A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products

Advances in in vitro cultivation techniques for comprehensive analysis of human gut microbiome

The role of gut microbiota in human health and disease is becoming increasingly recognized. Historically, the impact of human gut microbiota on health has been studied using clinical trials and animal models. However, clinical studies often struggle with controlling variables and pinpointing disease-causing factors, while animal models fall short of accurately replicating the human gut environment. Additionally, continuous sample collection for gut microbiota analysis in vivo presents significant ethical and technical challenges. To address these limitations, in vitro fermentation models have emerged as promising alternatives. These models aim to simulate the structural and functional characteristics of the human gut in a controlled setting, offering valuable insights into microbial behavior. This review highlights current knowledge and technological advances in in vitro cultivation systems for human gut microbiota, focusing on key elements such as three-dimensional scaffolds, culture media, fermentation systems, and analytical techniques. By examining these components, the review establishes a framework for improving methods to cultivate and study human gut microbiota, enhancing research methodologies for better understanding microbial interactions, behavior, and adaptation in diverse environments.

Personalized nutrition studies of human gut microbiome-polyphenol interactions utilizing continuous multistaged in vitro fermentation models-a narrative review

The gut microbiota, a complex community of microorganisms primarily inhabiting the human large intestine, plays a crucial role in human health. Gut dysbiosis, characterized by an imbalance in gut bacterial populations, has been increasingly recognized as a significant factor in the pathogenesis of metabolic diseases such as type 2 diabetes, inflammatory bowel disease, and colorectal cancer. Polyphenols are critical modulators of gut microbial composition and metabolism. However, the extent of polyphenol-induced modulation of the gut microbiome remains largely unexplored. In vitro models offer a convenient and ethical alternative to in vivo studies for investigating nutrient-gut microbiome interactions, facilitating easy sampling and controlled experimental conditions. Among these, continuous multistaged in vitro fermentation models, which simulate different sections of the human gastrointestinal tract (e.g., proximal colon, transverse colon, and distal colon), provide a more accurate representation of the human gut environment compared to single-batch fermentation. Various configurations of these multistaged models have been developed and widely employed in studies examining the effects of polyphenols on the gut microbiome. This review aims to summarize the different configurations of multistaged in vitro fermentation models and recent advancements in their development, highlight key aspects of experimental design, outline commonly used analytical workflows with complementary analyses, and review the restorative effects of polyphenol interventions on dysregulated gut microbiota.

Bacillusmegaterium DSM 32963 Enhances Specialized Pro-Resolving Mediator Production from an n-3 PUFA Salt in a Dynamic Model of the Human Intestine

BACKGROUND

Omega-3 polyunsaturated fatty acids (n-3 PUFA) have been used in the treatment of inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS), and their effects are potentiated upon conversion to specialized pro-resolving mediators (SPM). Recent studies indicated that the probiotic bacterial strain Bacillus megaterium DSM 32963 can be used to enhance the production of SPM and its precursors in vivo.

METHODS

Here, we explored the contribution of Bacillus megaterium DSM 32963 to SPM production in a validated, dynamic model of the upper and lower intestine. The TIM-1 and TIM-2 models were applied, with the TIM-2 model inoculated with the fecal microbiota of healthy individuals and probed with an n-3 PUFA lysine salt with and without Bacillus megaterium DSM 32963 or an SPM-enriched fish oil or placebo. Kinetics of SPM production were assessed by metabololipidomics analysis, and survival and engraftment of the Bacillus megaterium strain was monitored by plate counting and by strain-specific qPCR.

RESULTS

Bacillus megaterium DSM 32963 poorly survived TIM-1 conditions but propagated in the TIM-2 model, where it enabled the metabolism of n-3 PUFA to SPM (resolvin E2 and protectin DX) and SPM precursors (e.g., 5-hydroxyeicosapentaenoic acid (5-HEPE), 15-HEPE, 18-HEPE, 4-hydroxydocosahexaenoic acid (4-HDHA), 10-HDHA, and 17-HDHA, among other EPA- and DHA-derived metabolites) with significantly higher levels of lipid mediator production compared to the n-3 PUFA lysine salt alone; esterified n-3 PUFA were hardly converted by the microbiota.

CONCLUSIONS

These findings reinforce that Bacillus megaterium DSM 32963 facilitates SPM production in situ from bioavailable n-3 PUFA in the large intestine, highlighting its use to complement eukaryotic SPM biosynthesis by the host and its possible therapeutic use for, e.g., IBD and IBS.

Simulator of the Human Intestinal Microbial Ecosystem (SHIME®): Current Developments, Applications, and Future Prospects

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.

Cellular and Microbial In Vitro Modelling of Gastrointestinal Cancer

Human diseases are multifaceted, starting with alterations at the cellular level, damaging organs and their functions, and disturbing interactions and immune responses. In vitro systems offer clarity and standardisation, which are crucial for effectively modelling disease. These models aim not to replicate every disease aspect but to dissect specific ones with precision. Controlled environments allow researchers to isolate key variables, eliminate confounding factors and elucidate disease mechanisms more clearly. Technological progress has rapidly advanced model systems. Initially, 2D cell culture models explored fundamental cell interactions. The transition to 3D cell cultures and organoids enabled more life-like tissue architecture and enhanced intercellular interactions. Advanced bioreactor-based devices now recreate the physicochemical environments of specific organs, simulating features like perfusion and the gastrointestinal tract's mucus layer, enhancing physiological relevance. These systems have been simplified and adapted for high-throughput research, marking significant progress. This review focuses on in vitro systems for modelling gastrointestinal tract cancer and the side effects of cancer treatment. While cell cultures and in vivo models are invaluable, our main emphasis is on bioreactor-based in vitro modelling systems that include the gut microbiome.

Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum

Substantial functional metabolic diversity exists within species of cultivated grain crops that directly or indirectly provide more than half of all calories consumed by humans around the globe. While such diversity is the molecular currency used for improving agronomic traits, diversity is poorly characterized for its effects on human nutrition and utilization by gut microbes. Moreover, we know little about agronomic traits' potential tradeoffs and pleiotropic effects on human nutritional traits. Here, we applied a quantitative genetics approach using a meta-analysis and parallel genome-wide association studies of Sorghum bicolor traits describing changes in the composition and function of human gut microbe communities, and any of 200 sorghum seed and agronomic traits across a diverse sorghum population to identify associated genetic variants. A total of 15 multiple-effect loci (MEL) were initially found where different alleles in the sorghum genome produced changes in seed that affected the abundance of multiple bacterial taxa across 2 human microbiomes in automated in vitro fermentations. Next, parallel genome-wide studies conducted for seed, biochemical, and agronomic traits in the same population identified significant associations within the boundaries of 13/15 MEL for microbiome traits. In several instances, the colocalization of variation affecting gut microbiome and agronomic traits provided hypotheses for causal mechanisms through which variation could affect both agronomic traits and human gut microbes. This work demonstrates that genetic factors affecting agronomic traits in sorghum seed can also drive significant effects on human gut microbes, particularly bacterial taxa considered beneficial. Understanding these pleiotropic relationships will inform future strategies for crop improvement toward yield, sustainability, and human health.

Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2)

AIMS

This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism.

METHODS AND RESULTS

To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control.

CONCLUSIONS

The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.

Progress and challenges in designing dynamic in vitro gastric models to study food digestion

Understanding the mechanisms involved in food breakdown in the human gastrointestinal (GI) tract is essential in food digestion research. Research to study food digestion in the human GI tract requires in vivo and in vitro approaches. In vivo methods involving human or animal subjects are often cost-prohibitive and raise ethical concerns. For these reasons, in vitro approaches are becoming more common. Several dynamic in vitro models that mimic one or more components of the GI tract have been developed at various research institutions and by commercial companies. While there is evidence of considerable novelty and innovation in the design of these models, there are many differences among them in how the mechanical breakdown of solid foods is accomplished. In some systems, modulating water pressure is used to achieve peristaltic contractions of the gastric antrum, whereas, in other models, the flexible walls of a gastric chamber are compressed by the movement of rollers or clamps outside the walls of the test chamber. Although much progress has been made in standardizing the biochemical environment appropriate to the food digestion process, there is a lack of standard protocols to measure mechanical forces that result in the breakdown of solid foods. Similarly, no standardized methods are available to evaluate the results obtained from in vitro trials for validation purposes. Due to the large variability in the design features of in vitro models used for food digestion studies, developing consensus-based standards for the mechanical aspects of food breakdown is needed.

Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties

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).

In Vitro Human Gastrointestinal Tract Simulation Systems: A Panoramic Review

Simulated human gastrointestinal (GI) tract systems are important for their applications in the fields of probiotics, nutrition and health. To date, various in vitro gut systems have been available to study GI tract dynamics and its association with health. In contrast to in vivo investigations, which are constrained by ethical considerations, in vitro models have several benefits despite the challenges involved in mimicking the GI environment. These in vitro models can be used for a range of research, from simple to dynamic, with one compartment to several compartments. In this review, we present a panoramic development of in vitro GI models for the first time through an evolutionary timeline. We tried to provide insight on designing an in vitro gut model, especially for novices. Latest developments and scope for improvement based on the limitations of the existing models were highlighted. In conclusion, designing an in vitro GI model suitable for a particular application is a multifaceted task. The bio-mimicking of the GI tract specific to geometrical, anatomical and mechanical features remains a challenge for the development of effective in vitro GI models. Advances in computer technology, artificial intelligence and nanotechnology are going to be revolutionary for further development. Besides this, in silico high-throughput technologies and miniaturisation are key players in the success of making in vitro modelling cost-effective and reducing the burden of in vivo studies.

Intraintestinal fermentation of fructo- and galacto-oligosaccharides and the fate of short-chain fatty acids in humans

Consumption of fructo- (FOS) and galacto-oligosaccharides (GOS) has health benefits which have been linked in part to short-chain fatty acids (SCFA) production by the gut microbiota. However, detailed knowledge of this process in the human intestine is lacking. We aimed to determine the acute fermentation kinetics of a FOS:GOS mixture in healthy males using a naso-intestinal catheter for sampling directly in the ileum or colon. We studied the fate of SCFA as substrates for glucose and lipid metabolism by the host after infusion of 13C-SCFA. In the human distal ileum, no fermentation of FOS:GOS, nor SCFA production, or bacterial cross-feeding was observed. The relative composition of intestinal microbiota changed rapidly during the test day, which demonstrates the relevance of postprandial intestinal sampling to track acute responses of the microbial community toward interventions. SCFA were vividly taken up and metabolized by the host as shown by incorporation of 13C in various host metabolites.

Gut Microbiome Integration in Drug Discovery and Development of Small Molecules

Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions

A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.

Fermentation characteristics and prebiotic potential of enzymatically synthesized butyryl-fructooligosaccharides

Existing prebiotics, such as fructo-oligosaccharides (FOSs), can be modified to enhance their functionality or introduce additional functionalities. This study aimed to investigate the fermentation characteristics and prebiotic potential of enzymatically synthesized butyryl-FOSs. The esters were successfully synthesized through the reaction of butyric acid and FOSs using both chemical and enzymatic methods, denoted as A-FOSs and B-FOSs, respectively, for comparative analysis. The esterification degree of each component in A-FOSs was significantly higher than that of B-FOSs. Subsequently, the obtained esters were characterized for their fermentation properties, degradation mode and potential prebiotic effects using an in vitro simulated colonic fermentation model. Enzymes of human gut microbiota were found to preferentially cleave the glycosidic bond to the unit without butyryl group and release the sugars for utilization. A significant increase in butyric acid levels was observed during fermentation after the supplementation of B-FOSs. The 16S rRNA gene sequencing, absolute quantification of microbiota, and selected probiotic strains culture showed that B-FOSs supplementation promoted the growth of beneficial bacteria while reducing harmful ones. These results suggest that B-FOSs hold promise as novel prebiotics, possessing dual functions of modulating gut microbiota and delivering butyric acid to the colon in a targeted manner, ultimately contributing to improved gut health.

