Search Results (42)

The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality. Full article

Objective: This study assessed the ability of capsule formulations to improve the oral delivery and retain activity of an acid-sensitive enzyme during gastrointestinal transit. Methods: The dissolution characteristics of five capsule formulations—single DRcaps^® [DR], single Vcaps^® Plus [VCP], and three DUOCAP^® capsule-in-capsule combinations, DRcaps^® inside DRcaps^® (DR-in-DR), DRcaps^® inside Vcaps^® Plus (DR-in-VCP), and Vcaps^® Plus inside DRcaps^® (VCP-in-DR)—were evaluated in an in vitro simulation of a healthy human upper gastrointestinal tract under fasting and fed conditions using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME)^® platform. Capsules contained caffeine as a marker of capsule dissolution, and pancreatin as an active ingredient for which activity was determined by the conversion of tributyrin. Readouts included visual capsule scoring, the analysis of caffeine release, and the quantification of tributyrin-to-butyrate conversion at the end of each gastrointestinal tract segment. Results: The single VCP capsules had a high level of caffeine release at the end of the stomach incubation with low butyrate recovery (16–21%), suggesting the rapid release and gastric degradation of the unprotected enzyme. The single DR, DR-in-VCP, and VCP-in-DR formulations showed caffeine release at the end of the duodenum and/or jejunum and had high butyrate recovery, ranging from 53% to 87%. The DR-in-DR formulation had the most delayed release, with incomplete caffeine release and low-to-moderate butyrate recovery (10–36%). Conclusions: Fast capsule dissolution led to the reduced enzymatic activity of the active ingredient, while delayed dissolution resulted in inadequate time for the enzymatic conversion of tributyrin to butyrate. These results highlight that capsule selection should align with the intended use and targeted nutrient delivery, with DUOCAP^® formulations being best suited for small intestinal (VCP-in-DR and DR-in-VCP) and colonic (DR-in-DR) delivery. Full article

Faced with the challenge of reducing food waste, transforming discarded fruit into functional ingredients useful for the food industry is a valuable solution. Ingredients from fruit such as persimmons, which are rich in indigestible carbohydrates and bioactive compounds with antiradical capacity, could positively impact on the health of certain population groups due to their potential prebiotic effect. This study aimed to select the most suitable drying conditions and milling intensity for obtaining powdered persimmon ingredients with a prebiotic-like effects observed in vitro for postmenopausal women, and to evaluate this effect by considering the stimulation of health-promoting bacterial growth and short-chain fatty acids (SCFAs) production. First, the effect of the drying method (hot air drying at 60 and 70 °C, and freeze-drying) and grinding intensity on antiradical capacity, particle size, and the release of bioactive antiradical components into the intestinal lumen after an in vitro gastrointestinal digestion was determined. Next, the effect of these conditions on the microbiota composition of postmenopausal women was preliminary assessed in a batch colonic fermentation experiment for 24 h. The results showed that the ingredient dried with air at 70 °C had the highest phenol and flavonoid content, suffered the least degradation during in vitro gastrointestinal digestion and promoted the differential growth of fiber-degrader genera. Consequently, this was the ingredient selected as the most suitable. Lastly, the impact of this ingredient on the microbiota composition of 4 postmenopausal women has been evaluated in a long-term study using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®) coupled to high throughput sequencing. The growth stimulation of health-associated bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii or Phascolarctobacterium faecium, and the promotion of beneficial metabolic pathways, such as the sugar uptake-specific phosphotransferase system, sugar metabolism and propionate and isobutyrate production, were detected along 14 days of persimmon powder supplementation. A holistic framework for promoting human health while advancing environmental sustainability is represented by the combination of sustainable by-product valorization and microbiota-targeted functional food development. Full article

Recently, the role of mucosal intestinal microbiota in human health has received increasing attention. Nevertheless, data on the response of this microbiota to various interventions remain limited. Here, we have employed the Mucosal Simulator of Human Gastrointestinal Microbial Ecosystem (M-SHIME^®) and luminal SHIME^® (L-SHIME^®) to examine mucosal microbiota responses to interventions that are known to impact the intestinal microbial community in humans and study relationships between the responses of mucosal and luminal microbiota. Specifically, we evaluated the effects of varying macronutrient levels over a 28-day standard, balanced dietary intervention and a parallel 14-day administration of Lacticaseibacillus rhamnosus GG. Observed shifts in mucosal microbiota in response to interventions differed significantly from those observed in luminal microbiota (p < 0.05). In particular, we found that the mucosal microbiota compared to luminal microbiota was more stable and that the abundance of several genera (i.e., Subdoligranulum, Parabacteroides and Fusobacterium) in the M-SHIME^® correlated positively with the intake of dietary macronutrients, especially protein, which was in line with results reported in previous human studies. This study demonstrates the reliability of advanced in vitro models in capturing diet-induced dynamics of the human mucosal microbiota, a compartment that remains understudied despite its critical role in intestinal immune regulation. Full article

