INTRODUCTION:Specific foods are associated with abdominal bloating, which can significantly affect quality of life. To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses. METHODS:Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics), and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized before each challenge to identify factors predicting response and after the challenge to elucidate mechanisms underpinning food-induced bloating. RESULTS:Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, 7 (7/39, 17.9%) participants were fructan responders and 8 (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and nonresponders to both challenges, including greater abdominal girth (fructan, P = 0.009; α-GOS, P = 0.030). α-GOS responders had higher breath hydrogen (H 2 ) prechallenge than α-GOS nonresponders ( P = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (prechallenge, adjusted P -value ( P adj) = 0.024; postchallenge, P adj = 0.042) and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders ( P adj = 0.041). DISCUSSION:A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H 2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.

Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome. IMPORTANCE:An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.

The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.

Meta-analyses suggest that yogurt consumption reduces type 2 diabetes incidence in humans, but the molecular basis of these observations remains unknown. Here we show that dietary yogurt intake preserves whole-body glucose homeostasis and prevents hepatic insulin resistance and liver steatosis in a dietary mouse model of obesity-linked type 2 diabetes. Fecal microbiota transplantation studies reveal that these effects are partly linked to the gut microbiota. We further show that yogurt intake impacts the hepatic metabolome, notably maintaining the levels of branched chain hydroxy acids (BCHA) which correlate with improved metabolic parameters. These metabolites are generated upon milk fermentation and concentrated in yogurt. Remarkably, diet-induced obesity reduces plasma and tissue BCHA levels, and this is partly prevented by dietary yogurt intake. We further show that BCHA improve insulin action on glucose metabolism in liver and muscle cells, identifying BCHA as cell-autonomous metabolic regulators and potential mediators of yogurt's health effects.

Background Individual diet components and specific dietary regimens have been shown to impact the gut microbiome. Objectives Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort. Methods Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants. Results Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P <= 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P <= 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P <= 1.2 x 10(-7)), which was better explained by diet than health status. Conclusions We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.

We assessed the utility of representing dietary intake data in hierarchical tree structures that consider relationships among foods. Dietary intake was collected from 1909 adults (≥18 years) using a food frequency questionnaire (FFQ; VioScreen) from the American Gut Project. FFQ food items were formatted into hierarchical tree structures based on 1) USDA's Food Nutrient and Database for Dietary Studies (FNDDS) classifications, 2) nutrient content, and 3) molecular compound information detected via mass spectrometry to capture the non-nutrient composition of foods. Next, we compared how well representing dissimilarities (or distances) between individuals based on their diet corresponded with indices such as the Healthy Eating Index (HEI-2015), when those distances are calculated using tree-based versus non-tree-based metrics. We performed an Adonis test (PERMANOVA) to measure the amount of variation explained (R2) in these diet-based distances by HEI-2015. We observed that dietary ordinations generated using tree-based relationships between foods have better agreement with HEI than ordinations generated without considering relatedness between foods. The variation explained by HEI-2015 increased by 35% when using the FNDDS tree compared to using a non-tree based quantitative metric (Bray-Curtis (not tree-based) R2 = 0.02931 vs. Weighted UniFrac (tree-based) R2 = 0.03969), by >20% when using the nutrient tree (vs. Weighted UniFrac R2 = 0.03627), and only marginally (6%) when using the molecular compound tree (vs. Weighted UniFrac R2 = 0.03116). We show that tree-based measurements of dietary similarity lead to better agreement with diet indices (e.g., HEI) than when relationships among foods are not considered. We also show that representing dietary intake in a tree-like structure can offer interactive visualizations of data that can be used to inform hypotheses regarding dietary characteristics. Danone Nutricia Research.

While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms. Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism. Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms. This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010.

