Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review

Investigating the gut bacteria structure and function of hibernating bats through 16S rRNA high-throughput sequencing and culturomics

The gut microbiota of bats is vital for their roles in health and the ecosystem, yet studies on hibernating bats in southwest China, particularly in the unique karst landscape of Guizhou, are limited. We captured three hibernating bat species-Pipistrellus (PB), Rhinolophus (RB), and Myotis (MB)-in Liping County, collecting rectal samples for 16S rRNA amplicon sequencing. Data processing involved Trimmomatic, Flash, and Qiime2 for operational taxonomic unit (OTU) standardization and species annotation via the Greengenes database. Differential abundance was analyzed using LEfSe, and diversity metrics were assessed through alpha and beta diversity analyses. The RB group was predominantly composed of Proteobacteria (80.99%), while MB and PB exhibited diverse compositions with significant OTU richness (729 in MB). Notable genera included Hafnia and Yersinia in RB and Cosenzaea myxofaciens in MB. High proportions of unclassified taxa were observed, particularly in RB (83.81%). Functional predictions indicated metabolic pathways, with a significant representation of human diseases in PB. Culturomics revealed the successful cultivation of Huaxiibacter chinensis and Enterobacter chengduensis from bats for the first time and appears to have identified a new bacterium that is likely closely related to Clostridium paraputrificum.IMPORTANCEOur research reveals significant differences in the composition and diversity of the gut microbiota among three bat groups (PB, MB, and RB) from Guizhou. While Proteobacteria predominates in all groups, its abundance varies. Notably, the high richness of operational taxonomic units (OTUs) in the MB group suggests a more diverse microbial ecosystem, underscoring the complex interactions between species diversity, diet, gut microbiota, and overall ecological dynamics in bats. Furthermore, the substantial presence of unknown bacterial species in their intestines highlights the critical importance of cultivation-based approaches. The presence of specific taxa may have potential health implications for both bats and humans. These findings emphasize the need for further investigations into the functional roles of these microbiota and their contributions to host health. Future research should focus on longitudinal studies to elucidate these intricate interactions.

How to Study the Effects of Dietary Lipids on the Small Intestinal Microbiome? Methodological Design and Evaluation of the Human HealThy fAt, haPpy mIcRobiome (TAPIR) Proof-of-Concept Study

Background

Emerging evidence highlights the importance of the small intestinal microbiota in digestion and metabolism, underscoring the challenging need for human studies beyond fecal analyses.

Objective

The TAPIR (acronym of "healthy fat, happy microbiome") proof-of-concept study was primarily designed to confirm the interaction between the small intestinal microbiota and dietary lipids in healthy adults with a challenge test. We also aimed to assess the impact of a plant-based mild-ketogenic preconditioning diet on microbiome composition and function. Here, we comprehensively describe our extensive study protocol and evaluate the study execution.

Methods

Participants consumed an 8-day preconditioning diet, followed by a high-fat shake challenge test on day 9. During this test, fasting and postprandial small intestinal aspirates were collected every 20 min via a naso-intestinal catheter, and blood samples were collected hourly. Participants ingested small intestine aspiration capsules before (day 0), on day 6 of the preconditioning diet, and during the challenge test. Dietary compliance, capsule retrieval, sample collection, stool pattern, and gastrointestinal complaints were monitored to evaluate study execution.

Results

Twenty adults with a mean age of 48 y (19-88 y) and a mean body mass index (BMI) of 24.3 kg/m2 (19.5-30 kg/m2) consumed a preconditioning diet with a 96% compliance. There were no significant changes in gastrointestinal complaints and stool patterns during the study. Mean aspiration capsule retrieval rate was 94.7%, with mean sample weights per timepoint between 84.2 and 95.4 mg and median transit times between 32.8 and 49.3 h. The average success rate of aspirate collection by catheter was 49%, varying significantly between time points.

Conclusion

The dietary intervention was successful and well-tolerated. We sampled in the small intestine with capsules and catheters, each with its own (dis)advantages. The comprehensive description and evaluation of our study execution offer practical insights supporting future study designs in food-microbe interactions in the small intestine.The trial is registered at clinicaltrials.gov as NCT06064266.

Inulin as a Biopolymer; Chemical Structure, Anticancer Effects, Nutraceutical Potential and Industrial Applications: A Comprehensive Review

Inulin is a versatile biopolymer that is non-digestible in the upper alimentary tract and acts as a bifidogenic prebiotic which selectively promotes gut health and modulates gut-organ axes through short-chain fatty acids and possibly yet-to-be-known interactions. Inulin usage as a fiber ingredient in food has been approved by the FDA since June 2018 and it is predicted that the universal inulin market demand will skyrocket in the near future because of its novel applications in health and diseases. This comprehensive review outlines the known applications of inulin in various disciplines ranging from medicine to industry, covering its benefits in gut health and diseases, metabolism, drug delivery, therapeutic pharmacology, nutrition, and the prebiotics industry. Furthermore, this review acknowledges the attention of researchers to knowledge gaps regarding the usages of inulin as a key modulator in the gut-organ axes.

Establishing baselines for prebiotic production in controlled environments for applications in space and vertical farming

Prebiotics might contribute to astronauts' health in space, yet their production in Bioregenerative Life Support Systems (BLSS) remains largely unexplored. Here, chicory (Cichorium intybus L.) exhibited the most appropriate characteristics among seven candidate species as the ideal crop for space prebiotic production systems. Furthermore, we evaluated chicory's performance under different light intensities (250 μmol m-2 s-1 and 500 μmol m-2 s-1 of photosynthetically active radiation) and growing cycle lengths (76 and 91 days after sowing) to optimize prebiotic production. Our findings reveal chicory's remarkable adaptability to fully controlled growing conditions and its ability to accumulate high levels of inulin in the young taproot, despite the short growing cycle. The length of the growing period influenced the productivity of biomass and inulin, the latter depending more on taproot biomass than on inulin content. A growing area of 6.3 m2 might be sufficient for a daily production of 12 g of inulin, the amount of "native chicory inulin" recognized by EFSA to promote health benefits in humans. These results establish important baselines for prebiotic production in BLSS or Controlled Environment Agriculture (CEA) and may be used to design fully controlled cropping systems for space and Earth based vertical farming facilities.

Classifying compounds as prebiotics - scientific perspectives and recommendations

Microbiomes provide key contributions to health and potentially important therapeutic targets. Conceived nearly 30 years ago, the prebiotic concept posits that targeted modulation of host microbial communities through the provision of selectively utilized growth substrates provides an effective approach to improving health. Although the basic tenets of this concept remain the same, it is timely to address certain challenges pertaining to prebiotics, including establishing that prebiotic-induced microbiota modulation causes the health outcome, determining which members within a complex microbial community directly utilize specific substrates in vivo and when those microbial effects sufficiently satisfy selectivity requirements, and clarification of the scientific principles on which the term 'prebiotic' is predicated to inspire proper use. In this Expert Recommendation, we provide a framework for the classification of compounds as prebiotics. We discuss ecological principles by which substrates modulate microbiomes and methodologies useful for characterizing such changes. We then propose statistical approaches that can be used to establish causal links between selective effects on the microbiome and health effects on the host, which can help address existing challenges. We use this information to provide the minimum criteria needed to classify compounds as prebiotics. Furthermore, communications to consumers and regulatory approaches to prebiotics worldwide are discussed.

Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics

Diet may influence the gut microbiota and subsequently affect the host's health. Recent developments in methods analyzing the composition and function of the gut microbiota allow a deeper understanding of diet-gut microbiota relationships. A state-of-the-art methodology, shotgun metagenomics sequencing, offers a higher taxonomic resolution of the gut microbiota at the bacterial species and strain levels, and more accurate information regarding the functional potential of gut microbiota. Here, the available evidence on the relationship between diet and gut microbiota was critically reviewed, focusing on results emerging from recent metagenomics sequencing studies applied in randomized controlled trials and observational studies. The PubMed and Embase databases were used to search publications between January 2011 and September 2023. Thus far, the number of studies is limited, and the study designs and methods utilized have been variable. Nevertheless, the cumulative evidence from interventions relates to dietary fiber as a modifier of bacterial species, such as Anaerostipes hadrus and Faecalibacterium prausnitzii. Furthermore, observational studies have detected associations between different dietary patterns and food groups with certain microbial species. Utilization of metagenomics sequencing is becoming more common and will undoubtedly provide further insights into diet-gut microbiota relationships at the species level as well as their functional pathways in the near future. For reproducible results and to draw reliable conclusions across various studies on diet-gut microbiota relationships, there is a need for harmonization of the study designs and standardized ways of reporting.

Prebiotics: Comprehensive analysis of sources, structural characteristics and mechanistic roles in disease regulation

Prebiotics are nondigestible components that comprise short-chain carbohydrates, primarily oligosaccharides, which are converted into beneficial compounds by probiotics. Various plant substances with prebiotic properties provide substantial health benefits and are used to prevent different diseases and for medical and clinical applications. Consuming prebiotics gives impeccable benefits since it aids in gut microbial balance. Prebiotic research is primarily concerned with the influence of intestinal disorders. The proposed review will describe recent data on the sources, structures, implementation of prebiotics and potential mechanisms in preventing and treating various disorders, with an emphasis on the gut microbiome. Prebiotics have a distinctive impact on the gastro intestine by explicitly encouraging the growth of probiotic organisms like Bifidobacteria and Lactobacilli. This in turn augments the body's inherent ability to fend off harmful pathogens. Prebiotic carbohydrates may also provide other non-specific advantages due to their fermentation in the large intestine. Additional in vivo research is needed to fully comprehend the interactions between prebiotics and probiotics ingested by hosts to improve their nutritional and therapeutic benefits.

Investigating the response of the butyrate production potential to major fibers in dietary intervention studies

Interventions involving dietary fibers are known to benefit host health. A leading contribution of gut microbiota is commonly recognized with production of short chain fatty acids (SCFA) suspected to play a key role. However, the detailed mechanisms are largely unknown, and apart from a well-described bifidogenic effect of some fibers, results for other bacterial taxa are often incongruent between studies. We performed pooled analyses of 16S rRNA gene data derived from intervention studies (n = 14) based on three fibers, namely, inulin-type fructans (ITF), resistant starch (RS), and arabinoxylan-oligosaccharides (AXOS), harmonizing the bioinformatics workflow to reveal taxa stimulated by those substrates, specifically focusing on the SCFA-production potential. The results showed an increased butyrate production potential after ITF (p < 0.05) and RS (p < 0.1) treatment via an increase in bacteria exhibiting the enzyme butyryl-CoA:acetate CoA-transferase (but) that was governed by Faecalibacterium, Anaerostipes (ITF) and Agathobacter (RS) respectively. AXOS did not promote an increase in butyrate producers, nor were pathways linked to propionate production stimulated by any intervention. A bifidogenic effect was observed for AXOS and ITF, which was only partly associated with the behavior of but-containing bacteria and largely represented a separate response. Low and high Ruminococcus abundances pre-intervention for ITF and RS, respectively, promoted an increase in but-containing taxa (p < 0.05) upon interventions, whereas initial Prevotella abundance was negatively associated with responses of butyrate producers for both fibers. Collectively, our data demonstrate targeted stimulation of specific taxa by individual fibers increasing the potential to synthesize butyrate, where gut microbiota composition pre-intervention strongly controlled outcomes.

The impact of daily supplementation with rhamnogalacturonan-I on the gut microbiota in healthy adults: A randomized controlled trial

Pectin and its derivatives have been shown to modulate immune signaling as well as gut microbiota in preclinical studies, which may constitute the mechanisms by which supplementation of specific pectic polysaccharides confers protection against viral respiratory infections. In a double-blind, placebo-controlled rhinovirus (RV16) challenge study, healthy volunteers were randomized to consume placebo (0.0 g/day) (N = 46), low-dose (0.3 g/day) (N = 49) or high-dose (1.5 g/day) (N = 51) of carrot derived rhamnogalacturonan-I (cRG-I) for eight weeks and they were subsequently challenged with RV-16. Here, the effect of 8-week cRG-I supplementation on the gut microbiota was studied. While the overall gut microbiota composition in the population was generally unaltered by this very low dose of fibre, the relative abundance of Bifidobacterium spp. (mainly B. adolescentis and B. longum) was significantly increased by both doses of cRG-1. Moreover, daily supplementation of cRG-I led to a dose-dependent reduction in inter- and intra-individual microbiota heterogeneity, suggesting a stabilizing effect on the gut microbiota. The severity of respiratory symptoms did not directly correlate with the cRG-I-induced microbial changes, but several dominant groups of the Ruminococcaceae family and microbiota richness were positively associated with a reduced and hence desired post-infection response. Thus, the present results on the modulation of the gut microbiota composition support the previously demonstrated immunomodulatory and protective effect of cRG-I during a common cold infection.

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.

The Role of the FODMAP Diet in IBS

The low FODMAP (fermentable oligosaccharide, disaccharide, monosaccharide, and polyol) diet is a beneficial therapeutic approach for patients with irritable bowel syndrome (IBS). However, how the low FODMAP diet works is still not completely understood. These mechanisms encompass not only traditionally known factors such as luminal distension induced by gas and water but also recent evidence on the role of FOMAPs in the modulation of visceral hypersensitivity, increases in intestinal permeability, the induction of microbiota changes, and the production of short-chain fatty acids (SCFAs), as well as metabolomics and alterations in motility. Although most of the supporting evidence is of low quality, recent trials have confirmed its effectiveness, even though the majority of the evidence pertains only to the restriction phase and its effectiveness in relieving abdominal bloating and pain. This review examines potential pathophysiological mechanisms and provides an overview of the existing evidence on the effectiveness of the low FODMAP diet across various IBS subtypes. Key considerations for its use include the challenges and disadvantages associated with its practical implementation, including the need for professional guidance, variations in individual responses, concerns related to microbiota, nutritional deficiencies, the development of constipation, the necessity of excluding an eating disorder before commencing the diet, and the scarcity of long-term data. Despite its recognized efficacy in symptom management, acknowledging these limitations becomes imperative for a nuanced comprehension of the role of a low FODMAP diet in managing IBS. By investigating its potential mechanisms and evidence across IBS subtypes and addressing emerging modulations alongside limitations, this review aims to serve as a valuable resource for healthcare practitioners, researchers, and patients navigating the intricate landscape of IBS.