Background/Objectives: This study examines the application of the novel double emulsion gel system for the delivery and release of encapsulated cannabidiol (CBD) and the probiotic strain Lactiplantibacillus plantarum DSM 24624. Methods: During a six-week experimental period comprising stabilization, treatment, and wash-out phases, the dynamic Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®) model was employed to assess a system. The evaluation focused on the delivery of CBD and probiotics, as well as the system’s effects on microbial composition, diversity, and metabolic activity throughout the digestion process using 16S rRNA gene sequencing and digital PCR methods. Results: Microbial community analysis revealed significant shifts in both mucosal and luminal microbiota following supplementation. The treatment increased beneficial bacterial families such as Lachnospiraceae and Clostridiaceae, demonstrated effective delivery, release, and persistence of the probiotic L. plantarum, as well as enhanced butyrate and lactate production. Diversity analyses highlighted a transient rise in alpha diversity within the mucin layer and a decrease in the lumen, with significant changes in beta diversity across experimental phases. Conclusions: Findings suggest that double emulsion gel can be employed for the delivery of probiotics and CBD to the gastrointestinal tract. In addition, an innovative CBD-probiotic formulation can modulate gut microbiota composition and metabolic activity, suggesting its potential as a functional food innovation for intestinal health. However, the results are based on an in vitro model, which lacks the complexity of the human host environment, and further clinical studies are necessary to confirm the biological relevance and therapeutic potential of such delivery systems for gastrointestinal health. Full article

Microplastics (MPs) have become widespread environmental contaminants, with increasing evidence of their harmful impacts on human health. MPs generally enter the human body via ingestion, inhalation, or dermal exposure, with the gastrointestinal tract acting as a crucial entrance route. This work utilized the SHIME system to evaluate the effects of polystyrene (PS) MPs on gut microbiota and short-chain fatty acid (SCFA) metabolism in distinct colonic areas. The results demonstrated regional and individual-specific variations in microbial diversity, significant shifts in Firmicutes/Bacteroidetes (F/B) ratio, and declines in beneficial bacteria, such as Bifidobacteriaceae. Moreover, SHIME supernatants were then tested with a co-cultured cell model (Caco-2/HT29-MTX-E12). Results indicated a deteriorative effect on the intestinal model, characterized by enhanced oxidative stress and mitochondrial malfunction. No significant effect on intestinal barrier integrity or mucus secretion was detected. These findings highlight the potential systemic toxicity of PS-MPs on human gut microbiota-mediated mechanisms, emphasizing the necessity for immediate mitigation efforts. Full article

Xanthohumol (XN), a polyphenol from hops (Humulus lupulus), exhibits antioxidant, anti-inflammatory, antihyperlipidemic, and chemo-preventive activity. Preclinical evidence suggests gut microbiota are critical to mediating some of these bioactivities. Nevertheless, its precise impact on human gut microbiota, particularly at supplemental doses, remains poorly characterized. We evaluated 200 mg/day XN for 3 weeks on human gut microbiota in a eubiotic and dysbiotic model using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®). Functional assessments of microbiota included quantification of XN metabolites, short-chain fatty acids (SCFAs), and untargeted metabolomics of the digestive metabolome. Bacterial composition was assessed by 16S rRNA gene sequencing. XN reduced alpha-diversity and short-chain fatty acid production in both models, as well as altered taxa abundance variably between models. XN disrupted bile acid metabolism through inhibition of microbial bile salt hydrolase (BSH). The modulation of bile acid metabolism has important implications for host-level bioactivity of XN. Full article