Presence of digestible starch impacts in vitro fermentation of resistant starch

Starch is an important energy source for humans. Starch escaping digestion in the small intestine will transit to the colon to be fermented by gut microbes. Many gut microbes express α-amylases that can degrade soluble starch, but only a few are able to degrade intrinsic resistant starch (RS), which is insoluble and highly resistant to digestion (≥80% RS). We studied the in vitro fermentability of eight retrograded starches (RS-3 preparations) differing in rapidly digestible starch content (≥70%, 35-50%, ≤15%) by a pooled adult faecal inoculum and found that fermentability depends on the digestible starch fraction. Digestible starch was readily fermented yielding acetate and lactate, whereas resistant starch was fermented much slower generating acetate and butyrate. Primarily Bifidobacterium increased in relative abundance upon digestible starch fermentation, whereas resistant starch fermentation also increased relative abundance of Ruminococcus and Lachnospiraceae. The presence of small fractions of total digestible starch (±25%) within RS-3 preparations influenced the fermentation rate and microbiota composition, after which the resistant starch fraction was hardly fermented. By short-chain fatty acid quantification, we observed that six individual faecal inocula obtained from infants and adults were able to ferment digestible starch, whereas only one adult faecal inoculum was fermenting intrinsic RS-3. This suggests that, in contrast to digestible starch, intrinsic RS-3 is only fermentable when specific microbes are present. Our data illustrates that awareness is required for the presence of digestible starch during in vitro fermentation of resistant starch, since such digestible fraction might influence and overrule the evalution of the prebiotic potential of resistant starches.

Type of intrinsic resistant starch type 3 determines in vitro fermentation by pooled adult faecal inoculum

Resistant starch (RS) results in relatively high health-beneficial butyrate levels upon fermentation by gut microbiota. We studied how physico-chemical characteristics of RS-3 influenced butyrate production during fermentation. Six highly resistant RS-3 substrates (intrinsic RS-3, 80-95 % RS) differing in chain length (DPn 16-76), Mw distribution (PI) and crystal type (A/B) were fermented in vitro by pooled adult faecal inoculum. All intrinsic RS-3 substrates were fermented to relatively high butyrate levels (acetate/butyrate ≤ 2.5), and especially fermentation of A-type RS-3 prepared from polydisperse α-1,4 glucans resulted in the highest relative butyrate amount produced (acetate/butyrate: 1). Analysis of the microbiota composition after fermentation revealed that intrinsic RS-3 stimulated primarily Lachnospiraceae, Bifidobacterium and Ruminococcus, but the relative abundances of these taxa differed slightly depending on the RS-3 physico-chemical characteristics. Especially intrinsic RS-3 of narrow disperse Mw distribution stimulated relatively more Ruminococcus. Selected RS fractions (polydisperse Mw distribution) obtained after pre-digestion were fermented to acetate and butyrate (ratio ≤ 1.8) and stimulated Lachnospiraceae and Bifidobacterium. This study indicates that especially the α-1,4 glucan Mw distribution dependent microstructure of RS-3 influences butyrate production and microbiota composition during RS-3 fermentation.

Colon-targeted delivery of polyphenols: construction principles, targeting mechanisms and evaluation methods

Polyphenols have received considerable attention for their promotive effects on colonic health. However, polyphenols are mostly sensitive to harsh gastrointestinal environments, thus, must be protected. It is necessary to design and develop a colon-targeted delivery system to improve the stability, colon-targeting and bioavailability of polyphenols. This paper mainly introduces research on colon-targeted controlled release of polyphenols. The physiological features affecting the dissolution, release and absorption of polyphenol-loaded delivery systems in the colon are first discussed. Simultaneously, the types of colon-targeted carriers with different release mechanisms are described, and colon-targeting assessment models that have been studied so far and their advantages and limitations are summarized. Based on the current research on polyphenols colon-targeting, outlook and reflections are proposed, with the goal of inspiring strategic development of new colon-targeted therapeutics to ensure that the polyphenols reach the colon with complete bioactivity.

Fermentation patterns of prebiotics fructooligosaccharides-SCFA esters inoculated with fecal microbiota from ulcerative colitis patients

Ulcerative colitis (UC) is believed to arise from an imbalance between the intestinal microbiota and mucosal immunity, leading to excessive intestinal inflammation. Modulating the gut microbial community through dietary components presents a valuable strategy in aiding the treatment of UC. In this study, esters formed by binding of well-known prebiotics, fructooligosaccharides (FOS), with short chain fatty acids (SCFAs) via both enzymatic and chemical methods were evaluated for their impact on the gut microbiota of UC patients. An in vitro human colonic fermentation model was employed to monitor changes in total carbohydrates and SCFAs production during the fermentation of these esters by microbiota from patients with active and remission UC. The results showed that pronounced abundance of [Ruminococcus]_gnavus_group, Escherichia_Shigella, Lachnoclostridium, Klebsiella and other potential pathogens were detected in the fecal samples from UC patients, with a milder condition observed during the remission phase. Significant higher levels of corresponding SCFA were observed in the groups with addition of FOS-SCFAs esters during fermentation. Butyrylated fructooligosaccharides (B-FOS) and propionylated fructooligosaccharides (P-FOS) by enzymatic synthesis successfully promoted the proliferation of Bifidobacterium and inhibited Clostridium_sensu_stricto_1 and Klebsiella. Overall, B-FOS and P-FOS exhibit promising potential for restoring intestinal homeostasis and alleviating intestinal inflammation in individuals with UC.

