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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.

The human gut microbiome influence on brain function and mental health is an emerging area of intensive research. Animal and human research indicates adolescence as a sensitive period when the gut-brain axis is fine-tuned, where dietary interventions to change the microbiome may have long-lasting consequences for mental health. This study reports a systematic review and meta-analysis of microbiota-targeted (psychobiotics) interventions on anxiety in youth, with discussion of a consultation on the acceptability of psychobiotic interventions for mental health management amongst youth with lived experience. Six databases were searched for controlled trials in human samples (age range: 10–24 years) seeking to reduce anxiety. Post intervention outcomes were extracted as standard mean differences (SMDs) and pooled based on a random-effects model. 5416 studies were identified: 14 eligible for systematic review and 10 eligible for meta-analysis (total of 324 experimental and 293 control subjects). The meta-analysis found heterogeneity I2 was 12% and the pooled SMD was −0.03 (95% CI: −0.21, 0.14), indicating an absence of effect. One study presented with low bias risk, 5 with high, and 4 with uncertain risk. Accounting for risk, sensitivities analysis revealed a SMD of −0.16 (95% CI: −0.38, 0.07), indicative of minimal efficacy of psychobiotics for anxiety treatment in humans. There is currently limited evidence for use of psychobiotics to treat anxiety in youth. However, future progress will require a multidisciplinary research approach, which gives priority to specifying mechanisms in the human models, providing causal understanding, and addressing the wider context, and would be welcomed by anxious youths.

Culinary herbs and spices have previously been recognised for their potential impact on health through antioxidant and antimicrobial properties. They may also be promotors of positive microbial modulation by stimulating beneficial gut bacteria during fermentation, increasing the production of short chain fatty acids and thereby exhibiting a prebiotic effect. In the present paper, current literature around herb and spice consumption, gut microbiota modulation and prospective health benefits were reviewed. Herb and spice consumption can positively modulate gut microbes and possibly play an important role in inflammation related afflictions such as obesity. Current literature indicates that few human studies have been conducted to confirm the impact of herb and spice consumption on gut microbiota in connection with prospective health outcomes and inconsistencies in conclusions therefore remain.

The 2019 Dudrick Research Symposium, entitled "Targeted Approaches for In Situ Gut Microbiome Manipulation," was held on March 25, 2019, at the American Society for Parenteral and Enteral Nutrition (ASPEN) 2019 Nutrition Science & Practice Conference in Phoenix, AZ. The Dudrick Symposium honors the many pivotal and innovative contributions to the development and advancement of parenteral nutrition (PN) made by Dr Stanley J. Dudrick, physician scientist, academic leader, and a founding member of ASPEN. As the 2018 recipient of the Dudrick award, Dr Gail Cresci organized and chaired the symposium. The symposium addressed the evolving field of nutrition manipulation of the gut microbiome as a means to mitigate disease and support health. Presentations focused on (1) the role of prebiotics as a means to beneficially support gut microbiome composition and function and health; (2) designer synbiotics targeted to support metabolic by-products altered by ethanol exposure and microbial effectors that manipulate host metabolic outcomes; and, lastly, (3) types of intervention designs used to study diet-gut microbiome interactions in humans and a review of findings from recent interventions, which tested the effects of diet on the microbiome and the microbiome's effect on dietary exposures. New molecular techniques and multiomic approaches have improved knowledge of the structure and functional activity of the gut microbiome; however, challenges remain in establishing causal relationships between changes in the gut microbial-community structure and function and health outcomes in humans.

In 2010, British Journal of Nutrition published a consensus review article entitled Prebiotic effects: metabolic and health benefits(1). This was commissioned by International Life Sciences Institute, Europe and had twenty-one co-authors. The current article summarises how this review was planned and written. It deals with three questions regarding the context/background of the paper; what it told us and what happened next.

Short chain fatty acids (SCFAs) derived from the human gut microbiota, and in particular propionate, may beneficially influence metabolic processes such as appetite regulation. Development of prebiotics that induce high propionate levels during fermentation is desirable. A total of 11 candidate prebiotics were screened to investigate their fermentation characteristics, with a focus on propionate production in mixed anaerobic batch culture of faecal bacteria. Further to this, a continuous 3-stage colonic fermentation model (simulating the human colon) was used to evaluate changes in microbial ecology, lactate and SCFA production of three 50:50 blends, comprising both slow and rapidly fermented prebiotics. In mixed batch culture: xylo-oligosaccharide, polydextrose and α-gluco-oligosaccharide were associated with the greatest increase in propionate. Polydextrose, α-gluco-oligosaccharide, β-1,4 glucan and oat fibre induced the greatest reductions in the acetate to propionate ratio. The most bifidogenic prebiotics were the oligosaccharides. Fermentation of a 50:50 blend of inulin and arabinoxylan, through the continuous 3-stage colonic fermentation model, induced a substantial and sustained release of propionate. The sustained release of propionate through the colon, if replicable in vivo, could potentially influence blood glucose, blood lipids and appetite regulation, however, dietary intervention studies are needed. Bifidogenic effects were also observed for the inulin and arabinoxylan blend and an increase synthesis of butyrate and lactate, thus indicating wider prebiotic potential.

Purpose Resistant dextrin (RD) supplementation has been shown to alter satiety, glycaemia, and body weight, in overweight Chinese men; however, there are limited data on its effects in other demographic groups. Here, we investigated the effects of RD on satiety in healthy adults living in the United Kingdom. Methods 20 normal weight and 16 overweight adults completed this randomised controlled cross-over study. Either RD (14 g/day NUTRIOSE® FB06) or maltodextrin control was consumed in mid-morning and mid-afternoon preload beverages over a 28-day treatment period with crossover after a 28-day washout. During 10-h study visits (on days 1, 14, and 28 of each treatment period), satietogenic, glycaemic and anorectic hormonal responses to provided meals were assessed. Results Chronic supplementation with RD was associated with higher fasted satiety scores at day 14 (P = 0.006) and day 28 (P = 0.040), compared to control. RD also increased satiety after the mid-morning intervention drink, but it was associated with a reduction in post-meal satiety following both the lunch and evening meals (P P P = 0.035) and 28 (P = 0.030), compared to day 1, following RD supplementation in the normal weight group. Energy intake and anthropometrics were unaffected. Conclusions RD supplementation modified satiety and glycaemic responses in this cohort, further studies are required to determine longer-term effects on body weight control and metabolic markers. Clinicaltrials.gov registration NCT02041975 (22/01/2014)

Adhesion ability to the host is a classical selection criterion for potential probiotic bacteria that could result in a transient colonisation that would help to promote immunomodulatory effects, as well as stimulate gut barrier and metabolic functions. In addition, probiotic bacteria has a potential protective role against enteropathogens through different mechanisms including production of antimicrobial compounds, reduction of pathogenic bacterial adhesion and competition for host cell binding sites. The competitive exclusion by probiotic bacteria not only has a beneficial effect on the gut but also in the urogenital tract and oral cavity. On the other hand, prebiotics may also act as barriers to pathogens and toxins by preventing their adhesion to epithelial receptors.\ud In vitro studies with different intestinal cell lines has been widely used along the last decades to assess the adherence ability of probiotic bacteria and pathogen antagonism. However, extrapolation of these results to in vivo conditions still remain unclear, leading to the need of optimization of more complex in vitro approaches that includes interaction with the resident microbiota to address the current limitations. \ud The aim of this mini-review is to provide a comprehensive overview on the potential effect of the adhesive properties of probiotics and prebiotics on the host by focusing on the most recent findings related with adhesion and immunomodulatory and antipathogenic effect on human health.

Rationale The gut-brain axis includes bidirectional communication between intestinal microbiota and the central nervous system. Bifidobacterium and Lactobacillus spp. have been implicated in psychological health, such as depression, through various pathways (e.g. inflammation). Research needs a better understanding of direct and indirect effects through examination of psychological factors that make people susceptible to, or offer protection against, depression. Objective This study investigated the relationships between gut microbiota, inflammation and psychological risk and resilience factors for depression. Methods Forty participants (13 m/27 f) recruited from the general population completed self-report questionnaires for depression, self-judgement, over-identification and affective and cognitive empathy. Faecal and blood samples were taken to assay microbiota (Bifidobacterium; Lactobacillus spp.) and pro-inflammatory molecules (C-reactive protein, CRP and interleukin-6, IL-6), respectively. Results Hierarchical regression analyses (controlling for sex, age and the shared variance of risk and resilience factors) showed that (i) cognitive depression was significantly predicted by negative self-judgement and reduced cognitive empathy; (ii) abundance of Lactobacillus spp. was directly related to positive self-judgement but only indirectly to cognitive depression and lower affective empathy (both through self-judgement); and (iii) CRP was the strongest predictor of reduced cognitive empathy, with suppression effects seen for age (negative) and IL-6 (positive) after controlling for CRP. Conclusions Findings suggest that lactobacilli and inflammation may be differentially associated with mood disorder via brain mechanisms underpinning self-judgement and cognitive empathy, respectively. Further trials investigating interventions to increase Lactobacillus spp. in depression would benefit from direct measures of self-judgement and affective empathic distress, whilst those that aim to reduce inflammation should investigate cognitive empathy. Electronic supplementary material The online version of this article (10.1007/s00213-019-05230-2) contains supplementary material, which is available to authorized users.

\ud Background\ud The role of the gut microbiota in health and disease is becoming increasingly apparent. Faeces is the most accessible sample to collect from human volunteers for studying the gut microbiota. However, the impact of stool collection and storage conditions on microbial and metabolic profiles have not been fully evaluated. By understanding the effect of different stool collection and storage conditions on microbial and metabolic composition, we can consider these parameters in the design of in vitro fermentation studies.\ud \ud Methods\ud Stool samples from 3 volunteers were stored under 5 different conditions to mimic methods that researchers may use to collect and store stool samples for study of the gut microbiota, including: fresh sample used within 10 min; stored on wet ice (4 °C) for 60 min; stored in an anaerobic chamber in a temperature-controlled bag (4 °C) for 60 min; freezing at −20 °C for 60 min and freezing at −20 °C for 60 min and then at −80 °C for 2 weeks. The stored samples were added to basal medium in batch culture fermenters alone (negative control) or with 5 g 2’-Fucosyllactose (2’FL) Human Milk Oligosaccharide (HMO) (as a positive fermentation control). Samples were collected at 3 timepoints (0, 12 and 24 h) for analysis by Flow Cytometry-Fluorescent In Situ Hybridisation (FC-FISH) and 1H-Nuclear Magnetic Resonance (NMR) spectroscopy to assess the impact on microbial and metabolic profiles, respectively.\ud \ud Results\ud Freezing stool significantly impacted microbial numbers and activity during in vitro fermentations, whereas storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min had minimal effects on microbial and metabolic profiles throughout the 24 h batch culture fermentation experiments.\ud \ud Discussion\ud For in vitro batch culture fermentation studies where it may not be practical or possible to use fresh stool, either storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min could be plausible alternatives to maintain microbial and metabolic profiles for analysis.

Cow’s milk protein allergy (CMPA) is associated with dysbiosis of the infant gut microbiome, with allergic and immune development implications. Studies show benefits of combining synbiotics with hypoallergenic formulae, although evidence has never been systematically examined. This review identified seven publications of four randomised controlled trials comparing an amino acid formula (AAF) with an AAF containing synbiotics (AAF-Syn) in infants with CMPA (mean age 8.6 months; 68% male, mean intervention 27.3 weeks, n = 410). AAF and AAF-Syn were equally effective in managing allergic symptoms and promoting normal growth. Compared to AAF, significantly fewer infants fed AAF-Syn had infections (OR 0.35 (95% CI 0.19–0.67), p = 0.001). Overall medication use, including antibacterials and antifectives, was lower among infants fed AAF-Syn. Significantly fewer infants had hospital admissions with AAF-Syn compared to AAF (8.8% vs. 20.2%, p = 0.036; 56% reduction), leading to potential cost savings per infant of £164.05–£338.77. AAF-Syn was associated with increased bifidobacteria (difference in means 31.75, 95% CI 26.04–37.45, p < 0.0001); reduced Eubacterium rectale and Clostridium coccoides (difference in means −19.06, 95% CI −23.15 to −14.97, p < 0.0001); and reduced microbial diversity (p < 0.05), similar to that described in healthy breastfed infants, and may be associated with the improved clinical outcomes described. This review provides evidence that suggests combining synbiotics with AAF produces clinical benefits with potential economic implications.

Intestinal dysbiosis has been described in patients with certain gastrointestinal conditions including irritable bowel syndrome (IBS) and ulcerative colitis. 2′-fucosyllactose (2′-FL), a prebiotic human milk oligosaccharide, is considered bifidogenic and butyrogenic. To assess prebiotic effects of 2′-FL, alone or in combination with probiotic strains (potential synbiotics), in vitro experiments were conducted on stool from healthy, IBS, and ulcerative colitis adult donors. In anaerobic batch culture fermenters, Bifidobacterium and Eubacterium rectale-Clostridium coccoides counts, and short-chain fatty acids (SCFAs) including butyrate increased during fermentation with 2′-FL and some of the 2′-FL/probiotic combinations. In a subsequent open-label pilot trial, the effect of a 2′-FL-containing nutritional formula was evaluated in twelve adults with IBS or ulcerative colitis. Gastrointestinal Quality of Life Index (GIQLI) total and gastrointestinal symptoms domain scores, stool counts of Bifidobacterium and Faecalibacterium prausnitzii, and stool SCFAs including butyrate, increased after six weeks of intervention. Consistent with documented effects of 2′-FL, the batch culture fermentation experiments demonstrated bifidogenic and butyrogenic effects of 2′-FL during fermentation with human stool samples. Consumption of the 2′-FL-containing nutritional formula by adults with IBS or ulcerative colitis was associated with improvements in intra- and extra-intestinal symptoms, and bifidogenic and butyrogenic effects.

SummaryBackgroundThe human gut microbiome and its effect on brain function and mental health is emerging as an area of intensive research. Both animal and human research point towards adolescence as a sensitive period when the gut-brain axis is fine-tuned, and when we can use dietary intervention to change the microbiome, with long-lasting consequences for mental health. Here we report the results of a systematic review/meta-analysis of microbiota-targeted (psychobiotics) interventions on anxiety in youth, together with a summary of consultation work of youth with lived experience.MethodsSeven databases were searched (no date cut-offs), and controlled trials in clinical and healthy human samples (age range: 10-24) seeking to reduce anxiety were included. All data on between group-differences post intervention and outcomes were extracted as standard mean differences (SMDs) and pooled together based on a random-effects model.Findings5416 studies were identified, 14 were eligible for the qualitative summary, of which 10 were included in the meta-analyses (total of 324 experimental and 293 control subjects). The heterogeneity I2 was12% and the pooled SMD was −0.04 (95% CI: −0.21, 0.14). One study presented with low bias risk whereas 5 with high and 4 with uncertain risk, accounting for that, sensitivities analysis revealed a SMD of −0.16 (95%CI: −0.39, 0.06).InterpretationThere is currently limited evidence for use of psychobiotics to treat anxiety in youth. However, future progress will require a multidisciplinary research approach, which gives priority to specifying mechanisms in the human models, providing causal understanding and addressing the wider context.

In May 2019, the International Scientific Association for Probiotics and Prebiotics (ISAPP) convened a panel of nutritionists, physiologists and microbiologists to review the definition and scope of synbiotics. The panel updated the definition of a synbiotic to “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host”. The panel concluded that defining synbiotics as simply a mixture of probiotics and prebiotics could suppress the innovation of synbiotics that are designed to function cooperatively. Requiring that each component must meet the evidence and dose requirements for probiotics and prebiotics individually could also present an obstacle. Rather, the panel clarified that a complementary synbiotic, which has not been designed so that its component parts function cooperatively, must be composed of a probiotic plus a prebiotic, whereas a synergistic synbiotic does not need to be so. A synergistic synbiotic is a synbiotic for which the substrate is designed to be selectively utilized by the co-administered microorganisms. This Consensus Statement further explores the levels of evidence (existing and required), safety, effects upon targets and implications for stakeholders of the synbiotic concept., Gut microbiota can be manipulated to benefit host health, including the use of probiotics, prebiotics and synbiotics. This Consensus Statement outlines the definition and scope of the term ‘synbiotics’ as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in May 2019.

The recent COVID-19 pandemic has altered the face of biology, social interaction and public health worldwide. It has had a destructive effect upon millions of people and is approaching a devastating one million fatalities. Emerging evidence has suggested a link between the infection and gut microbiome status. This is one of the several factors that may contribute towards severity of infection. Given the fact that the gut is heavily linked to immunity, inflammatory status and the ability to challenge pathogens, it is worthwhile to consider dietary intervention of the gut microbiota as means of potentially challenging the viral outcome. In this context, probiotics and prebiotics have been used to mitigate similar respiratory infections. Here, we summarise links between the gut microbiome and COVID-19 infection, as well as propose mechanisms whereby probiotic and prebiotic interventions may act.

Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.

For pesticide registration a post application assessment is made on the safety of any residue remaining in the edible portion of the treated crop. This assessment does not typically consider the bioaccessibility of pesticide residues. The effects of this on potential exposure to incurred difenoconazole residues passing through the human gastrointestinal tract were studied, including the impact of commodity processing. It has previously been demonstrated that solvent extraction methods have the potential to overestimate the bioaccessible fraction, so in vitro simulated gut systems may offer a better approach to determine residue bioaccessibility to refine the risk assessment process. The bioaccessibility of difenoconazole residues associated with processed rice samples was assessed using in vitro intestinal extraction and colonic fermentation methods. The mean bioaccessibility following intestinal digestion was 33.3% with a range from 13% to 70.6%. Quantification of the colonic bioaccessible fraction was not possible due to compound metabolism. Mechanical processing methods generally increased the residue bioaccessibility, while chemical methods resulted in a decrease. Both mechanical and chemical processing methods reduced the total difenoconazole residue level by ca. 50%.

In summary, orally administered probiotic strains can reduce the incidence and severity of viral RTIs. At a time when doctors are using drugs with little anti- COVID-19 data, probiotic strains documented for anti-viral and respiratory activities (not low-quality undocumented imitations) should become part of the armamentarium to reduce the burden and severity of this pandemic. Government funding is being used to test numerous drugs but just as important, they should fund probiotic trials. In addition, use of recognized prebiotics (e.g., fructans, galactans) to enhance propagation of probiotic strains and indigenous beneficial microbes should be recommended as part of the overall strategy to flatten the curve (11, 50).

Dietary protein residue can result in microbial generation of various toxic metabolites in the gut, such as ammonia. A prebiotic is "a substrate that is selectively utilised by host microorganisms conferring a health benefit" (G. R. Gibson, R. Hutkins, M. E. Sanders, S. L. Prescott, et al., Nat Rev Gastroenterol Hepatol 14:491-502, 2017, https://doi.org/10.1038/nrgastro.2017.75). Prebiotics are carbohydrates that may have the potential to reverse the harmful effects of gut bacterial protein fermentation. Three-stage continuous colonic model systems were inoculated with fecal samples from omnivore and vegetarian volunteers. Casein (equivalent to 105 g protein consumption per day) was used within the systems as a protein source. Two different doses of inulin-type fructans (Synergy1) were later added (equivalent to 10 g per day in vivo and 15 g per day) to assess whether this influenced protein fermentation. Bacteria were enumerated by fluorescence in situ hybridization with flow cytometry. Metabolites from bacterial fermentation (short-chain fatty acid [SCFA], ammonia, phenol, indole, and p-cresol) were monitored to further analyze proteolysis and the prebiotic effect. A significantly higher number of bifidobacteria was observed with the addition of inulin together with reduction of Desulfovibrio spp. Furthermore, metabolites from protein fermentation, such as branched-chain fatty acids (BCFA) and ammonia, were significantly lowered with Synergy1. Production of p-cresol varied among donors, as we recognized four high producing models and two low producing models. Prebiotic addition reduced its production only in vegetarian high p-cresol producers.IMPORTANCE Dietary protein levels are generally higher in Western populations than in the world average. We challenged three-stage continuous colonic model systems containing high protein levels and confirmed the production of potentially harmful metabolites from proteolysis, especially replicates of the transverse and distal colon. Fermentations of proteins with a prebiotic supplementation resulted in a change in the human gut microbiota and inhibited the production of some proteolytic metabolites. Moreover, we observed both bacterial and metabolic differences between fecal bacteria from omnivore donors and vegetarian donors. Proteins with prebiotic supplementation showed higher Bacteroides spp. and inhibited Clostridium cluster IX in omnivore models, while in vegetarian modes, Clostridium cluster IX was higher and Bacteroides spp. lower with high protein plus prebiotic supplementation. Synergy1 addition inhibited p-cresol production in vegetarian high p-cresol-producing models while the inhibitory effect was not seen in omnivore models.

Dietary protein residue can result in microbial generation of various toxic metabolites in the gut, such as ammonia. A prebiotic is “a substrate that is selectively utilised by host microorganisms conferring a health benefit” (G. R. Gibson, R. Hutkins, M. E. Sanders, S. L. Prescott, et al., Nat Rev Gastroenterol Hepatol 14:491–502, 2017, https://doi.org/10.1038/nrgastro.2017.75). Prebiotics are carbohydrates that may have the potential to reverse the harmful effects of gut bacterial protein fermentation. Three-stage continuous colonic model systems were inoculated with fecal samples from omnivore and vegetarian volunteers. Casein (equivalent to 105 g protein consumption per day) was used within the systems as a protein source. Two different doses of inulin-type fructans (Synergy1) were later added (equivalent to 10 g per day in vivo and 15 g per day) to assess whether this influenced protein fermentation. Bacteria were enumerated by fluorescence in situ hybridization with flow cytometry. Metabolites from bacterial fermentation (short-chain fatty acid [SCFA], ammonia, phenol, indole, and p-cresol) were monitored to further analyze proteolysis and the prebiotic effect. A significantly higher number of bifidobacteria was observed with the addition of inulin together with reduction of Desulfovibrio spp. Furthermore, metabolites from protein fermentation, such as branched-chain fatty acids (BCFA) and ammonia, were significantly lowered with Synergy1. Production of p-cresol varied among donors, as we recognized four high producing models and two low producing models. Prebiotic addition reduced its production only in vegetarian high p-cresol producers. IMPORTANCE Dietary protein levels are generally higher in Western populations than in the world average. We challenged three-stage continuous colonic model systems containing high protein levels and confirmed the production of potentially harmful metabolites from proteolysis, especially replicates of the transverse and distal colon. Fermentations of proteins with a prebiotic supplementation resulted in a change in the human gut microbiota and inhibited the production of some proteolytic metabolites. Moreover, we observed both bacterial and metabolic differences between fecal bacteria from omnivore donors and vegetarian donors. Proteins with prebiotic supplementation showed higher Bacteroides spp. and inhibited Clostridium cluster IX in omnivore models, while in vegetarian modes, Clostridium cluster IX was higher and Bacteroides spp. lower with high protein plus prebiotic supplementation. Synergy1 addition inhibited p-cresol production in vegetarian high p-cresol-producing models while the inhibitory effect was not seen in omnivore models.

Background: The influence of gut microorganisms in health and disease is well documented, however, the role of yeasts has not been as widely studied as bacteria, despite associations with gastrointestinal disorders, such as Irritable Bowel Syndrome (IBS). For instance, Candida albicans is an opportunistic pathogen that has been linked to gastrointestinal symptoms. Methods: Urine, stool and blood samples will be collected from 40 healthy controls, 40 IBS and 40 inflammatory bowel disease (IBD) patients for microbial and metabolic analysis using primarily flow cytometry-fluorescence in situ hybridisation (FC-FISH) and proton nuclear magnetic resonance (1H-NMR) spectroscopy, respectively. Calprotectin and anti-Saccharomyces cerevisiae antibodies (ASCA) levels will assess gastrointestinal inflammation. Statistical analysis will identify yeasts and their metabolites associated with the cohorts of interest. Preliminary results: Preliminary tests to assess the presence and functionality of yeasts in healthy and IBS faecal samples using in vitro batch culture fermentation highlighted significant metabolic differences between the phenotypes: Trimethylamine (TMA), short chain fatty acids (SCFA) and ethanol predominantly distinguished in the IBS metabolic profile, compared to gamma-amino-N-butyrate (GABA) in the healthy donor. The addition of C. albicans shifted the healthy phenotype to resemble the IBS donor, whereas nystatin shifted the IBS phenotype towards the healthy metabolic profile. Conclusion: This study will further define the preliminary results that indicate the implication of yeasts in IBS pathogenesis. Understanding the role of yeasts within the healthy and diseased human gut is necessary to develop targeted therapies to improve patient’s quality of lives and relieve burdens on the economy and healthcare systems.

This study aimed to determine the impact of fat intake combined with Bacillus coagulans or trans-galactooligosaccharides (B-GOS) on bacterial composition and immune markers in an in vitro model. A three-stage continuous gut model system was used to simulate specific human colonic regions. Peripheral blood mononuclear cells were exposed to cell free supernatants and subsequent levels of inflammatory cytokines were measured by flow cytometry. Although fat addition decreased bifidobacteria from 8.76 ± 0.12 to 8.63 ± 0.13 and from 8.83 ± 0.08 to 8.67 ± 0.07 in pre- and probiotic models respectively, the changes were not significant. