, and the digested fluids were further fermented in triplicate with faecal microbiota from a healthy volunteer. The effect of digested beer on human gut microbiota was evaluated in terms of microbial metabolism (short-chain fatty acids (SCFAs) and ammonium ion), microbial diversity and bacterial populations (plate counting and 16S rRNA gene sequencing). Monitoring beer polyphenols through the different digestion phases showed their extensive metabolism, mainly at the colonic stage. In addition, a higher abundance of taxa related to gut health, especially Bacteroides, Bifidobacterium, Mitsuokella and Succinilasticum at the genus level, and the Ruminococcaceae and Prevotellaceae families were found in the presence of beers. Regarding microbial metabolism, beer feeding significantly increased microbial SCFA production (mainly butyric acid) and decreased ammonium content. Overall, these results evidence the positive actions of moderate beer consumption on the metabolic activity of colonic microbiota, suggesting that the raw materials and brewing methods used may affect the beer gut effects.

Survival Strategies and Metabolic Interactions between Ruminococcus gauvreauii and Ruminococcoides bili, Isolated from Human Bile.

Little is known about the bacteria that reside in the human gallbladder and the mechanisms that allow them to survive within this harsh environment. Here we describe interactions between two strains from a human bile sample, one Ruminococcus gauvreauii (IPLA60001), belonging to the Lachnospiraceae family, and the other, designated as Ruminococcoides bili (IPLA60002T; DSM 110008) most closely related to Ruminococcus bromii within the family Ruminococcaceae. We provide evidence for bile salt resistance and sporulation for these new strains. Both differed markedly in their carbohydrate metabolism. The R. bili strain mainly metabolized resistant starches to form formate, lactate and acetate. R. gauvreauii mainly metabolized sugar alcohols, including inositol and also utilized formate to generate acetate employing the Wood Ljungdahl pathway. Amino acid and vitamin biosynthesis genomic profiles also differed markedly between the two isolates, likely contributing to their synergistic interactions, as revealed by transcriptomic analysis of cocultures. Transcriptome analysis also revealed that R. gauvreauii IPLA60001 is able to grow using the end-products of starch metabolism formed by the R. bili strain such as formate, and potentially other compounds (such as ethanolamine and inositol) possibly provided by the autolytic behavior of R. bili. IMPORTANCE Unique insights into metabolic interaction between two isolates; Ruminococcus gauvreauii IPLA60001 and Ruminococcoides bili IPLA60002, from the human gallbladder, are presented here. The R. bili strain metabolized resistant starches while R. gauvreauii failed to do so but grew well on sugar alcohols. Transcriptomic analysis of cocultures of these strains, provides new data on the physiology and ecology of two bacteria from human bile, with a particular focus on cross-feeding mechanisms. Both biliary strains displayed marked resistance to bile and possess many efflux transporters, potentially involved in bile export. However, they differ markedly in their amino acid catabolism and vitamin synthesis capabilities, a feature that is therefore likely to contribute to the strong synergistic interactions between these strains. This is therefore the first study that provides evidence for syntrophic metabolic cooperation between bacterial strains isolated from human bile.

Gastrointestinal co-digestion of wine polyphenols with glucose/whey proteins affects their bioaccessibility and impact on colonic microbiota.

Interactions between food components during their gastrointestinal digestion are constant and could affect compounds digestibility and bioaccessibility. These interactions could have a key role in the bioactivity of dietary polyphenols. This study aimed to investigate the food matrix effects during the co-digestion of red wine with glucose and whey proteins using the gastrointestinal dynamic simulator simgi®. Bioaccessibility of wine polyphenols and nutrients and the effect of co-digestion on colonic microbiota composition and metabolism were evaluated. Co-digestion with red wine led to a reduction of over 50% of glucose bioaccessibility and lowered α-lactalbumin gastric degradation. Still, co-digestion with the food matrices modified polyphenols profiles, including their bioaccessible and non-bioaccessible fractions. For instance, the (-)-epicatechin bioaccessible fraction increased 70% when the wine was co-digested with glucose. Hence, the combined feeding of wine and each food matrix affected microbiota composition and functionality at colonic level. Glucose and whey proteins reduced bacterial diversity, but homogenization of beta-diversity by wine was observed. Moreover, wine presence favoured intestinal health-related taxa as Akkermansia or Bifidobacterium, and the co-digestion of wine and food matrices significantly increased total short- and medium-chain fatty acids production, especially butyric acid. Overall, this study provides evidence of the convenience of the simgi® system to evaluate the effects of co-digestion and highlights the importance of food matrix effects on our understanding of polyphenol bioactivity.