Prebiotics in food and dietary supplements: a roadmap to EU health claims

Numerous studies have established that prebiotic ingredients in foods and dietary supplements may play a role in supporting human health. Over the three decades that have passed since prebiotics were first defined as a concept, research has revealed a complex universe of prebiotic-induced changes to the human microbiota. There are strong indications of a direct link between these prebiotic-induced changes and specific health benefits. However, at the present time, the EU has not permitted use of the term 'prebiotic' in connection with an approved health claim. This paper is the outcome of a workshop organized on the 25th October 2023 by the European branch of the International Life Science Institute (ILSI). It provides an overview of the regulatory requirements for authorized health claims in the EU, key areas of prebiotic research, and findings to date in relation to prebiotics and digestive, immune, metabolic and cognitive health. Research gaps and documentation challenges are then explored and a roadmap proposed for achieving authorization of 'prebiotic' in the wording of future EU health claims.

Experimental Capacity of Human Fecal Microbiota to Degrade Fiber and Produce Short-Chain Fatty Acids Is Associated with Diet Quality and Anthropometric Parameters

BACKGROUND

Short-chain fatty acids (SCFAs) are considered beneficial to human health. The associations between bacterial capacity to produce SCFAs, diet, and health are not fully understood.

OBJECTIVE

We aimed to evaluate the capacity of human fecal microbiota to produce SCFAs and to metabolize soluble and insoluble fiber and to study its associations with human diet, anthropometric parameters, and carbohydrate and lipid metabolism.

METHODS

A cross-sectional study was carried out with 200 adult participants. Diet was evaluated using food records. Capacity to produce acetate, butyrate, and propionate and to degrade soluble fiber were assessed in an ex vivo experiment where fecal samples were inoculated in a pectin-containing broth. Fecal β-glucosidase activity was measured to assess potential to degrade insoluble fiber.

RESULTS

The main dietary determinants of high capacity to metabolize fiber were high intake of vegetables, fruits, nuts, and seeds. After adjusting analyses for confounders, glucose and lipid parameters were not significantly associated with any of the studied microbial capacities, but the capacity to produce propionic acid was significantly associated with hip circumference (β = -0.018, P = 0.044), which was seen especially in people eating healthy.

CONCLUSIONS

We confirmed that high intake of fiber-rich products is positively associated with the capacity of fecal microbiota to degrade soluble and insoluble dietary fiber and that people eating healthy food might benefit from enhanced microbial capacity to produce propionic acid.

Individual and Group-Based Effects of In Vitro Fiber Interventions on the Fecal Microbiota

The development of microbiome-targeted strategies is limited by individual differences in gut microbiome composition and metabolic responses to interventions. In vitro models that can replicate this variation allow us to conduct pre-clinical studies and assess efficacy. This study describes the exposure of 16 individual fecal microbiota samples to 5 different fibers using an in vitro system for the anaerobic cultivation of bacteria. The individual microbiota differed in composition and metabolite profiles (short-chain fatty acids and branched-chain fatty acids) after incubation with the fibers. Furthermore, microbiota composition after fiber incubation was significantly different between subjects with good intestinal health and subjects with Inflammatory Bowel Disease (IBD). α-diversity was differently affected by dietary fibers; for example, exposure to psyllium resulted in increased diversity in the healthy group and in decreased diversity in the IBD group. Instead, the functional metabolic profile did not differ between the two groups. Finally, the combination of all fibers, tested on the microbiota from IBD subjects, resulted in stronger overall effects on both microbiota composition and metabolite production compared to the single fibers. These results confirm that incubation with dietary fiber results in different compositional and functional effects on individual microbiota and that in vitro models represent successful tools for studying individual fiber effects.

Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans

Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of <0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.

Dietary Patterns, Gut Microbiota Remodeling, and Cardiometabolic Disease

The cardiovascular and metabolic disorders, collectively known as cardiometabolic disease (CMD), are high morbidity and mortality pathologies associated with lower quality of life and increasing health-care costs. The influence of the gut microbiota (GM) in dictating the interpersonal variability in CMD susceptibility, progression and treatment response is beginning to be deciphered, as is the mutualistic relation established between the GM and diet. In particular, dietary factors emerge as pivotal determinants shaping the architecture and function of resident microorganisms in the human gut. In turn, intestinal microbes influence the absorption, metabolism, and storage of ingested nutrients, with potentially profound effects on host physiology. Herein, we present an updated overview on major effects of dietary components on the GM, highlighting the beneficial and detrimental consequences of diet-microbiota crosstalk in the setting of CMD. We also discuss the promises and challenges of integrating microbiome data in dietary planning aimed at restraining CMD onset and progression with a more personalized nutritional approach.

HMOs Exert Marked Bifidogenic Effects on Children's Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition

Prebiotics are substrates that are selectively utilized by host microorganisms, thus conferring a health benefit. There is a growing awareness that interpersonal and age-dependent differences in gut microbiota composition impact prebiotic effects. Due to the interest in using human milk oligosaccharides (HMOs) beyond infancy, this study evaluated how HMOs [2'Fucosyllactose (2'FL), Lacto-N-neotetraose (LNnT), 3'Sialyllactose (3'SL), 6'Sialyllactose (6'SL)] and blends thereof affect the microbiota of 6-year-old children (n = 6) and adults (n = 6), compared to prebiotics inulin (IN) and fructooligosaccharides (FOS). The ex vivo SIFR® technology was used, given its demonstrated predictivity in clinical findings. First, HMOs and HMO blends seemed to maintain a higher α-diversity compared to FOS/IN. Further, while 2'FL/LNnT were bifidogenic for both age groups, 3'SL/6'SL and FOS/IN were exclusively bifidogenic for children and adults, respectively. This originated from age-related differences in microbiota composition because while 3'SL/6'SL stimulated B. pseudocatenulatum (abundant in children), FOS/IN enhanced B. adolescentis (abundant in adults). Moreover, all treatments significantly increased acetate, propionate and butyrate (only in adults) with product- and age-dependent differences. Among the HMOs, 6'SL specifically stimulated propionate (linked to Bacteroides fragilis in children and Phocaeicola massiliensis in adults), while LNnT stimulated butyrate (linked to Anaerobutyricum hallii in adults). Indole-3-lactic acid and 3-phenyllactic acid (linked to immune health) and gamma-aminobutyric acid (linked to gut-brain axis) were most profoundly stimulated by 2'FL and HMO blends in both children and adults, correlating with specific Bifidobacteriaceae. Finally, 2'FL/LNnT increased melatonin in children, while 3'SL remarkably increased folic acid in adults. Overall, age-dependent differences in microbiota composition greatly impacted prebiotic outcomes, advocating for the development of age-specific nutritional supplements. HMOs were shown to be promising modulators in the adult, and particularly the children's microbiota. The observed HMO-specific effects, likely originating from their structural heterogeneity, suggest that blends of different HMOs could maximize treatment effects.

