Experimental studies suggested potential adverse effects of preservative food additives, but epidemiological data are lacking. We aim to investigate associations between exposure to these compounds and type 2 diabetes incidence in the NutriNet-Santé prospective cohort (n = 108,723; 79.2

The relationship between the intestinal microbiota and the mucosal immune system is a key determinant of health in that it plays a pivotal role in managing pathogens and avoiding chronic inflammatory diseases. Diet is a central mediator of this relationship, influencing microbiota composition as well as the function of gut bacteria and host cells. This article will review impacts of the myriad of dietary components capable of influencing the microbiota-immune system interrelationship. Such components include macronutrients, micronutrients, phytochemicals, fibers naturally present in traditional foods as well the array of food additives, including sweeteners, metals, fibers and emulsifiers that are widely incorporated into highly processed foods. We will discuss how presence and/or absence of these food components impacts health-related outcomes in mice, and mechanisms that might underlie these outcomes, including the role of the microbiota therein. We will also discuss emerging approaches to better understand the microbiota-immune system-diet interrelationship, including how they can be leveraged to improve health of humans.

Microbiota-derived metabolites are central mediators between commensal microbes and host immune system at mucosal barrier surfaces. Insights from mouse models have revealed precise molecular mechanisms by which numerous metabolites, including short-chain fatty acids, tryptophan catabolites and bile acid derivatives, regulate epithelial integrity, innate immune tone, and adaptive immunity and tolerance. Parallel studies in humans increasingly confirm these pathways and link metabolite dysregulation to diseases, such as inflammatory bowel disease, asthma, and atopic dermatitis. This review synthesizes current understanding of how microbial metabolites orchestrate gastrointestinal barrier immunity, while also integrating emerging insights into the gut-lung and gut-skin axes. Crucially, we examine these interactions through a developmental lens, highlighting how metabolite exposure during critical early-life "windows of opportunity" shapes long-term immune trajectories. We integrate evidence from experimental models and human data to highlight conserved mechanisms, species-specific divergences, and the therapeutic potential of targeting these metabolic pathways as strategies to promote barrier health and durable immune homeostasis.

Recent years have highlighted the profound influence of the gut microbiota not only on local immunity but also on systemic host physiology. However, the translational potential of findings from preclinical animal models remains limited, in part owing to their microbiomes shaped in the absence of natural environmental cues. To address this gap, we developed a scalable, cost-effective, and reproducible preclinical model of environmental exposure (ENV), in which local soil-derived microbiota colonize laboratory mice. Sustained colonization with environmental microbes, particularly Gram-negative bacteria, was associated with a shift toward local and systemic anti-inflammatory immune responses, supporting the expansion of regulatory T cells (Tregs) and IL-10⁺ innate and adaptive populations. These changes confer protection against colitis, obesity, diabetes, and sepsis, ultimately extending both health span and lifespan. Thus, natural microbial exposure lays the foundation for future studies into microbiota‒host interactions, therapeutic resistance, and the development of more physiologically relevant models for human disease.

Background and Aims The rising incidence of Crohn's disease (CD) in Westernized countries has been linked to changes in diet and increased consumption of food additives, yet the mechanisms by which these factors fuel intestinal inflammation remain unclear. Adherent-invasive Escherichia coli (AIEC), a pathobiont involved in CD pathogenesis, lacks a clear genetic hallmark but exhibits intestinal colonization and virulence traits, raising questions about the evolutionary forces promoting its emergence among select individuals. Here, we investigated how chronic exposure to two common dietary emulsifiers, carboxymethylcellulose (CMC) and polysorbate 80 (P80), along with host inflammation, drives AIEC genomic evolution and pathogenic potential.Methods Wild-type and Il10-deficient mice were monocolonized with AIEC and chronically exposed to CMC, P80, or water. Bacterial isolates were collected and analyzed for genomic diversification, mutations, and phenotype both in vitro and in vivo.Results Emulsifiers accelerated AIEC genomic diversification and selected for mutations linked to increased motility, invasion, and pro-inflammatory activity. Moreover, dietary emulsifier-evolved strains displayed a marked fitness advantage in vivo, outcompeting their counterparts in murine hosts, with the greatest advantage observed when evolution occurred under inflammatory conditions. Notably, evolutionary pathways and phenotypic outcomes were shaped by both emulsifier and the host's inflammatory status, highlighting synergy between diet and host genetics in fostering pro-inflammatory pathobionts.Conclusion These findings provide an evolutionary framework connecting modern dietary habits to the emergence of pathogenic AIEC strains, and underscore the importance of dietary interventions in individuals at risk for inflammatory bowel disease.

