Search Results (15)

Celiac disease (CeD) is a chronic, immune-mediated enteropathy triggered by dietary gluten in genetically susceptible individuals, with environmental and epigenetic factors also contributing to its pathogenesis. Once considered a rare pediatric malabsorptive disorder, CeD is now recognized as a systemic condition that can manifest with both gastrointestinal and extraintestinal symptoms across the lifespan. Although strict adherence to a gluten-free diet (GFD) remains the cornerstone of treatment, up to 30–40% of patients experience persistent symptoms and/or ongoing mucosal injury despite reported compliance. This therapeutic gap, combined with advances in molecular understanding of disease mechanisms, has driven the development of novel strategies targeting key pathogenic pathways. Intraluminal interventions include gluten-degrading enzymes and gluten-sequestering agents, while other approaches target tissue transglutaminase 2, induce antigen-specific immune tolerance, or modulate cytokine-driven inflammation, with particular emphasis on interleukin-15 (IL-15) signaling. Additional strategies aim to inhibit lymphocyte trafficking to the intestinal mucosa and enhance intestinal barrier function through zonulin modulation. Adjunctive therapies under investigation include nutraceuticals, microbiota-targeted interventions, and vaccine-based approaches. More recently, advanced experimental and computational platforms, such as human intestinal organoids, organ-on-chip systems, and machine learning–driven analytics, are being leveraged in efforts to accelerate translational research and support the rational design of precision medicine approaches. This narrative review synthesizes current evidence for therapies beyond the GFD, examines challenges in clinical implementation, and discusses how technological innovations may reshape the future therapeutic landscape of CeD. Full article

Background: The interaction between probiotics and the vitamin D/vitamin D receptor (VDR) pathway has been increasingly explored as a potential mechanism for immune modulation in inflammatory bowel disease (IBD). Lactobacillus rhamnosus GG (LGG) has shown promising results in ulcerative colitis (UC) patients, but its effect on the VDR pathway remains unexplored in humans. Aim: To test the hypothesis that LGG can stimulate the vitamin D/VDR pathway and modulate mucosal-adherent microbiota. Methods: In this study, we analyzed a subgroup of 13 patients from the LGGinUC trial, in which UC patients with mild-to-moderate disease activity received LGG monotherapy for four weeks. Colonic biopsy samples were collected before and after treatment to evaluate VDR expression via RT-qPCR and immunohistochemistry. Mucosal-adherent microbiota was also analyzed by DNA extraction and next-generation sequencing (NGS). Results: LGG administration significantly increased VDR mRNA expression in colonic mucosa (p < 0.05), with a corresponding rise in VDR protein levels in both epithelial and sub-epithelial compartments. Microbiota analysis revealed a reduction in α-diversity, primarily due to a decrease in commensal bacterial species, while β-diversity remained largely unchanged. Conclusions: Although the present results have to be considered preliminary, this is the first human study demonstrating that probiotic supplementation can upregulate VDR expression in colonic mucosa. We propose that LGG may exert its beneficial effects in UC by stimulating the VDR pathway, which in turn modulates mucosal immunity and microbiota composition. Further studies with larger sample sizes and longer treatment durations are needed to validate these findings and explore their therapeutic implications. Full article

The increasing interest in fermented foods stems from their health benefits, mediated by foodborne microorganisms. This study aimed to characterize the fermentative microbiota of Pecorino di Picinisco, a traditional Italian cheese made from ovine raw milk, and to evaluate the probiotic and technological potential of selected lactic acid bacteria strains. Three strains representative of the different species found (Lactococcus lactis, Lactiplantibacillus plantarum and Latilactobacillus curvatus) were chosen and analyzed. All three strains were able to adhere to human intestinal Caco-2 cells, were resistant to simulated in vitro digestion and significantly prolonged the lifespan of Caenorhabditis elegans, used as a simplified in vivo model, with respect to the commercial probiotic strain Lacticaseibacillus rhamnosus GG. The L. plantarum Pic37.4 strain was particularly promising; therefore, its cell-free supernatant was employed to evaluate the antimicrobial activity against indicator strains of foodborne and intestinal pathogens or spoilage bacteria. The results demonstrated the effectiveness of the supernatant against all strains tested, with the strongest effect on the intestinal pathogen enterotoxigenic Escherichia coli K88. In addition, the inhibitory effect on pathogen adhesion to intestinal mucosa was investigated on Caco-2 cells, resulting in a significant reduction in adhesion mediated by the L. plantarum Pic37.4 supernatant. The antimicrobial properties of the L. plantarum strain were confirmed in vivo in C. elegans. These promising results lay the ground for further investigations aimed at substantiating the probiotic and technological potential of the L. plantarum Pic37.4 investigated in this work. Full article