PET microplastics affect human gut microbiota communities during simulated gastrointestinal digestion, first evidence of plausible polymer biodegradation during human digestion.

Microplastics (MPs) are a widely recognized global problem due to their prevalence in natural environments and the food chain. However, the impact of microplastics on human microbiota and their possible biotransformation in the gastrointestinal tract have not been well reported. To evaluate the potential risks of microplastics at the digestive level, completely passing a single dose of polyethylene terephthalate (PET) through the gastrointestinal tract was simulated by combining a harmonized static model and the dynamic gastrointestinal simgi model, which recreates the different regions of the digestive tract in physiological conditions. PET MPs started several biotransformations in the gastrointestinal tract and, at the colon, appeared to be structurally different from the original particles. We report that the feeding with microplastics alters human microbial colonic community composition and hypothesize that some members of the colonic microbiota could adhere to MPs surface promoting the formation of biofilms. The work presented here indicates that microplastics are indeed capable of digestive-level health effects. Considering this evidence and the increasing exposure to microplastics in consumer foods and beverages, the impact of plastics on the functionality of the gut microbiome and their potential biodegradation through digestion and intestinal bacteria merits critical investigation.

Polyphenols and Ulcerative Colitis: An Exploratory Study of the Effects of Red Wine Consumption on Gut and Oral Microbiome in Active-Phase Patients.

SCOPE: This paper explores the effects of moderate red wine consumption on the clinical status and symptomatology of patients with ulcerative colitis (UC), including the study of the oral and intestinal microbiome. METHODS AND RESULTS: A case control intervention study in UC patients is designed. Intervention patients (n = 5) consume red wine (250 mL day-1 ) for 4 weeks whereas control patients (n = 5) do not. Moderate wine consumption significantly (p < 0.05) improves some clinical parameters related to serum iron, and alleviates intestinal symptoms as evaluated by the IBDQ-32 questionnaire. 16S rRNA gene sequencing indicate a non-significant (p > 0.05) increase in bacterial alpha diversity after wine intervention in both saliva and fecal microbiota. Additional comparison of taxonomic data between UC patients (n = 10) and healthy subjects (n = 8) confirm intestinal dysbiosis for the UC patients. Finally, analysis of fecal metabolites (i.e., phenolic acids and SCFAs) indicates a non-significant increase (p > 0.05) for the UC patients that consumed wine. CONCLUSIONS: Moderate and regular red wine intake seems to improve the clinical status and symptoms of UC patients in the active phase of the disease. However, studies with a greater sample size are required to achieve conclusive results.

Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter.

Gallbladder metagenome involves a wide range of unidentified sequences comprising the so-called metagenomic dark matter. Therefore, this study aimed to characterise three gallbladder metagenomes and a fosmid library with an emphasis on metagenomic dark matter fraction. For this purpose, a novel data analysis strategy based on the combination of remote homology and molecular modelling has been proposed. According to the results obtained, several protein functional domains were annotated in the metagenomic dark matter fraction including acetyltransferases, outer membrane transporter proteins, membrane assembly factors, DNA repair and recombination proteins and response regulator phosphatases. In addition, one deacetylase involved in mycothiol biosynthesis was found in the metagenomic dark matter fraction of the fosmid library. This enzyme may exert a protective effect in Actinobacteria against bile components exposure, in agreement with the presence of multiple antibiotic and multidrug resistance genes. Potential mechanisms of action of this novel deacetylase were elucidated by molecular simulations, highlighting the role of histidine and aspartic acid residues. Computational pipelines presented in this work may be of special interest to discover novel microbial enzymes which had not been previously characterised.

Effects of Wine and Its Microbial-Derived Metabolites on Intestinal Permeability Using Simulated Gastrointestinal Digestion/Colonic Fermentation and Caco-2 Intestinal Cell Models.