Abstract The gut microbiota is central to human health, contributing to nutrient processing, metabolite production and protection against pathogens. Yet it is also an unintended target of antibiotic treatments, particularly after oral administration. Antibiotic exposure can therefore disrupt community structure, leading to dysbiosis and promoting the selection of resistant bacteria. Although studies in patients and animal models have shown that these effects vary markedly between individuals, host-related factors have made it difficult to isolate the specific contribution of the microbiota itself. Here, we used a controlled in vitro gut model (MBRA) to examine how 16 human gut microbiotas from the NutriNet-Santé cohort respond to the widely prescribed β-lactam amoxicillin (AMX). By combining dense temporal sampling, 16S amplicon sequencing and mass spectrometry, we observed highly heterogeneous response trajectories, ranging from near-stable communities to strong but reversible disruptions. These differences were not only reflected in the final magnitude of perturbation, but also in the timing, pace and recovery of microbiota change during treatment. Initial community composition partly structured these responses, as Lachnospiraceae / Bacteroidaceae ratio strongly correlated with perturbation. Dynamic quantification of AMX further showed that microbiotas differed in their capacity to deplete the drug over time, thereby altering the duration of exposure above critical concentration thresholds. Supplementation with clavulanic acid that inhibits β-lactamases confirmed that this process was largely mediated by β-lactamase activity. Finally, microbiotas displaying rapid AMX depletion showed reduced selection of resistant Enterobacteriaceae . Together, our results indicate that both initial community composition and the temporal dynamics of antibiotic inactivation jointly determine microbiota resilience and resistance selection.

The advent of the modern diet - characterized by increased consumption of ultra-processed foods rich in saturated fats and simple sugars, but deficient in fiber and micronutrients - has profoundly altered the biodiversity of the intestinal microbiota. This dysbiosis disrupts the intricate metabolic, immune, and nutritional interactions between the host and its microbiota, leading to significant downstream impacts on human health. Dietary imbalances result in reduced production of beneficial microbial metabolites, increased intestinal permeability, chronic inflammation, and heightened risks of obesity, diabetes, and inflammatory diseases. Conversely, diversified diets rich in fiber, unsaturated fatty acids, and plant-based proteins support a resilient and diverse microbial ecosystem that enhances gut barrier function, immunity, and the synthesis of protective compounds. A deeper understanding of these complex host-microbiota-nutrition interactions can pave the way for preventive and therapeutic strategies targeting the microbiome to promote human health.