Background: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota. Methods: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance. Results: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides. Conclusions: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota. Full article

In vitro models for culturing complex microbial communities are progressively being used to study the effects of different factors on the modeling of in vitro-cultured microorganisms. In previous work, we validated a 3D in vitro model of the human gut microbiota based on electrospun gelatin scaffolds covered with mucins. The aim of this study was to evaluate the effect of Bacillus cereus, a pathogen responsible for food poisoning diseases in humans, on the gut microbiota grown in the model. Real-time quantitative PCR and 16S ribosomal RNA-gene sequencing were performed to obtain information on microbiota composition after introducing B. cereus ATCC 14579 vegetative cells or culture supernatants. The adhesion of B. cereus to intestinal mucins was also tested. The presence of B. cereus induced important modifications in the intestinal communities. Notably, levels of Proteobacteria (particularly Escherichia coli), Lactobacillus, and Akkermansia were reduced, while abundances of Bifidobacterium and Mitsuokella increased. In addition, B. cereus was able to adhere to mucins. The results obtained from our in vitro model stress the hypothesis that B. cereus is able to colonize the intestinal mucosa by stably adhering to mucins and impacting intestinal microbial communities as an additional pathogenetic mechanism during gastrointestinal infection. Full article

The intestinal mucus lines the luminal surface of the intestinal epithelium. This mucus is a dynamic semipermeable barrier and one of the first-line defense mechanisms against the outside environment, protecting the body against chemical, mechanical, or biological external insults. At the same time, the intestinal mucus accommodates the resident microbiota, providing nutrients and attachment sites, and therefore playing an essential role in the host–pathogen interactions and gut homeostasis. Underneath this mucus layer, the intestinal epithelium is organized into finger-like protrusions called villi and invaginations called crypts. This characteristic 3D architecture is known to influence the epithelial cell differentiation and function. However, when modelling in vitro the intestinal host–pathogen interactions, these two essential features, the intestinal mucus and the 3D topography are often not represented, thus limiting the relevance of the models. Here we present an in vitro model that mimics the small intestinal mucosa and its interactions with intestinal pathogens in a relevant manner, containing the secreted mucus layer and the epithelial barrier in a 3D villus-like hydrogel scaffold. This 3D architecture significantly enhanced the secretion of mucus. In infection with the pathogenic adherent invasive E. coli strain LF82, characteristic of Crohn’s disease, we observed that this secreted mucus promoted the adhesion of the pathogen and at the same time had a protective effect upon its invasion. This pathogenic strain was able to survive inside the epithelial cells and trigger an inflammatory response that was milder when a thick mucus layer was present. Thus, we demonstrated that our model faithfully mimics the key features of the intestinal mucosa necessary to study the interactions with intestinal pathogens. Full article

Celiac disease (CD) is an autoimmune disease with the destruction of small intestinal villi, which occurs in genetically predisposed individuals. At the present moment, a gluten-free diet (GFD) is the only way to restore the functionality of gut mucosa. However, there is an open debate on the effects of long-term supplementation through a GFD, because some authors report an unbalance in microbial taxa composition. Methods: For microbiome analysis, fecal specimens were collected from 46 CD individuals in GFD for at least 2 years and 30 specimens from the healthy controls (HC). Data were analyzed using an ensemble of software packages: QIIME2, Coda-lasso, Clr-lasso, Selbal, PICRUSt2, ALDEx2, dissimilarity-overlap analysis, and dysbiosis detection tests. Results: The adherence to GFD restored the alpha biodiversity of the gut microbiota in celiac people but microbial composition at beta diversity resulted as different to HC. The microbial composition of the CD subjects was decreased in a number of taxa, namely Bifidobacterium longum and several belonging to Lachnospiraceae family, whereas Bacteroides genus was found to be more abundant. Predicted metabolic pathways among the CD bacterial communities revealed an important role in tetrapyrrole biosynthesis. Conclusions: CD patients in GFD had a non-dysbiotic microbial composition for the crude alpha diversity metrics. We found significant differences in beta diversity, in certain taxon, and pathways between subjects with inactive CD in GFD and controls. Collectively, our data may suggest the development of new GFD products by modulating the gut microbiota through diet, supplements of vitamins, and the addition of specific prebiotics. Full article