Insights into the fermentation patterns of wheat bran cell wall polysaccharides using an in-vitro batch fermentation model

We aimed to study the structural characteristics and fermentation properties of wheat bran cell wall polysaccharides (CWPs). Sequential extractions of CWPs from wheat bran produced the water-extractable (WE) and alkali-extractable (AE) fractions. The extracted fractions were structurally characterized based on their molecular weight (Mw) and monosaccharide composition. Our findings revealed that the Mw and the ratio of arabinose to xylose (A/X) of AE were higher than those of WE and that the two fractions were mainly composed of arabinoxylans (AXs). The substrates were then subjected to in vitro fermentation by human fecal microbiota. As fermentation progressed, the total carbohydrates of WE were significantly more utilized than that of AE (p < 0.05). The AXs in WE were utilized at a higher rate than those in AE. The relative abundance of Prevotella_9, which can efficiently utilize AXs, was significantly increased in AE. The presence of AXs in AE shifted the balance away from protein fermentation and caused a delay in protein fermentation. Our study demonstrated that wheat bran CWPs can modulate the gut microbiota in a structure-dependent manner. However, future studies should further characterize the fine structure of wheat CWPs to clarify their detailed relationship with gut microbiota and metabolites.

Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration

Research on gut microbiota has generally focused on fecal samples, representing luminal content of the large intestine. However, nutrient uptake is restricted to the small intestine. Abundant immune cell populations at this anatomical site combined with diminished mucus secretion and looser junctions (partly to allow for more efficient fluid and nutrient absorption) also results in intimate host-microbe interactions despite more rapid transit. It is thus crucial to dissect key differences in both ecology and physiology between small and large intestine to better leverage the immense potential of human gut microbiota imprinting, including probiotic engraftment at biological sensible niches. Here, we provide a detailed review unfolding how the physiological and anatomical differences between the small and large intestine affect gut microbiota composition, function, and plasticity. This information is key to understanding how gut microbiota manipulation, including probiotic administration, may strain-dependently transform host-microbe interactions at defined locations.

Structural characteristics and in vitro fermentation patterns of polysaccharides from Boletus mushrooms

The aim of this study was to investigate the structural characteristics and in vitro fermentation patterns of polysaccharides from Boletus mushrooms. Polysaccharides were solubilized from fruit bodies of selected mushrooms Boletus auripes, B. bicolor, and B. griseus using subcritical water extraction. Boletus polysaccharides were characterized for their general physicochemical pattern, constituent monosaccharides and molecular weight. A simulated in vitro fermentation model was used to study the utilization of Boletus polysaccharides by the gut microbiota and their consequent modulation of microbial communities. Results showed that the main constituent monosaccharides of Boletus polysaccharides were glucose, galactose and mannose, followed by fucose, xylose and rhamnose, with glucose being the most abundant. The polysaccharides from B. bicolor and B. griseus exhibited a relatively high proportion of galactose and mannose, respectively. Boletus polysaccharides exhibited a wide range of molecular weights (5 kDa to 2000 kDa), which covered multiple polysaccharide populations, but the proportions of these populations varied among the samples. Boletus polysaccharides were gradually utilized by the human fecal microbiota, promoting the production of SCFAs. Boletus polysaccharides contributed to a healthier gut microbiota composition by increasing the relative abundance of beneficial bacterial genera such as Bacteroides and Faecalibacterium and reducing the relative abundance of harmful bacterial genera such as Sutterella and Escherichia-Shigella. B. bicolor polysaccharides showed better fermentability and prebiotic effects than the other Boletus polysaccharide groups. Therefore, the consumption of select Boletus mushrooms, particularly B. bicolor, could be a potential approach to obtain polysaccharides for microbiota modulation and to support gut health.

Influence of Different Diets on the Degradation of Sulfasalazine by Colon Bacteria Determined Using MimiCol3

The microbiome of the colon is characterized by its great diversity. This varies not only intra- but also interindividually and is influenced by endogenous and exogenous factors, such as dietary and lifestyle factors. The aim of this work was to investigate the extent to which the degradation of the drug sulfasalazine is influenced by different microbiota. Therefore, the in vitro model MimiCol3 was used, which represents the physiological conditions of the ascending colon. In addition to a representative physiological volume, the pH value, redox potential and an anaerobic atmosphere are important to provide the bacteria with the best possible growth conditions. Stool samples were taken from three healthy subjects, comparing omnivorous, vegetarian and meat-rich diets, and cultured for 24 h. However, the nutrient medium used for cultivation led to the alignment of the bacterial composition of the microbiota. The previously observed differences between the diets could not be maintained. Nevertheless, the similar degradation of sulfasalazine was observed in all microbiota studied in MimiCol3. This makes MimiCol3 a suitable in vitro model for metabolism studies in the gut microbiome.

Casein structures differently affect postprandial amino acid delivery through their intra-gastric clotting properties

We aimed to assess if casein structure affects its digestion and its subsequent amino acid delivery kinetic. Higher nitrogen levels were recovered in dialysates after in vitro digestions of sodium caseinate (SC, formed of small aggregates) compared to micellar casein (MC, native form of casein) and calcium caseinate (CC, intermediate structure). Likewise, plasma indispensable amino-acid concentration peak was higher after SC compared to MC or CC ingestion in healthy volunteers in a randomized, double blind, cross-over study. In pigs, gamma-scintigraphy using labelled meals revealed that SC was mainly localized in the proximal part of the stomach whereas MC was distributed in the whole gastric cavity. Caseins were found in both solid and liquid phases and partly hydrolyzed casein in the solid phase shortly after SC drink ingestion. These data support the concept of slow (MC) and rapid (SC) casein depending of casein structure, likely due to their intra-gastric clotting properties.

2'-fucosyllactose alone or combined with resistant starch increases circulating short-chain fatty acids in lean men and men with prediabetes and obesity

Background

Infusion of short-chain fatty acids (SCFA) to the distal colon beneficially affects human substrate and energy metabolism. Here, we hypothesized that the combination of 2'-fucosyllactose (2'-FL) with resistant starch (RS) increases distal colonic SCFA production and improves metabolic parameters.