Short-chain fatty acids as a link between diet and cardiometabolic risk: a narrative review

AIM

Diet has a profound impact on cardiometabolic health outcomes such as obesity, blood glucose, blood lipids and blood pressure. In recent years, the gut microbiota has emerged as one of several potential key players explaining dietary effects on these outcomes. In this review we aim to summarise current knowledge of interaction between diet and gut microbiota focusing on the gut-derived microbial metabolites short-chain fatty acids and their role in modulating cardiometabolic risk.

FINDINGS

Many observational and interventional studies in humans have found that diets rich in fibre or supplemented with prebiotic fibres have a favourable effect on the gut microbiota composition, with increased diversity accompanied by enhancement in short-chain fatty acids and bacteria producing them. High-fat diets, particularly diets high in saturated fatty acids, have shown the opposite effect. Several recent studies indicate that the gut microbiota modulates metabolic responses to diet in, e.g., postprandial blood glucose and blood lipid levels. However, the metabolic responses to dietary interventions, seem to vary depending on individual traits such as age, sex, ethnicity, and existing gut microbiota, as well as genetics. Studies mainly in animal models and cell lines have shown possible pathways through which short-chain fatty acids may mediate these dietary effects on metabolic regulation. Human intervention studies appear to support the favourable effect of short-chain fatty acid in animal studies, but the effects may be modest and vary depending on which cofactors were taken into consideration.

CONCLUSION

This is an expanding and active field of research that in the near future is likely to broaden our understanding of the role of the gut microbiota and short-chain fatty acids in modulating metabolic responses to diet. Nevertheless, the findings so far seem to support current dietary guidelines encouraging the intake of fibre rich plant-based foods and discouraging the intake of animal foods rich in saturated fatty acids.

Response of murine gut microbiota to a prebiotic based on oligosaccharides derived via hydrolysis of fungal α-(1→3)-d-glucan: Preclinical trial study on mice

We investigated the modulating effect of α-(1→3)-glucooligosaccharides (GOS), i.e. a product of fungal α-(1→3)-d-glucan hydrolysis, on the gut microbiota composition. Mice were fed with a GOS-supplemented diet and two control diets for 21 days, and fecal samples were collected at 0, 1, and 3-week time points. The bacterial community composition was determined by 16S rRNA gene Illumina sequencing. The gut microbiota of the GOS-supplemented mice showed profound time-dependent changes in the taxonomic composition; however, we did not observe significant changes in α-diversity indices. The biggest number of genus abundance shifts after 1 week of the treatment was noticed between the group of the GOS-supplemented mice and the controls; however, the differences were still relevant after the 3-week treatment. The GOS-supplemented mice displayed higher abundance of Prevotella spp., with a concomitant decrease in the abundance of Escherichia-Shigella. Hence, GOS seems to be a promising candidate for a new prebiotic.

Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential

Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.

The Potential of Pectins to Modulate the Human Gut Microbiota Evaluated by In Vitro Fermentation: A Systematic Review

Pectin is a dietary fiber, and its health effects have been described extensively. Although there are limited clinical studies, there is a growing body of evidence from in vitro studies investigating the effect of pectin on human gut microbiota. This comprehensive review summarizes the findings of gut microbiota modulation in vitro as assessed by 16S rRNA gene-based technologies and elucidates the potential structure-activity relationships. Generally, pectic substrates are slowly but completely fermented, with a greater production of acetate compared with other fibers. Their fermentation, either directly or by cross-feeding interactions, results in the increased abundances of gut bacterial communities such as the family of Ruminococcaceae, the Bacteroides and Lachnospira genera, and species such as Lachnospira eligens and Faecalibacterium prausnitzii, where the specific stimulation of Lachnospira and L. eligens is unique to pectic substrates. Furthermore, the degree of methyl esterification, the homogalacturonan-to-rhamnogalacturonan ratio, and the molecular weight are the most influential structural factors on the gut microbiota. The latter particularly influences the growth of Bifidobacterium spp. The prebiotic potential of pectin targeting specific gut bacteria beneficial for human health and well-being still needs to be confirmed in humans, including the relationship between its structural features and activity.

Essential Factors for a Healthy Microbiome: A Scoping Review

Recent discoveries of the purpose and potential of microbial interactions with humans have broad implications for our understanding of metabolism, immunity, the host−microbe genetic interactions. Bioavailability and bioaccessibility of phytonutrients in foods not only enrich microbial diversity in the lower human gastrointestinal tract (GIT) but also direct the functioning of the metagenome of the microbiota. Thus, healthy choices must include foods that contain nutrients that satisfy both the needs of humans and their microbes. Physical activity interventions at a moderate level of intensity have shown positive effects on metabolism and the microbiome, while intense training (>70% VO2max) reduces diversity in the short term. The microbiome of elite endurance athletes is a robust producer of short-chain fatty acids. A lifestyle lacking activity is associated with the development of chronic disease, and experimental conditions simulating weightlessness in humans demonstrate loss of muscle mass occurring in conjunction with a decline in gut short-chain fatty acid (SCFA) production and the microbes that produce them. This review summarizes evidence addressing the relationship between the intestinal microbiome, diet, and physical activity. Data from the studies reviewed suggest that food choices and physical fitness in developed countries promote a resource “curse” dilemma for the microbiome and our health.

A comparative study between Fusarium solani and Neocosmospora vasinfecta revealed differential profile of fructooligosaccharide production

Fructooligosaccharides (FOS) are fructose-based oligosaccharides employed as additives to improve the food's nutritional and technological properties. The rhizosphere of plants that accumulate fructopolysaccharides as inulin has been revealed as a source of filamentous fungi. These fungi can produce FOS either by inulin hydrolysis or by biosynthesis from sucrose, including unusual FOS with enhanced prebiotic properties. Here, we investigated the ability of Fusarium solani and Neocosmospora vasinfecta to produce FOS from different carbon sources. Fusarium solani and N. vasinfecta grew preferentially in inulin instead of sucrose, resulting in the FOS production as the result of endo-inulinase activities. N. vasinfecta was also able to produce the FOS 1-kestose and 6-kestose from sucrose, indicating transfructosylating activity, absent in F. solani. Moreover, the results showed how these carbon sources affected fungal cell wall composition and the expression of genes encoding for β-1,3-glucan synthase and chitin synthase. Inulin and fructose promoted changes in fungal macroscopic characteristics partially explained by alterations in cell wall composition. However, these alterations were not directly correlated with the expression of genes related to cell wall synthesis. Altogether, the results pointed to the potential of both F. solani and N. vasinfecta to produce FOS at specific profiles.

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.