The Western diet, rich in lipids and in n-6 polyunsaturated fatty acids (PUFAs), favors gut dysbiosis observed in Crohn’s disease (CD). The aim of this study was to assess the effects of rebalancing the n-6/n-3 PUFA ratio in CEABAC10 transgenic mice that mimic CD. Mice in individual cages with running wheels were randomized in three diet groups for 12 weeks: high-fat diet (HFD), HFD + linseed oil (HFD-LS-O) and HFD + extruded linseed (HFD-LS-E). Then, they were orally challenged once with the Adherent-Invasive Escherichia coli (AIEC) LF82 pathobiont. After 12 weeks of diet, total energy intake, body composition, and intestinal permeability were not different between groups. After the AIEC-induced intestinal inflammation, fecal lipocalin-2 concentration was lower at day 6 in n-3 PUFAs supplementation groups (HFD-LS-O and HFD-LS-E) compared to HFD. Analysis of the mucosa-associated microbiota showed that the abundance of Prevotella, Paraprevotella, Ruminococcus, and Clostridiales was higher in the HFD-LS-E group. Butyrate levels were higher in the HFD-LS-E group and correlated with the Firmicutes/Proteobacteria ratio. This study demonstrates that extruded linseed supplementation had a beneficial health effect in a physically active mouse model of CD susceptibility. Additional studies are required to better decipher the matrix influence in the linseed supplementation effect. Full article

Celiac Disease (CD) is an autoimmune disease characterized by inflammation of the intestinal mucosa due to an immune response to wheat gliadins. It presents in subjects with genetic susceptibility (HLA-DQ2/DQ8 positivity and non-HLA genes) and under the influence of environmental triggers, such as viral infections and intestinal microbiota dysbiosis. The only treatment currently available in CD is a gluten-free diet for life. Despite this, the intestinal dysbiosis that is recorded in celiac subjects persists, even with adherence to dietary therapy. In this review, we have analyzed the literature over the past several decades, which have focused on the use of pro-, pre- and post-biotics in vitro and in vivo in CD. The study of probiotics and their products in CD could be interesting for observing their various effects on several different pathways, including anti-inflammatory properties. Full article

Colorectal cancer (CRC) is a leading cause of cancer death worldwide, and its incidence is correlated with infections, chronic inflammation, diet, and genetic factors. An emerging aspect is that microbial dysbiosis and chronic infections triggered by certain bacteria can be risk factors for tumor progression. Recent data suggest that certain bacterial toxins implicated in DNA attack or in proliferation, replication, and death can be risk factors for insurgence and progression of CRC. In this study, we recruited more than 300 biopsy specimens from people undergoing colonoscopy, and we analyzed to determine whether a correlation exists between the presence of bacterial genes coding for toxins possibly involved in CRC onset and progression and the different stages of CRC. We also analyzed to determine whether CRC-predisposing genetic factors could contribute to bacterial toxins response. Our results showed that CIF toxin is associated with polyps or adenomas, whereas pks+ seems to be a predisposing factor for CRC. Toxins from Escherichia coli as a whole have a higher incidence rate in adenocarcinoma patients compared to controls, whereas Bacteroides fragilis toxin does not seem to be associated with pre-cancerous nor with cancerous lesions. These results have been obtained irrespectively of the presence of CRC-risk loci. Full article