BACKGROUND AND AIMS:Host-microbe interactions critically shape cellular metabolism and immune responses. The bacterial siderophore enterobactin (Ent) is known for pilfering iron from the host, but recent evidence suggests that it may also deliver iron to host mitochondria. Its impact on mitochondrial respiration, however, remains poorly understood. Here, we assess the interplay among Ent, iron, and lipocalin-2 (Lcn2, which sequesters Ent) on mitochondrial function. We also examine the effects of the 2, 3-dihydroxybenzoic acid (2, 3-DHBA), the monomeric derivative of Ent, and the mammalian siderophore 2, 5-DHBA in a murine model of colitis. METHODS:Murine bone marrow-derived macrophages (BMDMs) and the human model intestinal epithelial cells (IEC) were treated with Ent, with or without iron or rec-Lcn2, and mitochondrial respiration was assessed via Seahorse XFe96 analyzer. For in vivo study, mice were treated with dextran sulfate sodium (DSS) to induce colitis and administered with 2, 3-DHBA or 2, 5-DHBA. RESULTS:Iron-free Ent impaired mitochondrial oxidative phosphorylation in BMDMs and IEC, as evidenced by reduced ATP production and elevated reactive oxygen species. These effects of Ent were mitigated by iron saturation or upon co-administered with rec-Lcn2. Intriguingly, administration of 2, 3-DHBA, but not 2, 5-DHBA, to mice with DSS-induced colitis attenuated inflammation, increased expression of tight junction proteins, preserved epithelial architecture, and promoted mucosal repair. 2, 3-DHBA treatment also enhanced mitochondrial biogenesis, dynamics, and redox balance. CONCLUSIONS:Ent in its 2, 3-DHBA form confers mucosal protection, despite its inhibitory effects on mitochondrial respiration. These findings suggest that modulating mitochondrial activity, thus reducing cellular metabolism, may be beneficial during colitis and position 2, 3-DHBA as a promising microbiota-derived metabolite for therapeutic intervention in inflammatory bowel disease.

Mono- and dimethyl fumarates are oral fumarate esters widely prescribed for relapsing-remitting multiple sclerosis and psoriasis. While these drugs appear to be effective, their effects on the gut microbiota and their precise bacterial targets remain unclear. In this study, we investigated how these drugs affect bacteria through a chemical modification called succination, where they react with protein thiol groups (-SH), particularly in cysteine residues. Using proteomics, enzymology and microscopy, we show how this post-translational modification disrupts several key bacterial functions and triggers oxidative and protein stress in E.coli. We also found that fumarate esters can be toxic to various gut bacteria in isolated cultures. Notably, our results demonstrate that when bacteria are studied together in microbial communities, the effect of fumarates can change, either weakening or intensifying. Our findings thus shed light on fumarate esters and microbiota interactions and allow identifying new molecular targets of succination relevant to microbiome health. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-10-LABX-62-IBEID Institut Pasteur, https://ror.org/0495fxg12, Groot-21 FUMA

Abstract Microbial dysbiosis is a hallmark of inflammatory bowel diseases (IBD); however, its drivers and impact on disease pathophysiology are poorly understood. Applying neural network-based feature attribution to metabolomics and metagenomics datasets from >5000 individuals, we identified epimerized host derived bile acids (BAs) produced by microbial hydroxysteroid dehydrogenases (HSDHs) as a novel hallmark of IBD-associated dysbiosis. Epimerized BAs reduce FXR activity in intestinal epithelial cells and dampen their production of FGF19, a negative feedback regulator of host-derived bile acid (HBA) production in the liver. Increased HBA levels drive colonic epithelial remodeling by impacting goblet cell maturation and select for HSDH-carrying bacteria that transform bactericidal HBA into less toxic, epimerized forms. Confirming the translational relevance of these findings, we demonstrated that high HBA levels limit fecal microbiota transplant engraftment and show that BA sequestering drugs support microbiome recovery in patients with high HBA levels. Together, we discover that elevated HBAs deplete BA-sensitive commensals and favor the growth of HSDH-encoding pathobionts that disrupt host BA feedback signaling, establishing a causal link between changes in microbial ecology and IBD pathophysiology.

BACKGROUND AND AIMS:Experimental studies suggest that some preservative food additives may exert adverse cardiovascular effects, yet human data are lacking. The associations between exposure to these compounds and incidence of hypertension and cardiovascular diseases (CVD) were investigated in the NutriNet-Santé cohort (France, 2009-2024). METHODS:Dietary intakes were assessed using repeated 24-h dietary records (up to 96), including commercial brands. Exposure to food additives was evaluated through multiple composition databases and ad hoc laboratory assays in food matrices. Associations between cumulative time-dependent exposures to preservative food additives during follow-up and outcomes were characterized using multi-adjusted Cox models. RESULTS:Overall, 112 395 participants were included (78.7% women, mean age 42.8 ± 14.7 years) with a median follow-up of 7.9 years. The sum of total preservatives encompassed 58 substances consumed by at least one participant. Total non-antioxidant preservatives were positively associated with higher incidences of hypertension [n = 5544; hazard ratio (HR) higher vs. lower consumers: 1.29, 95% confidence interval (CI) 1.20-1.39] and CVD (n = 2450; HR 1.16, 95% CI 1.04-1.29), while total antioxidant preservatives were associated with higher incidence of hypertension (HR 1.22, 95% CI 1.13-1.31). Out of the 17 individual preservative food additives consumed by at least 10% of the study population, eight were associated with higher incidence of hypertension and one with higher incidence of CVD, after multiple test correction. CONCLUSIONS:Multiple associations between exposure to preservative food additives widely used in industrial foods and higher incidence of hypertension or CVD were observed in this large prospective cohort. Experimental research is needed to gain insight into underlying mechanisms. If confirmed, these new data call for the re-evaluation of regulations governing the use of these additives to improve consumer protection. TRIAL REGISTRATION:ClinicalTrials.gov NCT03335644.

Objective To investigate potential association between exposure to food colouring additives and type 2 diabetes incidence. Research Design and Methods 108,723 participants (79.2% female, mean age= 42.5 y, SD= 14.6) from the French NutriNet-Santé cohort were followed (2009-2023). Dietary data were assessed using repeated 24h-dietary records, including industrial food brands. Cumulative time-dependent exposure to food additives was evaluated through multiple composition databases and ad-hoc laboratory assays in food matrices. Associations between exposures to food colouring additives (sex-specific tertiles if proportion of exposed participants >2/3, or non-exposed/lower/higher exposed based on sex-specific median otherwise) and type 2 diabetes incidence were assessed using multivariable Cox proportional hazards models. Results 1,131 incident type 2 diabetes cases were diagnosed (median follow-up=8.05 y). After False Discovery Rate correction, intakes of following colours were associated with higher type 2 diabetes incidence: total food colouring additives (hazard ratio [HR]higher versus non/lower consumers (95% CI)= 1.38 [1.17-1.63], p=0.0002), total caramel (1.43 [1.21-1.67], p=0.0002), plain caramel (1.46 [1.26-1.70], p=0.0002), sulphite ammonia caramel (1.30 [1.07-1.59], p= 0.007), total carotene (1.27 [1.08-1.48], p=0.007), carotenoids (1.39 [1.19-1.62], p=0.0002), beta-carotene (1.44 [1.23-1.68], p=0.0002), paprika, capsanthin, and capsorubin (1.26 [1.08-1.46], p=0.004), lutein (1.20 [1.02-1.40], p=0.0002), curcumin (1.49 [1.29-1.73], p=0.0002), cochineal, carminic acid, and carmines (1.27 [1.10-1.48], p=0.003), and anthocyanins (1.40 [1.17-1.68], p=0.0002). Conclusion Several positive associations were observed between exposure to natural synthetic food colouring additives and type 2 diabetes incidence. Further studies are needed to gain insights into underlying mechanisms, and if confirmed, call for re-evaluation of food colouring additives to protect consumer health.

In 1998, Arlette Darfeuille-Michaud, Christel Neut and Jean-Frederic Colombel discovered a novel pathovar of Escherichia coli, adherent and invasive Escherichia coli (AIEC), in the ileum of patients with Crohn's disease (CD), that was genetically distinct from diarrheagenic E. coli, could adhere to and invade intestinal epithelial cells and survive in macrophages. The consistent association between AIEC and CD (approximately 30% across the world), their ability to exploit CD-associated genetic traits, and virulence in preclinical colitis models but not healthy hosts spurred global research to elucidate their pathogenicity. Research focused on integrating AIEC with the microbiome, metabolome, metagenome, host response and the impact of diet and antimicrobials has linked the luminal microenvironment and AIEC metabolism to health and disease. This deeper understanding has led to therapeutic trials and precision medicine targeting AIEC-colonised patients. In November 2023, prominent members of the AIEC research community met to present and discuss the many facets of basic, translational and clinical AIEC fields at 'AIEC: past, present and future' in NYC. This review is a summary of this international meeting highlighting the history of AIEC, knowledge accumulated over the past 25 years about its pathogenic properties and proposes a standardised approach for screening patients for AIEC.