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans

Dietary fibers act through the microbiome to improve cardiovascular health and prevent metabolic disorders and cancer. To understand the health benefits of dietary fiber supplementation, we investigated two popular purified fibers, arabinoxylan (AX) and long-chain inulin (LCI), and a mixture of five fibers. We present multiomic signatures of metabolomics, lipidomics, proteomics, metagenomics, a cytokine panel, and clinical measurements on healthy and insulin-resistant participants. Each fiber is associated with fiber-dependent biochemical and microbial responses. AX consumption associates with a significant reduction in LDL and an increase in bile acids, contributing to its observed cholesterol reduction. LCI is associated with an increase in Bifidobacterium. However, at the highest LCI dose, there is increased inflammation and elevation in the liver enzyme alanine aminotransferase. This study yields insights into the effects of fiber supplementation and the mechanisms behind fiber-induced cholesterol reduction, and it shows effects of individual, purified fibers on the microbiome.

Prebiotics as a Tool for the Prevention and Treatment of Obesity and Diabetes: Classification and Ability to Modulate the Gut Microbiota

Diabetes and obesity are metabolic diseases that have become alarming conditions in recent decades. Their rate of increase is becoming a growing concern worldwide. Recent studies have established that the composition and dysfunction of the gut microbiota are associated with the development of diabetes. For this reason, strategies such as the use of prebiotics to improve intestinal microbial structure and function have become popular. Consumption of prebiotics for modulating the gut microbiota results in the production of microbial metabolites such as short-chain fatty acids that play essential roles in reducing blood glucose levels, mitigating insulin resistance, reducing inflammation, and promoting the secretion of glucagon-like peptide 1 in the host, and this accounts for the observed remission of metabolic diseases. Prebiotics can be either naturally extracted from non-digestible carbohydrate materials or synthetically produced. In this review, we discussed current findings on how the gut microbiota and microbial metabolites may influence host metabolism to promote health. We provided evidence from various studies that show the ability of prebiotic consumption to alter gut microbial profile, improve gut microbial metabolism and functions, and improve host physiology to alleviate diabetes and obesity. We conclude among other things that the application of systems biology coupled with bioinformatics could be essential in ascertaining the exact mechanisms behind the prebiotic–gut microbe–host interactions required for diabetes and obesity improvement.

Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes

We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (-0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; -0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.

Intestinal gluconeogenesis shapes gut microbiota, fecal and urine metabolome in mice with gastric bypass surgery

Intestinal gluconeogenesis (IGN), gastric bypass (GBP) and gut microbiota positively regulate glucose homeostasis and diet-induced dysmetabolism. GBP modulates gut microbiota, whether IGN could shape it has not been investigated. We studied gut microbiota and microbiome in wild type and IGN-deficient mice, undergoing GBP or not, and fed on either a normal chow (NC) or a high-fat/high-sucrose (HFHS) diet. We also studied fecal and urine metabolome in NC-fed mice. IGN and GBP had a different effect on the gut microbiota of mice fed with NC and HFHS diet. IGN inactivation increased abundance of Deltaproteobacteria on NC and of Proteobacteria such as Helicobacter on HFHS diet. GBP increased abundance of Firmicutes and Proteobacteria on NC-fed WT mice and of Firmicutes, Bacteroidetes and Proteobacteria on HFHS-fed WT mice. The combined effect of IGN inactivation and GBP increased abundance of Actinobacteria on NC and the abundance of Enterococcaceae and Enterobacteriaceae on HFHS diet. A reduction was observed in the amounf of short-chain fatty acids in fecal (by GBP) and in both fecal and urine (by IGN inactivation) metabolome. IGN and GBP, separately or combined, shape gut microbiota and microbiome on NC- and HFHS-fed mice, and modify fecal and urine metabolome.

Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation

BACKGROUND

Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss of beneficial bacteria, commonly associated with chronic autoimmune and inflammatory diseases, including T1D and type 2 diabetes. Here, we addressed whether a metabolite-based dietary supplement has an impact on humans with T1D. We conducted a single-arm pilot-and-feasibility trial with high-amylose maize-resistant starch modified with acetate and butyrate (HAMSAB) to assess safety, while monitoring changes in the gut microbiota in alignment with modulation of the immune system status.

RESULTS

HAMSAB supplement was administered for 6 weeks with follow-up at 12 weeks in adults with long-standing T1D. Increased concentrations of SCFA acetate, propionate, and butyrate in stools and plasma were in concert with a shift in the composition and function of the gut microbiota. While glucose control and insulin requirements did not change, subjects with the highest SCFA concentrations exhibited the best glycemic control. Bifidobacterium longum, Bifidobacterium adolescentis, and vitamin B7 production correlated with lower HbA1c and basal insulin requirements. Circulating B and T cells developed a more regulatory phenotype post-intervention.

CONCLUSION

Changes in gut microbiota composition, function, and immune profile following 6 weeks of HAMSAB supplementation were associated with increased SCFAs in stools and plasma. The persistence of these effects suggests that targeting dietary SCFAs may be a mechanism to alter immune profiles, promote immune tolerance, and improve glycemic control for the treatment of T1D.

TRIAL REGISTRATION

ACTRN12618001391268. Registered 20 August 2018, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375792 Video Abstract.

The Archaeal Transcription Termination Factor aCPSF1 is a Robust Phylogenetic Marker for Archaeal Taxonomy

Archaea are highly diverse and represent a primary life domain, but the majority of them remain uncultured. Currently, 16S rRNA phylogeny is widely used in archaeal taxonomy and diversity surveys. However, highly conserved sequence of 16S rRNA possibly results in generation of chimera in the amplicons and metagenome-assembled genomes (MAGs) and therefore limits its application. The newly developed phylogenomic approach has overcome these flaws, but it demands high-quality MAGs and intensive computation. In this study, we investigated the use of the archaeal transcription termination factor aCPSF1 in archaeal classification and diversity surveys. The phylogenetic analysis of 1,964 aCPSF1 orthologs retrieved from the available archaeal (meta)genomes resulted in convergent clustering patterns with those of archaeal phylogenomics and 16S rRNA phylogeny. The aCPSF1 phylogeny also displayed comparable clustering with the methanoarchaeal McrABG phylogeny and the haloarchaeal phylogenomics. Normalization of 779 aCPSF1 sequences including 261 from cultured archaeal species yielded a taxonomic ranking system with higher resolutions than that obtained with 16S rRNA for genus and species. Using the aCPSF1 taxonomy, 144 unclassified archaea in NCBI database were identified to various taxonomic ranks. Moreover, aCPSF1- and 16S rRNA-based surveys of the archaeal diversity in a sample from a South China Sea cold seep produced similar results. Our results demonstrate that aCPSF1 is an alternative archaeal phylogenetic marker, which exhibits higher resolution than 16S rRNA, and is more readily usable than phylogenomics in the taxonomic study of archaea. IMPORTANCE Archaea represent a unique type of prokaryote, which inhabit in various environments including extreme environments, and so define the boundary of biosphere, and play pivotal ecological roles, particularly in extreme environments. Since their discovery over 40 years ago, environmental archaea have been widely investigated using the 16S rRNA sequence comparison, and the recently developed phylogenomic approach because the majority of archaea are recalcitrant to laboratory cultivation. However, the highly conserved sequence of 16S rRNA and intensive bioinformatic computation of phylogenomics limit their applications in archaeal species delineation and diversity investigations. aCPSF1 is a ubiquitously distributed and vertically inherited transcription termination factor in archaea. In this study, we developed an aCPSF1-based archaeal taxonomic system which exhibits congruent phylogenic clustering patterns with archaeal phylogenomics and higher resolution than 16S rRNA in distinguishing archaea at lower taxonomic ranks. Therefore, aCPSF1 is a new phylogenetic marker in the taxonomic and diversity studies of archaea.

Frutalose®, a mixture of fructans obtained from enzymatic hydrolysis of chicory inulin, and normal defecation: evaluation of a health claim pursuant to Article 13(5) of Regulation (EC) No 1924/2006

Following an application from Sensus B.V. (Royal Cosun), submitted for authorisation of a health claim pursuant to Article 13(5) of Regulation (EC) No 1924/2006 via the Competent Authority of the Netherlands, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on the scientific substantiation of a health claim related to Frutalose® and maintenance of normal defecation. The scope of the application was proposed to fall under a health claim based on newly developed scientific evidence. The Panel considers that Frutalose®, a mixture of fructans obtained from enzymatic hydrolysis of chicory inulin, is sufficiently characterised. The claimed effect proposed by the applicant is 'contributes to regular bowel function by increasing stool frequency'. The proposed target population is 'the general healthy adult population'. Maintenance of normal defecation is a beneficial physiological effect provided that it does not result in diarrhoea. One human intervention study showed an effect of Frutalose® on the maintenance of normal defecation by increasing stool frequency and improving stool consistency (softer stools) when consumed daily at a dose of 15 g for 8 weeks. The results have not been replicated in other studies. There is a plausible mechanism by which Frutalose® could exert the claimed effect. The Panel concludes that the evidence provided is insufficient to establish a cause and effect relationship between the consumption of Frutalose® and maintenance of normal defecation under the proposed conditions of use.

Manipulation of intestinal microbiome as potential treatment for insulin resistance and type 2 diabetes

PURPOSE

Increasing evidence suggests that the intestinal microbiome (IM) and bacterial metabolites may influence glucose homeostasis, energy expenditure and the intestinal barrier integrity and lead to the presence of systemic low-grade inflammation, all of which can contribute to insulin resistance (IR) and type 2 diabetes (T2D). The purpose of this review is to explore the role of the IM and bacterial metabolites in the pathogenesis and treatment of these conditions.

RESULTS

This review summarizes research focused on how to modulate the IM through diet, prebiotics, probiotics, synbiotics and fecal microbiota transplant in order to treat IR and T2D.

CONCLUSION

There is an abundance of evidence suggesting a role for IM in the pathogenesis of IR and T2D based on reviewed studies using various methods to modulate IM and metabolites. However, the results are inconsistent. Future research should further assess this relationship.

Prebiotic Enriched Exclusive Enteral Nutrition Suppresses Colitis via Gut Microbiome Modulation and Expansion of Anti-inflammatory T Cells in a Mouse Model of Colitis

BACKGROUND & AIMS

Exclusive enteral nutrition (EEN) is used to treat pediatric Crohn's disease (CD), but therapeutic benefits are variable, and EEN can lead to microbial dysbiosis. Because of reported lower efficacy EEN is not routinely used to treat pediatric ulcerative colitis (UC). Inulin-type fructans (IN) beneficially modulate the gut microbiome and promote expansion of anti-inflammatory immune cells. We hypothesized that enriching EEN with IN (EEN IN) would enhance treatment efficacy. To test this, we examined the effects of EEN IN on colitis development, the gut microbiome, and CD4⁺ T cells using an adoptive T-cell transfer model of colitis.

METHODS

TCR-β deficient (^-/-) mice were randomized to 1 of 4 groups: (1) Control, (2) Chow, (3) EEN, and (4) EEN IN, and naive CD4⁺ T cells were adoptively transferred into groups 2-4, after which mice were monitored for 5 weeks before experimental endpoint.

RESULTS

Mice fed EEN IN showed greater colitis protection, with colonic shortening, goblet cell, and crypt density loss reduced compared with EEN fed mice and reduced disease activity and immune cell infiltration compared with chow fed mice, and less crypt hyperplasia and higher survival compared with both groups. EEN IN mice had less deterioration in the colonic mucus layer and had increased levels of Foxp3⁺IL-10⁺ and Rorγt⁺IL-22⁺ and reduced levels of Tbet⁺IFNγ⁺ and Tbet⁺TNF⁺ CD4⁺ T cells. EEN IN also led to higher butyrate concentrations, Bifidobacterium spp. and Anaerostipes caccae relative abundance, and lower [Clostridium] innocuum group spp. and Escherichia-Shigella spp. relative abundance.

CONCLUSIONS

The EEN IN group showed reduced colitis development as compared with the chow and EEN groups. This highlights the potential benefits of EEN IN as a novel induction therapy for pediatric CD and UC patients.

Dietary Fibre Intervention for Gut Microbiota, Sleep, and Mental Health in Adults with Irritable Bowel Syndrome: A Scoping Review

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder affecting 4-5% of the global population. This disorder is associated with gut microbiota, diet, sleep, and mental health. This scoping review therefore aims to map existing research that has administrated fibre-related dietary intervention to IBS individuals and reported outcomes on at least two of the three following themes: gut microbiota, sleep, and mental health. Five digital databases were searched to identify and select papers as per the inclusion and exclusion criteria. Five articles were included in the assessment, where none reported on all three themes or the combination of gut microbiota and sleep. Two studies identified alterations in gut microbiota and mental health with fibre supplementation. The other three studies reported on mental health and sleep outcomes using subjective questionnaires. IBS-related research lacks system biology-type studies targeting gut microbiota, sleep, and mental health in patients undergoing diet intervention. Further IBS research is required to explore how human gut microbiota functions (such as short-chain fatty acids) in sleep and mental health, following the implementation of dietary pattern alteration or component supplementation. Additionally, the application of objective sleep assessments is required in order to detect sleep change with more accuracy and less bias.

Characterizing the Effects of Calcium and Prebiotic Fiber on Human Gut Microbiota Composition and Function Using a Randomized Crossover Design-A Feasibility Study

Consumption of prebiotic inulin has been found to increase calcium absorption, which may protect against gut diseases such as colorectal cancer. This dietary relation may be modulated by compositional changes in the gut microbiota; however, no human study has addressed this hypothesis. We determined the feasibility of a randomized crossover trial to evaluate the effect of three interventions (combined calcium and inulin supplementation, calcium supplementation alone, and inulin supplementation alone) on the intestinal microbiota composition and function. We conducted a 16-week pilot study in 12 healthy adults who consumed the three interventions in a random sequence. Participants provided fecal and blood samples before and after each intervention. Each intervention period lasted four weeks and was flanked by one-week washout periods. 16S ribosomal RNA sequencing and quantification of short chain fatty acids (SCFA) was determined in fecal samples. Systemic lipopolysaccharide binding protein (LBP) was quantified in serum. Of the 12 individuals assigned to an intervention sequence, seven completed the study. Reasons for dropout included time (n = 3), gastrointestinal discomfort (n = 1), and moving (n = 1). Overall, participants reported positive attitudes towards the protocol (n = 9) but were unsatisfied by the practicalities of supplement consumption (44%) and experienced digestive discomfort (56%). We found no appreciable differences in microbial composition, SCFA concentration, nor LBP concentrations when comparing intervention periods. In conclusion, an intervention study using a randomized crossover design with calcium and a prebiotic fiber is feasible. Improvements of our study design include using a lower dose prebiotic fiber supplement and a larger sample size.