Methods

In this randomized, crossover study, 10 lean (BMI 20-24.9 kg/m²) and nine men with prediabetes and overweight/obesity (BMI 25-35 kg/m²) were supplemented with either 2'-FL, 2'-FL+RS, or placebo one day before a clinical investigation day (CID). During the CID, blood samples were collected after a overnight fast and after intake of a liquid high-fat mixed meal to determine plasma SCFA (primary outcomes). Secondary outcomes were fasting and postprandial plasma insulin, glucose, free fatty acid (FFA), glucagon-like peptide-1, and peptide YY concentrations. In addition, fecal SCFA and microbiota composition, energy expenditure and substrate oxidation (indirect calorimetry), and breath hydrogen excretion were determined.

Results

In lean men, supplementation with 2'-FL increased postprandial plasma acetate (P = 0.017) and fasting H₂ excretion (P = 0.041) compared to placebo. Postprandial plasma butyrate concentration increased after 2'-FL and 2'-FL+RS as compared to placebo (P < 0.05) in lean men and men with prediabetes and overweight/obesity. Additionally, 2'-FL+RS decreased fasting and postprandial plasma FFA concentrations compared to placebo (P < 0.05) in lean men.

Conclusion

Supplementation of 2'-FL with/without RS the day before investigation increased systemic butyrate concentrations in lean men as well as in men with prediabetes and obesity, while acetate only increased in lean men. The combination of 2'-FL with RS showed a putatively beneficial metabolic effect by lowering plasma FFA in lean men, indicating a phenotype-specific effect.

Clinical trial registration

nr. NCT04795804.

Microbiota-dependent influence of prebiotics on the resilience of infant gut microbiota to amoxicillin/clavulanate perturbation in an in vitro colon model

Antibiotic exposure disturbs the developing infant gut microbiota. The capacity of the gut microbiota to recover from this disturbance (resilience) depends on the type of antibiotic. In this study, infant gut microbiota was exposed to a combination of amoxicillin and clavulanate (amoxicillin/clavulanate) in an in vitro colon model (TIM-2) with fecal-derived microbiota from 1-month-old (1-M; a mixed-taxa community type) as well as 3-month-old (3-M; Bifidobacterium dominated community type) breastfed infants. We investigated the effect of two common infant prebiotics, 2'-fucosyllactose (2'-FL) or galacto-oligosaccharides (GOS), on the resilience of infant gut microbiota to amoxicillin/clavulanate-induced changes in microbiota composition and activity. Amoxicillin/clavulanate treatment decreased alpha diversity and induced a temporary shift of microbiota to a community dominated by enterobacteria. Moreover, antibiotic treatment increased succinate and lactate in both 1- and 3-M colon models, while decreasing the production of short-chain (SCFA) and branched-chain fatty acids (BFCA). The prebiotic effect on the microbiota recovery depended on the fermenting capacity of antibiotic-exposed microbiota. In the 1-M colon model, the supplementation of 2'-FL supported the recovery of microbiota and restored the production of propionate and butyrate. In the 3-M colon model, GOS supplementation supported the recovery of microbiota and increased the production of acetate and butyrate.

An in vitro platform for study of the human gut microbiome under an oxygen gradient

The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. We have developed an in vitro 40-plex platform that provides an oxygen gradient to support simultaneous maintenance of microaerobic and anaerobic microbes from the gut microbiome that can aid in rapid characterization of microbial interactions and direct comparison of individual microbiome samples. In this report, we demonstrate that the platform more closely maintained the microbial diversity and composition of human donor fecal microbiome samples than strict anaerobic conditions. The oxygen gradient established in the platform allowed the stratification and subsequent sampling of diverse microbial subpopulations that colonize microaerobic and anaerobic micro-environments. With the ability to run forty samples in parallel, the platform has the potential to be used as a rapid screening tool to understand how the gut microbiome responds to environmental perturbations such as toxic compound exposure, dietary changes, or pharmaceutical treatments.

The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function

The human colon is inhabited by a complex community of microbes. These microbes are integral to host health and physiology. Understanding how and when the microbiome causally influences host health will require microbiome models that can be tightly controlled and manipulated. While in vivo models are unrivalled in their ability to study host-microbial interplay, in vitro models are gaining in popularity as methods to study the ecology and function of the gut microbiota, and benefit from tight controllability and reproducibility, as well as reduced ethical constraints. In this set of protocols, we describe the Robogut, a single-stage bioreactor system designed to replicate the conditions of the distal human colon, to culture whole microbial communities derived from stool and/or colonic biopsy samples, with consideration of methods to create culture medium formulations and to build, run, and sample the bioreactor apparatus. Cleaning and maintenance of the bioreactor system are also described. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth medium preparation Support Protocol 1: Preparing medium supplements Basic Protocol 2: Preparing the bioreactor vessels Support Protocol 2: Making acid and base bottles Support Protocol 3: Preparing the effluent bottles Support Protocol 4: Making acid solution Support Protocol 5: Making base solution Basic Protocol 3: Preparing inoculum and inoculating bioreactors Alternate Protocol 1: Preparing inoculum less than 0.5% (w/v) of vessel volume Alternate Protocol 2: Preparing synthetic community aliquots and inoculation via the septum Alternate Protocol 3: Preparing inoculum from a tissue sample Basic Protocol 4: Sampling the bioreactor vessel Basic Protocol 5: Harvesting bioreactor vessel contents at end of experiment Support Protocol 6: Cleaning and sterilizing sampling needles Basic Protocol 6: Cleaning the bioreactor vessel Support Protocol 7: Cleaning bioreactor support bottles.