Our study aimed to assess potential associations between food colouring additives and cancer incidence in the French NutriNet-Santé cohort. A total of 105,260 adults (78.3

L’essor de l’alimentation moderne, caractérisée par la consommation accrue de produits dits ultra-transformés, pauvres en fibres et riches en graisses saturées ainsi qu’en sucres simples, bouleverse l’écosystème du microbiote intestinal. Cette altération de la biodiversité microbienne, essentielle à la santé humaine, entraîne des modifications profondes des interactions métaboliques, immunitaires et nutritionnelles entre l’hôte et son microbiote. Une compréhension approfondie de ces relations ouvre la voie à des approches alimentaires préventives et thérapeutiques innovantes. Cette revue présente une synthèse des mécanismes par lesquels les différents composants alimentaires modernes modulent la composition et les fonctions du microbiote intestinal, et discute de leurs conséquences sur le risque de maladies chroniques.

OBJECTIVE:To investigate the association between intake of food additive preservatives and cancer incidence in a large prospective cohort. DESIGN:Prospective cohort. SETTING:French NutriNet-Santé cohort, 2009-23. PARTICIPANTS:105 260 participants (≥15 years) without prevalent cancer who completed at least two 24 hour dietary records at baseline. MAIN OUTCOME MEASURES:Cumulative time dependent intake of preservatives, including those in industrial food brands, assessed using repeated 24 hour dietary records and evaluated through multiple composition databases and ad hoc laboratory assays in food products for the most frequently consumed additive-food pairs. Associations between intake of three categories of preservatives (defined as sex specific thirds if preservative was consumed by at least a third of participants, otherwise defined as non-consumers and lower or higher consumers separated by the sex specific median) and cancer incidence were characterised using multivariable proportional hazards Cox models adjusted for potential confounders. RESULTS:Mean age of participants was 42.0 years (standard deviation (SD 14.5) years), and 78.7% were women. 4226 participants received a diagnosis of incident cancer (mean follow-up 7.57 (SD 4.56) years), comprising 1208 breast, 508 prostate, 352 colorectal, and 2158 other cancers). Higher intakes of several preservatives were associated with higher cancer incidence: total non-antioxidants with overall cancer (hazard ratio for higher v non-consumers or lower consumers 1.16 (95% confidence interval (CI) 1.07 to 1.26); absolute risk of cancer at age 60 years, respectively, 13.3%, 12.1%) and breast cancer (1.22 (1.05 to 1.41); 5.7%, 4.8%); total sorbates, specifically potassium sorbate, with overall cancer (1.14 (1.04 to 1.24); 13.4%, 11.8%) and breast cancer (1.26 (1.07 to 1.49); 5.7%, 4.6%); total sulfites with overall cancer (1.12 (1.02 to 1.24); 13.4%, 11.9%); potassium metabisulfite with overall cancer (1.11 (1.03 to 1.20); 13.5%, 12.0%) and breast cancer (1.20 (1.04 to 1.38); 5.7%, 4.9%); sodium nitrite with prostate cancer (1.32 (1.02 to 1.70); 4.2%, 3.4%); potassium nitrate with overall cancer (1.13 (1.05 to 1.23); 14.0%, 12.0%) and breast cancer (1.22 (1.05 to 1.41); 5.9%, 4.8%); total acetates with overall cancer (1.15 (1.06 to 1.25); 14.3%, 12.2%) and breast cancer (1.25 (1.07 to 1.45); 6.1%, 4.9%); acetic acid with overall cancer (1.12 (1.01 to 1.25); 14.4%, 12.4%); and sodium erythorbate with overall cancer (1.12 (1.04 to 1.22); 13.5%, 11.9%) and breast cancer (1.21 (1.04 to 1.41); 5.7%, 4.8%). 11 of the 17 individually studied preservatives were not associated with cancer incidence. CONCLUSION:Multiple positive associations between intake of preservatives widely used in industrial foods and higher cancer incidence (overall, breast, and prostate) were observed in this large prospective cohort. Epidemiology based on health effect biomarkers and experimental research are needed to gain insight into outcome pathways. If confirmed, these new data call for the re-evaluation of regulations governing the food industry's use of these additives, to improve consumer protection. In the meantime, the findings support recommendations for consumers to favour freshly made, minimally processed foods. TRIAL REGISTRATION:ClinicalTrials.gov NCT03335644.