Healthy, plant-based diets, rich in fermentable residues, may induce gas-related symptoms. The aim of this exploratory study was to assess the effects of a fermented milk product, containing probiotics, on the tolerance of a healthy diet in patients with disorders of gut–brain interactions (DGBI), complaining of excessive flatulence. In an open design, a 3-day healthy, mostly plant-based diet was administered to patients with DGBI (52 included, 43 completed) before and at the end of 28 days of consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria. As compared to a habitual diet, the flatulogenic diet increased the perception of digestive symptoms (flatulence score 7.1 ± 1.6 vs. 5.8 ± 1.9; p < 0.05) and the daily number of anal gas evacuations (22.4 ± 12.5 vs. 16.5 ± 10.2; p < 0.0001). FMP consumption reduced the flatulence sensation score (by –1.6 ± 2.2; p < 0.05) and the daily number of anal gas evacuations (by –5.3 ± 8.2; p < 0.0001). FMP consumption did not significantly alter the overall gut microbiota composition, but some changes in the microbiota correlated with the observed clinical improvement. The consumption of a product containing B. lactis CNCM I-2494 improved the tolerance of a healthy diet in patients with DGBI, and this effect may be mediated, in part, by the metabolic activity of the microbiota.

Eating habits have been shown to impact the gut microbiome. Here we aimed to define several types of dietary patterns in a U.S. adult cohort and test their associations with the gut microbiome. Using supervised and unsupervised approaches, we built dietary patterns based on a food frequency questionnaire of the American Gut Project database. Focusing on 1800 adult participants living in the United States, we defined patterns as partitions (groups of participants) or factors (combinations of food variables) driven by specific dietary criteria: fibers, proteins, Healthy Eating Index (HEI 2010), food items, food groups and micronutrients. We then associated these patterns with 16S gut microbiome data for 744 participants, excluding those reporting antibiotic intake in the last year or specific diseases. Analyses were adjusted for age, sex and BMI. Compared to individual features like fibers and proteins, or to factors representing reduced numbers of features, five unsupervised partitions based on food groups were best associated with gut microbiome beta-diversity. Two partitions presented a lower consumption of animal products, with one being almost completely exclusive and the other, close to a flexitarian diet, presenting the best diet quality as measured by HEI. A third one consisted mostly of participants under low carbohydrate diets with nearly no consumption of starchy foods or sweet products. Finally, the last two partitions presented Western-like diets with increased consumption of mixed dishes, sweet products and refined cereals, one of them being more diverse with increased nuts and whole cereals. Gut microbiome alpha-diversity was slightly increased in the flexitarian partition compared to the most westernized one. Strikingly, the low carbohydrate partition was associated with low levels of the Bifidobacterium genus. We showed in a U.S. adult cohort that a global diet may be more associated with gut microbiome variations than individual features like fibers or proteins. Five diet partitions were identified and their specific associations with gut microbiome were studied. These results confirm the importance to consider diet as a whole when studying gut microbiota diversity. Danone Research.

While several studies have documented associations between dietary habits and microbiota composition and function in healthy subjects, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially in relation to symptoms. Here, we used a novel approach that combined data from 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for IBS patients ( N =149) and healthy subjects ( N =52). Paired microbiota and food-based trees allowed to detect new association between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. IBS patients with severe symptoms had a diet enriched in food items of poorer quality, a high abundance of gut microbial enzymes involved in hydrogen metabolism in correlation with animal carbohydrate (mucin/meat-derived) metabolism. Our study provides unprecedented resolution of diet-microbiota-symptom interactions and ultimately paves the way for personalized nutritional recommendations.