The ability of bacteria to adhere to the intestinal mucosa is a critical property necessary for the long-term colonization of the intestinal tract. This ability can be highly sensitive to the presence of prebiotics. However, limited data are available in this respect for beneficial bacteria such as probiotics or resident gut microbiota. We previously demonstrated that the presence of prebiotics may decrease adherence in several pre- and probiotic combinations. Thus, characterizing the interactions between numerous combinations involving different classes of pre- and probiotics can be crucial in identifying new synbiotics. Accordingly, here, we extend our prior analyses to evaluate the adhesion of five lactobacilli, six bifidobacteria, and one probiotic Escherichia coli strains, as commercial probiotics or promising probiotic candidates, together with the cariogenic Bifidobacterium dentium strain. As an in vitro intestinal mucosa model, Caco-2 and mucin-secreting HT29-MTX cells were co-cultured at 9:1 in the presence or absence of prebiotics. Commercial inulin-type fructooligosaccharide prebiotics Orafti^® GR, Orafti^® P95, and galactooligosaccharide-based prebiotic formula Vivinal^®, including purified human milk oligosaccharides (HMOs) were added into the cultivation media as the sole sugar source (2.5% each). Adherence was tested using microtiter plates and was evaluated as the percentage of fluorescently labeled bacteria present in the wells after three washes. Consistent prebiotics-mediated enhanced adherence was observed only for the commercial probiotic strain E. coli O83. For the remaining strains, the presence of HMO or prebiotics Orafti^® P95 or Orafti^® GR decreased adherence, reaching statistical significance (p < 0.05) for three of out of eight (HMO) or five of out of 11 strains tested, respectively. Conversely, Vivinal^® enhanced adhesion in six out of the 12 strains tested, and notably, it significantly attenuated the adherence of the cariogenic Bifidobacterium dentium Culture Collection of Dairy Microorganisms (CCDM) 318. To our knowledge, this represents the first report on the influence of commercial prebiotics and HMOs on the adhesion of the cariogenic Bifidobacterium sp. Vivinal^® seems to be a promising prebiotic to be used in the formulation of synbiotics, supporting the adhesion of a wide range of probiotics, especially the strains B. bifidum BBV and BBM and the probiotic Escherichia coli O83. Full article

Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups. Full article

Besides genetic polymorphisms and environmental factors, the intestinal microbiota is an important factor in the etiology of Crohn’s disease (CD). Among microbiota alterations, a particular pathotype of Escherichia coli involved in the pathogenesis of CD abnormally colonizes the intestinal mucosa of patients: the adherent-invasive Escherichia coli (AIEC) pathobiont bacteria, which have the abilities to adhere to and to invade intestinal epithelial cells (IECs), as well as to survive and replicate within macrophages. AIEC have been the subject of many studies in recent years to unveil some genes linked to AIEC virulence and to understand the impact of AIEC infection on the gut and consequently their involvement in CD. In this review, we describe the lifestyle of AIEC bacteria within the intestine, from the interaction with intestinal epithelial and immune cells with an emphasis on environmental and genetic factors favoring their implantation, to their lifestyle in the intestinal lumen. Finally, we discuss AIEC-targeting strategies such as the use of FimH antagonists, bacteriophages, or antibiotics, which could constitute therapeutic options to prevent and limit AIEC colonization in CD patients. Full article

Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities. Full article

Mucosal healing after an inflammatory flare is associated with lasting clinical remission. The aim of the present work was to evaluate the impact of the amount of dietary protein on epithelial repair after an acute inflammatory episode. C57BL/6 DSS-treated mice received isocaloric diets with different levels of dietary protein: 14% (P14), 30% (P30) and 53% (P53) for 3 (day 10), 6 (day 13) and 21 (day 28) days after the time of colitis maximal intensity. While the P53 diet worsened the DSS- induced inflammation both in intensity and duration, the P30 diet, when compared to the P14 diet, showed a beneficial effect during the epithelial repair process by accelerating inflammation resolution, reducing colonic permeability and increasing epithelial repair together with epithelial hyperproliferation. Dietary protein intake also impacted mucosa-adherent microbiota composition after inflammation since P30 fed mice showed increased colonization of butyrate-producing genera throughout the resolution phase. This study revealed that in our colitis model, the amount of protein in the diet modulated mucosal healing, with beneficial effects of a moderately high-protein diet, while very high-protein diet displayed deleterious effects on this process. Full article