BACKGROUND:The potential cardiac toxicity of glutamate is debated and has been suggested by some epidemiological and experimental studies. To our knowledge, none have investigated the links between both naturally occurring and food additive glutamate and cardiovascular disease (CVD) risk. OBJECTIVES:Our objective was to assess the associations between intakes of total, food additive, and naturally occurring glutamate and risk of CVD, including cerebrovascular (CVA) and ischemic heart diseases (IHDs), in a large population-based study. METHODS:Participants {n = 108,932, NutriNet-Santé prospective cohort, 2009-2023, France, mean age = 42.4 y [standard deviation (SD) = 14.5], 79.3% females} completed repeated 24-h dietary records [mean = 21 (SD = 18), ≤84], including brands of industrial food consumed. Exposure to food additive glutamate was evaluated through multiple composition databases and ad hoc laboratory assays in food matrices. Associations between time-dependent continuous exposures to total, naturally occurring, and food additive glutamate and risk of CVD, CVA, and IHD were investigated using multivariable Cox models. RESULTS:During follow-up (median = 7.92 y), 2397 CVD, 1113 CVA, and 1284 IHD cases were diagnosed. Higher intakes of food additive glutamate [hazard ratio (HR) per 200 mg/d: 1.05; 95% confidence interval: 1.01, 1.09; P = 0.02], naturally occurring glutamic acid (HR3000 mg/d: 1.13; 95% CI: 1.03, 1.25; P = 0.009), and total glutamate (HR3000 mg/d = 1.15; 95% CI: 1.05, 1.26) P = 0.004) were associated with higher risks of IHD. For CVD, corresponding HRs were 1.03 (1.00, 1.06; P = 0.07), 1.09 (1.01, 1.18; P = 0.02), and 1.10 (1.02, 1.18; P = 0.01). No association was detected for CVA (all P ≥ 0.5). Residual confounding cannot be entirely ruled out, and causality cannot be established based on this single observational study. CONCLUSIONS:This large prospective study showed positive linear associations between higher glutamate intakes and increased risks of CVD. In particular, food additive glutamate, naturally occurring glutamic acid, and total glutamate intakes were all associated with higher IHD risk. This adds to previous experimental data showing a role of glutamate in regulating heart functioning at physiological doses, while also suggesting heart rate dysfunction at higher exposures. This trial was registered at clinicaltrials.gov as NCT03335644.

SUMMARY Food provides nutrients that are selectively absorbed by the intestine, but, at the same time, may contain elements that challenge the intestinal barrier and induce post-prandial inflammation (PPI). How PPI is controlled in order to avoid pathological perturbation of homeostasis remains unclear. Here, we report that during fasting, enterocytes increase their absorptive potential and oxidative metabolism, a program that is largely reversed upon food intake of lipids that perturb the intestinal barrier and induce PPI. Such perturbation is countered by ILC3s, in the absence of which PPI increases, program reversal does not occur, and enterocytes engage into excessive oxidative metabolism. This enterocyte state leads to critical hypoglycemia as a consequence of decreased glucose absorption and increased insulinemia, recapitulating the pathological situation found in patients suffering from intestinal damage and sepsis. We hereby uncover a critical function for ILC3s in maintaining enterocyte homeostasis upon challenging food intake.