Background: Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms. Our aim was to determine the potential of a fermented milk product with probiotics in improving digestive comfort with such diets. Methods: In an open design, a 3-day high-residue diet was administered to healthy subjects (n = 74 included, n = 63 completed) before and following 28 days consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria. Main outcomes: digestive sensations, number of daytime anal gas evacuations, and gas volume evacuated during 4 h after a probe meal. Results: As compared to the habitual diet, the high-residue diet induced gas-related symptoms (flatulence score 4.9 vs. 1.2; p ≤ 0.0001), increased the daily number of anal gas evacuations (20.7 vs. 8.7; p < 0.0001), and impaired digestive well-being (1.0 vs. 3.4; p < 0.05). FMP consumption reduced flatulence sensation (by −1.7 [−1.9; −1.6]; p < 0.0001), reduced the number of daily evacuations (by −5.8 [−6.5; −5.1]; p < 0.0001), and improved digestive well-being (by +0.6 [+0.4; +0.7]; p < 0.05). FMP consumption did not affect the gas volume evacuated after a probe meal. Conclusion: In healthy subjects, consumption of a FMP containing B. lactis CNCM I-2494 and lactic acid bacteria improves the tolerance of a flatulogenic diet by subjective and objective criteria (sensations and number of anal gas evacuations, respectively).

The gut barrier plays an important role in human health. When barrier function is impaired, altered permeability and barrier dysfunction can occur, leading to inflammatory bowel diseases, irritable bowel syndrome or obesity. Several bacteria, including pathogens and commensals, have been found to directly or indirectly modulate intestinal barrier function. The use of probiotic strains could be an important landmark in the management of gut dysfunction with a clear impact on the general population. Previously, we found that Lactobacillus rhamnosus CNCM I-3690 can protect intestinal barrier functions in mice inflammation model. Here, we investigated its mechanism of action. Our results show that CNCM I-3690 can (i) physically maintain modulated goblet cells and the mucus layer and (ii) counteract changes in local and systemic lymphocytes. Furthermore, mice colonic transcriptome analysis revealed that CNCM I-3690 enhances the expression of genes related to healthy gut permeability: motility and absorption, cell proliferation; and protective functions by inhibiting endogenous proteases. Finally, SpaFED pili are clearly important effectors since an L. rhamnosus ΔspaF mutant failed to provide the same benefits as the wild type strain. Taken together, our data suggest that CNCM I-3690 restores impaired intestinal barrier functions via anti-inflammatory and cytoprotective responses.

Background: Basophil activation contributes to inflammatory reactions, especially in allergy. It is controlled, both positively and negatively, by several mechanisms. High-affinity IgE receptors (Fc epsilon RI) generate a mixture of activation and inhibition signals when aggregated, the ratio of which depends on the concentration of allergen recognized by receptor-bound IgE. Low-affinity IgG receptors (Fc gamma RIIA/B) generate inhibition signals when coengaged with Fc epsilon RI by allergen-antibody immune complexes. Commensal and probiotic bacteria, such as Lactobacillus paracasei, generate inhibition signals through still unclear mechanisms. Objective: We sought to investigate whether mechanisms that control, both positively and negatively, basophil activation, which were unraveled and studied in basophils from healthy donors, are functional in allergic patients. Methods: Fc epsilon RI and Fc gamma RIIA/B expression, Fc epsilon RI-dependent activation, FceRI-dependent inhibition, and Fc gamma RIIB-dependent inhibition were examined in blood basophils incubated overnight with or without L paracasei and challenged under 10 experimental conditions. Basophils from healthy donors were compared with basophils from patients who consulted an allergology outpatient clinic over a period of 3 months with respiratory allergy, anaphylaxis antecedents, chronic urticaria, and/or atopic dermatitis. Results: Patients' basophils expressed neither more Fc epsilon RI nor less Fc gamma RIIB than basophils from healthy donors. They were neither hyperreactive to positive regulation nor hyporeactive to negative regulation, irrespective of the receptors or mechanisms involved and the allergic manifestations of the patients. Conclusion: Regulatory mechanisms that control basophil activation are fully functional in allergic patients. Intrinsic defects in these mechanisms do not explain allergic manifestations. Based on these mechanisms, immune checkpoint modifiers can be developed as novel therapeutic tools for allergy.