Background: Bile salt hydrolase (BSH) is a key probiotic trait, as it facilitates both host metabolism and bacterial survival into the gastrointestinal tract (GIT), through bile acid (BA) deconjugation, keeping intestinal homeostasis. Objectives: The present study aims to investigate the viability of the Lacticaseibacillus rhamnosus VB4 strain and its effects on bile acid deconjugation during the gastrointestinal tract (GIT) passage, under a fed condition, using the in vitro SHIME^® (Simulator of the Human Intestinal Microbial Ecosystem) model. Methods: Gastric, small intestinal and colonic fractions were monitored and a fecal slurry from a healthy donor was inoculated into the colonic compartment to establish the intestinal microbiota. Samples were collected at the end of stomach, duodenum, jejunum, ileum phases, and colon after 0, 16 and 24 h. Strain survival was assessed by culturing method, and bsh gene expression was revealed by quantitative PCR (qPCR). In addition, UHPLC/HR-MS was performed to reveal the hypothetical changes in BAs profile after strain administration. Results: Good survivability of the VB4 strain in the upper GIT was revealed. Furthermore, VB4-inculated sample showed sustained expression of bsh in both the stomach/small intestine and colon fractions at all sampling times. Analysis of the BAs profile shown that the VB4 strain reduced the levels of the main conjugated BAs in the small intestine under fed condition and improved the deconjugation efficiency during colonic transit compared with the control. Conclusions: These findings highlight the survivability of L. rhamnosus VB4 strain inside the gut and its potential as biotherapeutic BAs-mediator candidate, demonstrating that transcriptomic and metabolomic approaches coupled to a dynamic in vitro gut model represent a robust tool for selection of a BSH-positive probiotic candidate. Full article

Background/Objectives: With increasing knowledge of the role of the microbiota in health and disease, the need for the reliable simulation of its behavior in response to various factors, such as diet and probiotic administration in in vitro conditions, has emerged. Although many studies utilize developed systems, data on how accurately these systems represent individual microbiota responses are scarce. Methods: In the present study, the Simulator of Human Intestinal Microbial Ecosystem (SHIME^®) was exposed to experimental conditions mimicking the application of probiotics and dietary changes in the study participant. Next-generation 16S rRNA sequencing was used to reveal the structure of the microbial communities in the analyzed samples. Results: Analysis of 17 samples revealed that predominantly diet and, to a lesser extent, probiotics had a divergent effect on the microbiota’s fluctuations dependent on the culture environment. Despite this, results from both in vitro and in vivo conditions aligned well with previously published data on the expected impact of dietary changes on the intestinal microbial community. Conclusions: The anecdotal evidence presented in this study suggested that current in vitro technology enables the reproduction of some of the microbiota responses that are well known from in vivo research. However, further work is required to enable simulations of an individual microbiota. Full article

Background/Objectives: The probiotic Lacticaseibacillus paracasei DG (LpDG) has shown promising results for various gastrointestinal diseases. This study evaluated the survival, metabolic activity, and impact on colonic microbiota of LpDG in an in vitro gastrointestinal tract simulation. Methods: Encapsulated LpDG was tested under simulated fed, fasted, and shortened fasted conditions compared with a blank control in a modified Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®) reactor. Capsule integrity, and cell culturability and viability were assessed at the end of each digestion phase. Metabolic activity (pH, total gas production, and concentrations of short-chain fatty acids, lactate, and ammonium) was assessed after a 24 h colonic incubation with a faecal inoculum. The impact of LpDG on the colonic microbial community was analysed by quantitative polymerase chain reaction and shallow shotgun sequencing. Results: The capsule was completely degraded at the end of the jejunum under all conditions. A low pH had a minimal impact on LpDG culturability and viability. Compared with blank control, LpDG remained metabolically active in the microbial community following a 24 h colonic incubation (LpDG [0–24 h] vs. blank control [0–24 h]: ΔpH, decreased [0.29–0.38 vs. 0.12–0.34]; Δlactic acid, decreased [1.52–1.69 mM vs. 0.13–0.21 mM]; and Δbutyrate, increased [7.49–10.52 mM vs. 5.19–7.76 mM]). Under fed conditions, treatment with LpDG compared with blank control significantly decreased levels of Escherichia coli and Blautia wexlerae and increased Clostridiaceae, Eubacteriaceae, and Lachnospiraceae. Conclusions: LpDG remains viable and metabolically active in the gastrointestinal tract, positively affecting intestinal microbiota and metabolite production. Full article

Background/Objectives: Selective serotonin reuptake inhibitors (SSRIs), widely prescribed for anxiety disorders, may negatively impact the gut microbiota, contributing to dysbiosis. Considering the gut–brain axis’s importance in mental health, probiotics could represent an effective adjunctive strategy. This study evaluated the effects of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on microbiota composition, metabolic activity, and immune markers in fecal samples from patients with anxiety on SSRIs, using the SHIME^® (Simulator of the Human Intestinal Microbial Ecosystem) model. Methods: The fecal microbiotas of four patients using sertraline or escitalopram were inoculated in SHIME^® reactors simulating the ascending colon. After stabilization, a 14-day probiotic intervention was performed. Microbial composition was assessed by 16S rRNA sequencing. Short-chain fatty acids (SCFAs), ammonia, and GABA were measured, along with the prebiotic index (PI). Intestinal barrier integrity was evaluated via transepithelial electrical resistance (TEER), and cytokine levels (IL-6, IL-8, IL-10, TNF-α) were analyzed using a Caco-2/THP-1 co-culture system. The statistical design employed in this study for the analysis of prebiotic index, metabolites, intestinal barrier integrity and cytokines levels was a repeated measures ANOVA, complemented by post hoc Tukey’s tests to assess differences across treatment groups. For the 16S rRNA sequencing data, alpha diversity was assessed using multiple metrics, including the Shannon, Simpson, and Fisher indices to evaluate species diversity, and the Chao1 and ACE indices to estimate species richness. Beta diversity, which measures microbiota similarity across groups, was analyzed using weighted and unweighted UniFrac distances. To assess significant differences in beta diversity between groups, a permutational multivariate analysis of variance (PERMANOVA) was performed using the Adonis test. Results: Probiotic supplementation increased Bifidobacterium and Lactobacillus, and decreased Klebsiella and Bacteroides. Beta diversity was significantly altered, while alpha diversity remained unchanged. SCFA levels increased after 7 days. Ammonia levels dropped, and PI values rose. TEER values indicated enhanced barrier integrity. IL-8 and TNF-α decreased, while IL-6 increased. GABA levels remained unchanged. Conclusions: The probiotic combination of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 modulated gut microbiota composition, metabolic activity, and inflammatory responses in samples from individuals with anxiety on SSRIs, supporting its potential as an adjunctive strategy to mitigate antidepressant-associated dysbiosis. However, limitations—including the small pooled-donor sample, the absence of a healthy control group, and a lack of significant GABA modulation—should be considered when interpreting the findings. Although the SHIME^® model is considered a gold standard for microbiota studies, further clinical trials are necessary to confirm these promising results. Full article

This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit^TM), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME^® gastrointestinal model. A short-term single-stage colonic M-SHIME^® experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers. Full article

The human gastrointestinal microbiota plays a vital role in maintaining host health and preventing diseases, prompting the creation of simulators to replicate this intricate system. The Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®), a multicompartment dynamic simulator, has emerged as a pivotal in vitro model for studying the interactions and interferences within the human gut microbiota. The continuous and real-time monitoring hallmarks, along with the programmatically flexible setup, bestow SHIME^® with the ability to mimic the entire human intestinal ecosystem with high dynamics and stability, allowing the evaluation of various treatments on the bowel microbiota in a controlled environment. This review outlines recent developments in SHIME^® systems, including the M-SHIME^®, Twin-SHIME^®, Triple-SHIME^®, and Toddle SHIME^® models, highlighting their applications in the fields of food and nutritional science, drug development, gut health research, and traditional Chinese medicine. Additionally, the prospect of SHIME^® integrating with other advanced technologies is also discussed. The findings underscore the versatility of SHIME^® technology, demonstrating its significant contributions to current gut ecosystem research and its potential for future innovation in microbiome-related fields. Full article

Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine). Full article

Although various benefits of human milk oligosaccharides (HMOs) have been reported, such as promoting Bifidobacterium growth in the infant gut, their effects on adults have not been fully studied. This study investigated the effects of two types of sialyllactose, 3′-sialyllactose (3′-SL) and 6′-sialyllactose (6′-SL), on the adult intestinal microbiome using the simulator of human intestinal microbial ecosystem (SHIME^®), which can simulate human gastrointestinal conditions. HPLC metabolite analysis showed that sialyllactose (SL) supplementation increased the short-chain fatty acid content of SHIME culture broth. Moreover, 16S rRNA gene sequencing analysis revealed that SL promoted the growth of Phascolarctobacterium and Lachnospiraceae, short-chain fatty acid-producing bacteria, but not the growth of Bifidobacterium. Altogether, both types of SL stimulated an increase in short-chain fatty acids, including propionate and butyrate. Additionally, SHIME culture supernatant supplemented with SL improved the intestinal barrier function in Caco-2 cell monolayers. These results suggest that SL could act as a unique prebiotic among other HMOs with a nonbifidogenic effect, resulting in intestinal barrier protection. Full article