This paper explores the effects of wine polyphenols on intestinal permeability in in vitro conditions. A red wine (2500 mg/L of gallic acid equivalents) was sequentially subjected to gastrointestinal and colonic digestion in the Dynamic Gastrointestinal Simulator (simgi®) to obtain two simulated fluids: intestinal-digested wine (IDW) and colonic-digested wine (CDW). The two fluids were incubated with Caco-2 cell monolayers grown in Transwell® inserts, and paracellular permeability was measured as transport of FITC-dextran. Non-significant decreases (p > 0.05) in paracellular permeability were found, which was attributed to the relatively low phenolic concentration in the solutions tested (15.6 and 7.8 mg of gallic acid equivalents/L for IDW and CDW, respectively) as quercetin (200 µM) and one of its microbial-derived phenolic metabolites, 3,4-dihydroxyphenylacetic acid (200 µM), led to significant decreases (p < 0.05). The expression of tight junction (TJ) proteins (i.e., ZO-1 and occludin) in Caco-2 cells after incubation with IDW and CDW was also determined. A slight increase in mRNA levels for occludin for both IDW and CDW fluids, albeit without statistical significance (p > 0.05), was observed. Analysis of the microbiome and microbial activity during wine colonic fermentation revealed relevant changes in the relative abundance of some families/genera (i.e., reduction in Bacteroides and an increase in Veillonella, Escherichia/Shigella and Akkermansia) as well as in the microbial production of SCFA (i.e., a significant increase in propionic acid in the presence of IDW), all of which might affect paracellular permeability. Both direct and indirect (microbiota-mediated) mechanisms might be involved in the protective effects of (wine) polyphenols on intestinal barrier integrity. Overall, this paper reinforces (wine) polyphenols as a promising dietary strategy to improve gut functionality, although further studies are needed to evaluate the effect on the intestinal barrier under different conditions.

Gastrointestinal Digestion of a Grape Pomace Extract: Impact on Intestinal Barrier Permeability and Interaction with Gut Microbiome.

Grape pomace (GP) is a winemaking by-product rich in polyphenols and fibre. Supplementation with GP extracts has shown potential benefits against oxidative stress- and inflammation-related pathologies. As a new nutritional target, this paper explores the impact of the ingestion of a grape pomace extract on intestinal barrier functionality. A GP extract was sequentially subjected to gastrointestinal and colonic digestion using the dynamic gastrointestinal simulator (simgi®). This generated two simulated fluids: intestinal-digested extract (IDE) and colonic-digested extract (CDE). The effects of these two fluids on paracellular permeability and the expression of tight junction (TJ) proteins (i.e., zonula occludens-1 (ZO-1) and occludin) were assessed in Caco-2-cell monolayers grown in Transwell® inserts. The IDE fluid significantly (p < 0.001) reduced the paracellular transport of FITC-dextran with respect to the control, whereas no significant differences (p > 0.05) were found for CDE, which could be due, at least partially, to the pro-leaky effect of the colonic digestion medium. Accordant slight increases in the mRNA levels of both ZO-1 and occludin were observed for IDE, but without statistical significance. Additionally, the colonic fermentation of the GP extract promoted the production of short-chain fatty acids (SCFA) and phenolic metabolites and led to changes in the relative abundance of some bacteria that might affect paracellular permeability. Overall, this paper reports first trends about the effects of grape pomace extracts on intestinal permeability that would require further confirmation in future experiments.

Intestinal Bacteria Interplay With Bile and Cholesterol Metabolism: Implications on Host Physiology.