Analysing correlations between the observed health effects of ingested probiotics and their survival in digestive tract allows adapting their preparations for food. Tracking ingested probiotic in faecal samples requires accurate and specific tools to quantify live vs dead cells at strain level. Traditional culture-based methods are simpler to use but they do not allow quantifying viable but non-cultivable (VBNC) cells and they are poorly discriminant below the species level. We have set up a viable PCR (vPCR) assay combining propidium monoazide (PMA) treatment and either real time quantitative PCR (qPCR) or droplet digital PCR (ddPCR) to quantify a Lactobacillus rhamnosus and two Lactobacillus paracasei subsp. paracasei strains in piglet faeces. Adjustments of the PMA treatment conditions and reduction of the faecal sample size were necessary to obtain accurate discrimination between dead and live cells. The study also revealed differences of PMA efficiency among the two L. paracasei strains. Both PCR methods were able to specifically quantify each strain and provided comparable total bacterial counts. However, quantification of lower numbers of viable cells was best achieved with ddPCR, which was characterized by a reduced lower limit of quantification (improvement of up to 1.76 log(10) compared to qPCR). All three strains were able to survive in the piglets' gut with viability losses between 0.78 and 1.59 log(10)/g faeces. This study shows the applicability of PMA-ddPCR to specific quantification of small numbers of viable bacterial cells in the presence of an important background of unwanted microorganisms, and without the need to set up standard curves. It also illustrates the need to adapt PMA protocols according to the final matrix and target strain, even for closely related strains. The PMA-ddPCR approach provides a new tool to quantify bacterial survival in faecal samples from a preclinical and clinical trial.

INTRODUCTION:The microbiota controls a variety of biological functions, including immunity, and alterations of the microbiota in early life are associated with a higher risk of developing allergies later in life. Several probiotic bacteria, and particularly lactic acid bacteria, were described to reduce both the induction of allergic responses and allergic manifestations. Although specific probiotic strains were used in these studies, their protective effects on allergic responses also might be common for all lactobacilli.METHODS:To determine whether allergic effector cells inhibition is a common feature of lactobacilli or whether it varies among lactobacilli strains, we compared the ability of 40 strains of the same Lactobacillus paracasei species to inhibit IgE-dependent mouse mast cell and human basophil activation.RESULTS:We uncovered a marked heterogeneity in the inhibitory properties of the 40 Lactobacillus strains tested. These segregated into three to four clusters depending on the intensity of inhibition. Some strains inhibited both mouse mast cell and human basophil activation, others strains inhibited only one cell type and another group induced no inhibition of activation for either cell type.CONCLUSIONS:Individual Lactobacillus strains of the same species differentially inhibit IgE-dependent activation of mouse mast cells and human basophils, two cell types that are critical in the onset of allergic manifestations. Although we failed to identify specific bacterial genes associated with inhibition by gene-trait matching analysis, our findings demonstrate the complexity of the interactions between the microbiota and the host. These results suggest that some L. paracasei strains might be more beneficial in allergies than others strains and provide the bases for a rational screening of lactic acid bacteria strains as next-generation probiotics in the field of allergy.

Background Statistical models and scores have been recently suggested to predict remission of type 2 diabetes after bypass surgery, but their relevance in routine clinical practice still needs evaluation. Our objective was to assess these methods on a French cohort and to compare them with other easy-to-use models. Methods We investigated a cohort of 84 diabetic obese subjects who underwent Roux-en-Y gastric bypass surgery. Diabetes remission 1 year after surgery was defined based on the American Diabetes Association criteria. We tested six methods from the literature and four other models to predict remission of diabetes after bypass surgery using pre-operative bioclinical parameters. Predictive methods for diabetes remission were assessed using cross-validation error rates when appropriate. Results Sixty percent of the subjects had diabetes remission. Models from the literature had high error rates in our cohort (from 22.6 to 40.5 %), while published simple scoring systems behaved much better (15.9 and 16.7 %). Using other apprehensible models learned on our cohort did not improve the prediction error (from 17.2 to 19.9 %). Conclusions We showed that the scoring system DiaRem is easy to use and provides the best prediction error (15.9 %) compared to other methods. We additionally propose a DiaRem score threshold of ≤6 for likely remission of a subject 1 year after surgery, which may be considered in clinical decision-making.