Circulating bile acids as a link between the gut microbiota and cardiovascular health: impact of prebiotics, probiotics and polyphenol-rich foods

Beneficial effects of probiotic, prebiotic and polyphenol-rich interventions on fasting lipid profiles have been reported, with changes in the gut microbiota composition believed to play an important role in lipid regulation. Primary bile acids, which are involved in the digestion of fats and cholesterol metabolism, can be converted by the gut microbiota to secondary bile acids, some species of which are less well reabsorbed and consequently may be excreted in the stool. This can lead to increased hepatic bile acid neo-synthesis, resulting in a net loss of circulating low-density lipoprotein. Bile acids may therefore provide a link between the gut microbiota and cardiovascular health. This narrative review presents an overview of bile acid metabolism and the role of probiotics, prebiotics and polyphenol-rich foods in modulating circulating cardiovascular disease (CVD) risk markers and bile acids. Although findings from human studies are inconsistent, there is growing evidence for associations between these dietary components and improved lipid CVD risk markers, attributed to modulation of the gut microbiota and bile acid metabolism. These include increased bile acid neo-synthesis, due to bile sequestering action, bile salt metabolising activity and effects of short-chain fatty acids generated through bacterial fermentation of fibres. Animal studies have demonstrated effects on the FXR/FGF-15 axis and hepatic genes involved in bile acid synthesis (CYP7A1) and cholesterol synthesis (SREBP and HMGR). Further human studies are needed to determine the relationship between diet and bile acid metabolism and whether circulating bile acids can be utilised as a potential CVD risk biomarker.

Crystal structure of an inulosucrase from Halalkalicoccus jeotgali B3T, a halophilic archaeal strain

Several archaea harbor genes that code for fructosyltransferase (FTF) enzymes. These enzymes have not been characterized yet at structure-function level, but are of extreme interest in view of their potential role in the synthesis of novel compounds for food, nutrition, and pharmaceutical applications. In this study, 3D structure of an inulin-type fructan producing enzyme, inulosucrase (InuHj), from the archaeon Halalkalicoccus jeotgali was resolved in its apo form and with bound substrate (sucrose) molecule and first transglycosylation product (1-kestose). This is the first crystal structure of an FTF from halophilic archaea. Its overall five-bladed β-propeller fold is conserved with previously reported FTFs, but also shows some unique features. The InuHj structure is closer to those of Gram-negative bacteria, with exceptions such as residue E266, which is conserved in FTFs of Gram-positive bacteria and has possible role in fructan polymer synthesis in these bacteria as compared to fructooligosaccharide (FOS) production by FTFs of Gram-negative bacteria. Highly negative electrostatic surface potential of InuHj, due to a large amount of acidic residues, likely contributes to its halophilicity. The complex of InuHj with 1-kestose indicates that the residues D287 in the 4B-4C loop, Y330 in 4D-5A, and D361 in the unique α2 helix may interact with longer FOSs and facilitate the binding of longer FOS chains during synthesis. The outcome of this work will provide targets for future structure-function studies of FTF enzymes, particularly those from archaea.

Plant Prebiotics and Their Role in the Amelioration of Diseases

Prebiotics are either natural or synthetic non-digestible (non-)carbohydrate substances that boost the proliferation of gut microbes. Undigested fructooligosaccharides in the large intestine are utilised by the beneficial microorganisms for the synthesis of short-chain fatty acids for their own growth. Although various food products are now recognized as having prebiotic properties, several others, such as almonds, artichoke, barley, chia seeds, chicory, dandelion greens, flaxseeds, garlic, and oats, are being explored and used as functional foods. Considering the benefits of these prebiotics in mineral absorption, metabolite production, gut microbiota modulation, and in various diseases such as diabetes, allergy, metabolic disorders, and necrotising enterocolitis, increasing attention has been focused on their applications in both food and pharmaceutical industries, although some of these food products are actually used as food supplements. This review aims to highlight the potential and need of these prebiotics in the diet and also discusses data related to the distinct types, sources, modes of action, and health benefits.

Health benefits of whole grain: effects on dietary carbohydrate quality, the gut microbiome, and consequences of processing

Grains are important sources of carbohydrates in global dietary patterns. The majority of these carbohydrates, especially in refined-grain products, are digestible. Most carbohydrate digestion takes place in the small intestine where monosaccharides (predominantly glucose) are absorbed, delivering energy to the body. However, a considerable part of the carbohydrates, especially in whole grains, is indigestible dietary fibers. These impact gut motility and transit and are useful substrates for the gut microbiota affecting its composition and quality. For the most part, the profile of digestible and indigestible carbohydrates and their complexity determine the nutritional quality of carbohydrates. Whole grains are more complex than refined grains and are promoted as part of a healthy and sustainable diet mainly because the contribution of indigestible carbohydrates, and their co-passenger nutrients, is significantly higher. Higher consumption of whole grain is recommended because it is associated with lower incidence of, and mortality from, CVD, type 2 diabetes, and some cancers. This may be due in part to effects on the gut microbiota. Although processing of cereals during milling and food manufacturing is necessary to make them edible, it also offers the opportunity to still further improve the nutritional quality of whole-grain flours and foods made from them. Changing the composition and availability of grain carbohydrates and phytochemicals during processing may positively affect the gut microbiota and improve health.

Flexibility of Gut Microbiota in Ageing Individuals during Dietary Fiber Long-Chain Inulin Intake

SCOPE

During ageing, dysbiosis in the intestinal microbiota may occur and impact health. There is a paucity of studies on the effect of fiber on the elderly microbiota and the flexibility of the aged microbiota upon prebiotic intake. It is hypothesized that chicory long-chain inulin consumption can change microbiota composition, microbial fermentation products, and immunity in the elderly.

METHODS AND RESULTS

A double-blind, placebo-controlled trial is performed in healthy individuals (55-80 years), in which microbiota composition is studied before, during, and after two months of chicory long-chain inulin consumption. Fecal short chain fatty acid concentrations, T cell subsets, and antibody responses against a Hepatitis B (HB) vaccine are measured as well. Inulin consumption modified the microbiota composition, as measured by 16S rRNA sequencing. Participants consuming inulin have higher microbial diversity and a relatively higher abundance of the Bifidobacterium genus, as well as Alistipes shahii, Anaerostipes hadrus, and Parabacteroides distasonis. While the immune responses remain unchanged, the isobutyric acid levels, an undesired fermentation product, tend to be lower in the inulin group.

CONCLUSIONS

Overall, it is shown that the gut microbiota composition is still sensitive to chicory long-chain inulin induced changes in an ageing population, although this did not translate into an improved immune response to an HB vaccine.

Functional hydrocolloids, gut microbiota and health: picking food additives for personalized nutrition

The human gut microbiota respond to particular food components, interact with intestinal mucosa and thereby contribute to health and diseases. Key microbiome features are under comprehensive investigation and are likely to be developed as reliable evidences for clinical diagnosis. And the underlying mechanisms lay the foundation of assembling bespoke nutritional ingredients including functional food additives that may lead to favorable outcomes in facilitating amelioration of host dysfunctions. Functional hydrocolloids serve as multiple food additives with promising application prospects and outstanding adjunctive beneficial characteristics. Therefore, in this review, we introduce the latest advances in food additives-gut microbiota-host axis by summarizing the physiochemical and physiological properties of a collection of functional hydrocolloids from various sources, describing the functional hydrocolloids-related intestinal commensal markers, and deciphering the underlying mechanisms of their beneficial effects, and propose the feasibilities and guidelines for further developments of gut microbiota-oriented personalized nutrition.

Impact of prebiotics on immune response: from the bench to the clinic

Several preclinical and clinical studies have shown the immunomodulatory role exerted by prebiotics in regulating the immune response. In this review, we describe the mechanistic and clinical studies that decipher the cell signaling pathways implicated in the process. Prebiotic fibers are conventionally known to serve as substrate for probiotic commensal bacteria that release of short-chain fatty acids in the intestinal tract along with several other metabolites. Subsequently, they then act on the local as well as the systemic immune cells and the gut-associated epithelial cells, primarily through G-protein-coupled receptor-mediated pathways. However, other pathways including histone deacetylase inhibition and inflammasome pathway have also been implicated in regulating the immunomodulatory effect. The prebiotics can also induce a microbiota-independent effect by directly acting on the gut-associated epithelial and innate immune cells through the Toll-like receptors. The cumulative effect results in the maintenance of the epithelial barrier integrity and modulation of innate immunity through secretion of pro- and anti-inflammatory cytokines, switches in macrophage polarization and function, neutrophil recruitment and migration, dendritic cell and regulatory T-cell differentiation. Extending these in vitro and ex vivo observations, some prebiotics have been well investigated, with successful human and animal trials demonstrating the association between gut microbes and immunity biomarkers leading to improvement in health endpoints across populations. This review discusses scientific insights into the association between prebiotics, innate immunity and gut microbiome from in vitro to human oral intervention.

Dietary fibers reduce obesity-related disorders: mechanisms of action

PURPOSE OF REVIEW

Dietary fibers decrease risk of cardiovascular disease and obesity, but the most important mechanisms for fiber's protective properties are debated. The purpose of the review is to summarize the recent human studies that examine mechanisms how dietary fiber decreases risk of obesity-related disorders.

RECENT FINDINGS

Dietary fiber has effects throughout the digestive tract that decrease risk of obesity-related diseases. Soluble, viscous fibers slow absorption of and decrease serum cholesterol. Intake of dietary fiber enhances satiety and reduces food intake at future meals. The importance of gut fermentation and changes in the gut microbiota and metabolites are linked to decrease risk for obesity-related disorders. Dietary fibers alter the gut microbiota and produce metabolites such as short-chain fatty acids that may explain fiber's role in obesity prevention and treatment. Dietary fiber encompasses many plant compounds, so conclusions that dietary fiber reduces or treats obesity-related disorders must be considered by the fiber was fed in the study.

SUMMARY

Dietary fiber prevents and treats obesity-related disorders. Mechanisms for this protection include decreased absorption of macronutrients and enhanced satiety. Changes in the gut microbiota and short-chain fatty acids are emerging mechanisms to explain why high fiber diets protect against obesity and have a role in obesity treatment.

Does an Apple a Day Also Keep the Microbes Away? The Interplay Between Diet, Microbiota, and Host Defense Peptides at the Intestinal Mucosal Barrier

A crucial mechanism of intestinal defense includes the production and secretion of host defense peptides (HDPs). HDPs control pathogens and commensals at the intestinal interface by direct killing, by sequestering vital ions, or by causing bacterial cells to aggregate in the mucus layer. Accordingly, the combined activity of various HDPs neutralizes gut bacteria before reaching the mucosa and thus helps to maintain the homeostatic balance between the host and its microbes at the mucosal barrier. Defects in the mucosal barrier have been associated with various diseases that are on the rise in the Western world. These include metabolic diseases, such as obesity and type 2 diabetes, and inflammatory intestinal disorders, including ulcerative colitis and Crohn's disease, the two major entities of inflammatory bowel disease. While the etiology of these diseases is multifactorial, highly processed Western-style diet (WSD) that is rich in carbohydrates and fat and low in dietary fiber content, is considered to be a contributing lifestyle factor. As such, WSD does not only profoundly affect the resident microbes in the intestine, but can also directly alter HDP function, thereby potentially contributing to intestinal mucosal barrier dysfunction. In this review we aim to decipher the complex interaction between diet, microbiota, and HDPs. We discuss how HDP expression can be modulated by specific microbes and their metabolites as well as by dietary factors, including fibers, lipids, polyphenols and vitamins. We identify several dietary compounds that lead to reduced HDP function, but also factors that stimulate HDP production in the intestine. Furthermore, we argue that the effect of HDPs against commensal bacteria has been understudied when compared to pathogens, and that local environmental conditions also need to be considered. In addition, we discuss the known molecular mechanisms behind HDP modulation. We believe that a better understanding of the diet-microbiota-HDP interdependence will provide insights into factors underlying modern diseases and will help to identify potential dietary interventions or probiotic supplementation that can promote HDP-mediated intestinal barrier function in the Western gut.

Structure and Function of Bovine Whey Derived Oligosaccharides Showing Synbiotic Epithelial Barrier Protective Properties

Commensal gut microbiota and probiotics have numerous effects on the host’s metabolic and protective systems, which occur primarily through the intestinal epithelial cell interface. Prebiotics, like galacto-oligosaccharides (GOS) are widely used to modulate their function and abundance. However, important structure–function relations may exist, requiring a detailed structural characterization. Here, we detailed the structural characterization of bovine whey derived oligosaccharide preparations enriched with GOS or not, dubbed GOS-enriched milk oligosaccharides (GMOS) or MOS, respectively. We explore GMOS’s and MOS’s potential to improve intestinal epithelial barrier function, assessed in a model based on barrier disruptive effects of the Clostridioides difficile toxin A. GMOS and MOS contain mainly GOS species composed of β1-6- and β1-3-linked galactoses, and 3′- and 6′-sialyllactose. Both GMOS and MOS, combined with lactobacilli, like Lactobacillus rhamnosus (LPR, NCC4007), gave synergistic epithelial barrier protection, while no such effect was observed with Bifidobacterium longum (BL NCC3001), Escherichia coli (Nissle) or fructo-oligosaccharides. Mechanistically, for barrier protection with MOS, (i) viable LPR was required, (ii) acidification of growth medium was not enough, (iii) LPR did not directly neutralize toxin A, and (iv) physical proximity of LPR with the intestinal epithelial cells was necessary. This is the first study, highlighting the importance of structure–function specificity and the necessity of the simultaneous presence of prebiotic, probiotic and host cell interactions required for a biological effect.