Bile is a biological fluid synthesized in the liver, mainly constituted by bile acids and cholesterol, which functions as a biological detergent that emulsifies and solubilizes lipids, thereby playing an essential role in fat digestion. Besides, bile acids are important signaling molecules that regulate key functions at intestinal and systemic levels in the human body, affecting glucose and lipid metabolism, and immune homeostasis. Apart from this, due to their amphipathic nature, bile acids are toxic for bacterial cells and, thus, exert a strong selective pressure on the microbial populations inhabiting the human gut, decisively shaping the microbial profiles of our gut microbiota, which has been recognized as a metabolic organ playing a pivotal role in host health. Remarkably, bacteria in our gut also display a range of enzymatic activities capable of acting on bile acids and, to a lesser extent, cholesterol. These activities can have a direct impact on host physiology as they influence the composition of the intestinal and circulating bile acid pool in the host, affecting bile homeostasis. Given that bile acids are important signaling molecules in the human body, changes in the microbiota-residing bile biotransformation ability can significantly impact host physiology and health status. Elucidating ways to fine-tune microbiota-bile acids-host interplay are promising strategies to act on bile and cholesterol-related disorders. This manuscript summarizes the current knowledge on bile and cholesterol metabolism by intestinal bacteria, as well as its influence on host physiology, identifying knowledge gaps and opportunities to guide further advances in the field.

The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile.

BACKGROUND: The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of adequate methodologies to assess molecular studies. Although a few reports have described the biliary microbiota in some hepatobiliary diseases, the bile microbiota of healthy individuals has not been described. With this in mind, the goal of the present study was to generate fundamental knowledge on the composition and activity of the human bile microbiota, as well as establishing its potential relationship with human bile-related disorders. RESULTS: Human bile samples from the gallbladder of individuals from a control group, without any record of hepatobiliary disorder, were obtained from liver donors during liver transplantation surgery. A bile DNA extraction method was optimized together with a quantitative PCR (qPCR) assay for determining the bacterial load. This allows the selection of samples to perform functional metagenomic analysis. Bile samples from the gallbladder of individuals suffering from lithiasis were collected during gallbladder resection and the microbial profiles assessed, using a 16S rRNA gene-based sequencing analysis, and compared with those of the control group. Additionally, the metabolic profile of the samples was analyzed by nuclear magnetic resonance (NMR). We detected, for the first time, bacterial communities in gallbladder samples of individuals without any hepatobiliary pathology. In the biliary microecosystem, the main bacterial phyla were represented by Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Significant differences in the relative abundance of different taxa of both groups were found. Sequences belonging to the family Propionibacteriaceae were more abundant in bile samples from control subjects; meanwhile, in patients with cholelithiasis members of the families Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, and Veillonellaceae were more frequently detected. Furthermore, the metabolomics analysis showed that the two study groups have different metabolic profiles. CONCLUSIONS: Our results indicate that the gallbladder of human individuals, without diagnosed hepatobiliary pathology, harbors a microbial ecosystem that is described for the first time in this study. Its bacterial representatives and metabolites are different from those detected in people suffering from cholelithiasis. In this regard, since liver donors have been subjected to the specific conditions of the hospital's intensive care unit, including an antibiotic treatment, we must be cautious in stating that their bile samples contain a physiologically normal biliary microbiome. In any case, our results open up new possibilities to discover bacterial functions in a microbial ecosystem that has not previously been explored.

Diet: Cause or Consequence of the Microbial Profile of Cholelithiasis Disease?

Recent dietary habits and lifestyle could explain the shaping of the gut microbiota composition and, in consequence, the increasing prevalence of certain pathologies. However, little attention has been paid to the influence of diet on microbiotas, other than the gut microbiota. This is important in cholelithiasis, given that changes in the production of bile acids may affect gallbladder microbial communities. Our aim was to assess the association between regular dietary intake and gallbladder microbial composition. Fourteen adults with cholelithiasis and 14 controls, sex‒age-matched and without gastrointestinal pathology, were included. Diet was assessed through a food frequency questionnaire and quantification of gallbladder microbiota sequences by Illumina 16S rRNA gene-based analysis. The cholelithiasic patients showed greater intake of potatoes and lower consumption of vegetables, non-alcoholic drinks, and sauces, which resulted in a lower intake of energy, lipids, digestible polysaccharides, folate, calcium, magnesium, vitamin C, and some phenolic compounds. Regarding the altered bile microorganisms in cholelithiasic patients, dairy product intake was negatively associated with the proportions of Bacteroidaceae and Bacteroides, and several types of fiber, phenolics, and fatty acids were linked to the abundance of Bacteroidaceae, Chitinophagaceae, Propionibacteraceae, Bacteroides, and Escherichia‒Shigella. These results support a link between diet, biliary microbiota, and cholelithiasis.