Impact Assessment of vB_KpnP_K1-ULIP33 Bacteriophage on the Human Gut Microbiota Using a Dynamic In Vitro Model

New control methods are needed to counter antimicrobial resistances and the use of bacteriophages as an alternative treatment seems promising. To that end, the effect of the phage vB_KpnP_K1-ULIP33, whose host is the hypervirulent Klebsiella pneumoniae SA12 (ST23 and capsular type K1), was assessed on intestinal microbiota, using an in vitro model: the SHIME® system (Simulator of the Human Intestinal Microbial Ecosystem). After stabilization of the system, the phage was inoculated for 7 days and its persistence in the different colons was studied until its disappearance from the system. The concentration of short chain fatty acids in the colons showed good colonization of the bioreactors by the microbiota and no significant effect related to the phage treatment. Diversity (α and β), the relative abundance of bacteria, and qPCR analysis targeting different genera of interest showed no significant variation following phage administration. Even if further in vitro studies are needed to assess the efficacy of this phage against its bacterial host within the human intestinal ecosystem, the phage ULIP33 exerted no significant change on the global colonic microbiota.

Multi-Compartmental Dissolution Method, an Efficient Tool for the Development of Enhanced Bioavailability Formulations Containing Poorly Soluble Acidic Drugs

The purpose of this study was to investigate the applicability of the Gastrointestinal Simulator (GIS), a multi-compartmental dissolution model, to predict the in vivo performance of Biopharmaceutics Classification System (BCS) Class IIa compounds. As the bioavailability enhancement of poorly soluble drugs requires a thorough understanding of the desired formulation, the appropriate in vitro modelling of the absorption mechanism is essential. Four immediate release ibuprofen 200 mg formulations were tested in the GIS using fasted biorelevant media. In addition to the free acid form, ibuprofen was present as sodium and lysine salts in tablets and as a solution in soft-gelatin capsules. In the case of rapid-dissolving formulations, the dissolution results indicated supersaturation in the gastric compartment, which affected the resulting concentrations in the duodenum and the jejunum as well. In addition, a Level A in vitro-in vivo correlation (IVIVC) model was established using published in vivo data, and then the plasma concentration profiles of each formulation were simulated. The predicted pharmacokinetic parameters were consistent with the statistical output of the published clinical study. In conclusion, the GIS method was found to be superior compared to the traditional USP method. In the future, the method can be useful for formulation technologists to find the optimal technique to enhance the bioavailability of poorly soluble acidic drugs.

Gut microbiota-mediated metabolism of green tea catechins and the biological consequences: An updated review

Multiple beneficial effects have been attributed to green tea catechins (GTCs). However, the bioavailability of GTCs is generally low, with only a small portion directly absorbed in the small intestine. The majority of ingested GTCs reaches the large intestinal lumen, and are extensively degraded via biotransformation by gut microbiota, forming many low-molecular-weight metabolites such as phenyl-γ-valerolactones, phenolic acids, butyrate, and acetate. This process not only improves the overall bioavailability of GTC-derived metabolites but also enriches the biological activities of GTCs. Therefore, the intra- and inter-individual differences in human gut microbiota as well as the resulting biological contribution of microbial metabolites are crucial for the ultimate health benefits. In this review, the microbial degradation of major GTCs was characterized and an overview of the in vitro models used for GTC metabolism was summarized. The intra- and inter-individual differences of human gut microbiota composition and the resulting divergence in the metabolic patterns of GTCs were highlighted. Moreover, the potential beneficial effects of GTCs and their gut microbial metabolites were also discussed. Overall, the microbial metabolites of GTCs with higher bioavailability and bioactive potency are key factors for the observed beneficial effects of GTCs and green tea consumption.

A review on the evolution of methods for intestinal in vitro organ culture and its application in veterinary science

Different techniques have been reported in studies of intestinal in vitro organ culture (IVOC). A robust compilation of all available methods is lacking in the literature, making it difficult to choose a method that corresponds to the study's demands. In this review, readers can assess the most available methods, allowing them to evaluate which is more suitable for their purposes and requirements. A simplified view of culturing intestinal explants is presented, highlighting the approachability of IVOC. Relevant findings from diverse veterinarian studies, where explants played a major role, as well as the technique used in each, are described to illustrate its applications. Finally, the strengths and limitations of the innovative intestinal IVOC methods are discussed. This review provides a collection of methods for intestinal explant culture and their possible applications in veterinary research. In this way, it aims to broaden access to IVOC techniques and aid decision-making regarding the best suited for a study's purposes.

In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls

The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.

Evaluation of Different Advanced Approaches to Simulation of Dynamic In Vitro Digestion of Polyphenols from Different Food Matrices-A Systematic Review

Phenolic compounds have become interesting bioactive antioxidant compounds with implications for obesity, cancer and inflammatory gastrointestinal pathologies. As the influence of digestion and gut microbiota on antioxidant behavior is yet to be completely elucidated, and due to limitations associated to in vivo studies, dynamic in vitro gastrointestinal models have been promoted. A systematic review was conducted of different databases (PubMed, Web of Science and Scopus) following PRISMA guidelines to assess different dynamic digestion models and assay protocols used for phenolic compound research regarding bioaccesibility and interaction with colonic microbiota. Of 284 records identified, those including dynamic multicompartmental digestion models for the study of phenolic compound bioaccesibility, bioactivity and the effects of microbiota were included, with 57 studies meeting the inclusion criteria. Different conditions and experimental configurations as well as administered doses, sample treatments and microbiological assays of dynamic digestion studies on polyphenols were recorded and compared to establish their relevance for the dynamic in vitro digestion of phenolic compounds. While similarities were observed in certain experimental areas, a high variability was found in others, such as administered doses. A description of considerations on the study of the digestion of phenolic compounds is proposed to enhance comparability in research.

In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome

Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.

2'-Fucosyllactose inhibits proliferation of Clostridioides difficile ATCC 43599 in the CDi-screen, an in vitro model simulating Clostridioides difficile infection

Background

Clostridioides difficile is a Gram-positive anaerobic bacterium that can produce the toxins TcdA and/or TcdB and is considered an opportunistic pathogen. C. difficile is mainly transmitted as endospores, which germinate to produce the pathogenic vegetative cells under suitable conditions in the gut. To efficiently screen novel therapeutic- interventions against the proliferation of C. difficile within a complex microbial community, platforms are needed that facilitate parallel experimentation. In order to allow for screening of novel interventions a medium-to-high throughput in vitro system is desirable. To this end, we have developed the 96-well CDi-screen platform that employs an adapted simulated ileal effluent medium (CDi-SIEM) and allows for culturing of pathogenic C. difficile.

Methods

C. difficile strain ATCC 43599 was inoculated in the form of vegetative cells and spores into the CDi-screen in the presence and absence of a cultured fecal microbiota and incubated for 48h. To demonstrate its utility, we investigated the effect of the human milk oligosaccharide 2'-Fucosyllactose (2'-FL) at 4 and 8 mg/mL on C. difficile outgrowth and toxin production in the CDi-screen. The test conditions were sampled after 24 and 48 hours. C. difficile -specific primers were used to monitor C. difficile growth via qPCR and barcoded 16S rRNA gene amplicon sequencing facilitated the in-depth analysis of gut microbial community dynamics.

Results

C. difficile ATCC 43599 proliferated in CDi-SIEM, both when inoculated as spores and as vegetative cells. The strain reached cell numbers expressed as C. difficile genome equivalents of up to 10 8 cells per mL after 24h of incubation. 2'-FL significantly inhibited the outgrowth of the ATTC 43599 strain within a complex human gut microbial community in the CDi-screen. In addition, a dose-dependent modulation of the gut microbial community composition by 2'-FL supplementation was detected, with a significant increase in the relative abundance of the genus Blautia in the presence of 2'-FL.

Conclusion

The CDi-screen is suitable for studying C. difficile proliferation in a complex gut ecosystem and for screening for anti-pathogenic interventions that target C. difficile directly and/or indirectly through interactions with the gut microbiota. Different doses of compounds such as in this study the dose of the human milk oligosaccharide 2'-FL can be screened for efficacy in the inhibition of C. difficile proliferation.

Current in Vitro and Animal Models for Understanding Foods: Human Gut-Microbiota Interactions

The food-gut microbiota interaction is an important regulator of human health. Numerous in vitro and animal models have thus been developed in order to simulate the specific food-gut microbiota and/or host-gut microbiota interactions in the human colon. This review summarizes the design principles of each model and discusses their advantages and weaknesses in terms of studying food-gut microbiota interactions. In vitro fermentation models appear to be reliable methods to investigate various aspects involved in the food-gut microbiota interactions in humans. However, many physiological perspectives lack appreciation of these models, such as peristaltic movement, biochemical conditions, and gastrointestinal anatomy. Animal models provide more physiological relevance to human trials compared to in vitro models. However, they may have gastrointestinal tract aspects that are distinct from human subjects. This review contains important information that can help the development of more advanced models to study food-gut microbiota interactions in humans.

An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota

Lytic bacteriophages are considered safe for human consumption as biocontrol agents against foodborne pathogens, in particular in ready-to-eat foodstuffs. Phages could, however, evolve to infect different hosts when passing through the gastrointestinal tract (GIT). This underlines the importance of understanding the impact of phages towards colonic microbiota, particularly towards bacterial families usually found in the colon such as the Enterobacteriaceae. Here we propose in vitro batch fermentation as model for initial safety screening of lytic phages targeting Shiga toxin-producing Escherichia coli (STEC). As inoculum we used faecal material of three healthy donors. To assess phage safety, we monitored fermentation parameters, including short chain fatty acid production and gas production/intake by colonic microbiota. We performed shotgun metagenomic analysis to evaluate the outcome of phage interference with colonic microbiota composition and functional potential. During the 24 h incubation, concentrations of phage and its host were also evaluated. We found the phage used in this study, named E. coli phage vB_EcoS_Ace (Ace), to be safe towards human colonic microbiota, independently of the donors’ faecal content used. This suggests that individuality of donor faecal microbiota did not interfere with phage effect on the fermentations. However, the model revealed that the attenuated STEC strain used as phage host perturbed the faecal microbiota as based on metagenomic analysis, with potential differences in metabolic output. We conclude that the in vitro batch fermentation model used in this study is a reliable safety screening for lytic phages intended to be used as biocontrol agents.

Overview of the Nomenclature and Network of Contributors to the Development of Bioreactors for Human Gut Simulation Using Bibliometric Tools: A Fragmented Landscape

The evolution of complex in vitro models of the human gastrointestinal system to interrogate the biochemical functionality of the gut microbiome has augmented our understanding of its role in human physiology and pathology. With 5718 authors from 52 countries, gut bioreactor research reflects the growing awareness of our need to understand the contribution of the gut microbiome to human health. Although a large body of knowledge has been generated from in vitro models, it is scattered and defined by application-specific terminologies. To better grasp the capacity of bioreactors and further our knowledge of the human gastrointestinal system, we have conducted a cross-field bibliometric search and mapped the evolution of human gastrointestinal in vitro research. We present reference material with the aim of identifying key authors and bioreactor types to enable researchers to make decisions regarding the choice of method for simulating the human gut in the context of microbiome functionality.

Role, Relevance, and Possibilities of In vitro fermentation models in human dietary, and gut-microbial studies

Dietary studies play a crucial role in determining the health-benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short-chain fatty acids (SCFA). These diet-induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M-SHIME, CoMiniGut, and Dynamic Gastrointestinal Simulator (SIMGI) make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, i.e., proximal, transverse, and distal colon, making the findings physiologically more significant. Further, post-fermentation samples can be analyzed using metagenomic, metabolomic, qPCR and flow cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies. This article is protected by copyright. All rights reserved.

The Mini Colon Model: a benchtop multi-bioreactor system to investigate the gut microbiome

In vitro fermentation systems allow for the investigation of gut microbial communities with precise control of various physiological parameters while decoupling confounding factors from the human host. Current systems, such as the SHIME and Robogut, are large in footprint, lack multiplexing, and have low experimental throughput. Alternatives which address these shortcomings, such as the Mini Bioreactor Array system, are often reliant on expensive specialized equipment, which hinders wide replication across labs. Here, we present the Mini Colon Model (MiCoMo), a low-cost, benchtop multi-bioreactor system that simulates the human colon environment with physiologically relevant conditions. The device consists of triplicate bioreactors working independently of an anaerobic chamber and equipped with automated pH, temperature, and fluidic control. We conducted 14-d experiments and found that MiCoMo was able to support a stable complex microbiota community with a Shannon Index of 3.17 ± 0.65, from individual fecal samples after only 3-5 d of inoculation. MiCoMo also retained inter-sample microbial differences by developing closely related communities unique to each donor, while maintaining both minimal variations between replicate reactors (average Bray-Curtis similarity 0.72 ± 0.13) andday-to-day variations (average Bray-Curtis similarity 0.81±0.10) after this short stabilization period. Together, these results establish MiCoMo as an accessible system for studying gut microbial communities with high throughput and multiplexing capabilities.

Structure and function of non-digestible carbohydrates in the gut microbiome

Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.

Effects of Monascus application on in vitro digestion and fermentation characteristics of fish protein

The aim of this study was to investigate the digestion and fermentation properties of fish protein fermented by Monascus. Semi-dried fish was fermented by applying Monascus purpureus Went M 3.439. Our results show that the Monascus fermentation of the fish protein enriched the free amino acids and achieved a relatively higher glutamate content than the control group. The Monascus treatment promoted the decomposition of the fish protein during in vitro digestion, reduced the ammonia and indole content and tended to increase the propionic acid content during in vitro fermentation. The Monascus treatment considerably changed the gut microbiota composition, and particularly increased the relative abundance of Parabacteroides in the in vitro fermentation model of human distal colon. Consumption of Monascus fermented fish protein could result in positive changes in fermentation metabolites and gut microbiota, which brings potential health benefits.

An Advanced Bioreactor Simulating Dynamic Physiological Conditions in the Human Ascending Colon: MimiCol3

In recent years, the colon has become a hot topic in biopharmaceutical research as several in vitro models of the human colon have been presented. A major focus is on the characterization of the microbiota and its capabilities. The aim of the present study was to further develop the MimiCol, preserving its properties and accelerating data acquisition. Emphasis was placed on the simplicity of its design and easy scalability. To prove the viability of the concept, degradation of sulfasalazine was investigated, and the bacterial composition during the experiment was assessed by 16S rRNA sequencing. The transfer of the experimental conditions to the new model was successful. Commercially available components were implemented in the setup. The model MimiCol³ represented the colon ascendens satisfactorily in its properties regarding volume, pH value, and redox potential. 16S rRNA sequencing led to further insights into the bacterial composition in the vessels. Degradation of sulfasalazine was in good agreement with in vivo data. The new model of the colon ascendens MimiCol³ enabled us to collect more reliable data, as three experiments were conducted simultaneously under the same conditions.

Odorant Metabolism in Humans

Odorants are relatively small molecules which are easily taken up and distributed in the human body. Despite their relevance in everyday life, however, only a limited amount of evidence about their metabolism, pathways, and bioactivities in the human body exists. With this Review, we aim to encourage future interdisciplinary research on the function and mechanisms of the biotransformation of odorants, involving different disciplines such as nutrition, medicine, biochemistry, chemistry, and sensory sciences. Starting with a general overview of the different ways of odorant uptake and enzymes involved in the metabolism of odorants, a more precise description of biotransformation processes and their function in the oral cavity, the nose, the lower respiratory tract (LRT), and the gastrointestinal tract (GIT) is given together with an overview of the different routes of odorant excretion. Finally, perspectives for future research are discussed.

A Review of In Vitro Methods for Measuring the Glycemic Index of Single Foods: Understanding the Interaction of Mass Transfer and Reaction Engineering by Dimensional Analysis

The Glycemic Index (GI) has been described by an official method ISO (International Organization for Standardization) 26642:2010 for labeling purposes. The development of in vitro methods for GI measurement has faced significant challenges. Mass transfer and reaction engineering theory may assist in providing a quantitative understanding of in vitro starch digestion and glycemic response from an engineering point of view. We suggest that in vitro GI measurements should consider the mouth and the stomach in terms of fluid mechanics, mass transfer, length scale changes, and food-solvent reactions, and might consider a significant role for the intestine as an absorption system for the glucose that is generated before the intestine. Applying mass transfer and reaction engineering theory may be useful to understand quantitative studies of in vitro GI measurements. The relative importance of reactions and mass-transfer has been estimated from literature measurements through estimating the Damköhler numbers (Da), and the values estimated of this dimensionless group (0.04–2.9) suggest that both mass transfer and chemical reaction are important aspects to consider.

Structural Characterization and In Vitro Fermentation Characteristics of Enzymatically Extracted Black Mulberry Polysaccharides

In this study, we systematically investigated the structural characterization and in vitro fermentation patterns of crude black mulberry fruit polysaccharides (BMPs), either extracted by water (BMP) or by enzymatic treatment. Different enzymatic treatments were pectinase-extracted (PE)-BMP, pectin lyase-extracted (PL)-BMP, cellulase-extracted (CE)-BMP, and compound enzymes-extracted (M)-BMP (pectinase:pectin lyase:cellulase = 1:1:1). Our results show that enzymatic treatment improved the polysaccharide yield and led to a different chemical composition and structure for the polysaccharides. Change dynamics during the in vitro fermentation indicated that BMPs could indeed be degraded and consumed by human fecal microbiota and that different BMPs showed different degrees of fermentability. In addition, BMPs stimulated the growth of Bacteroidetes and Firmicutes, inhibited the growth of Fusobacteria and Proteobacteria (except for CE-BMP), and induced the production of short-chain fatty acids (SCFAs). Furthermore, we found that BMP and PL-BMP exhibited better fermentability and prebiotic potential than the other polysaccharides.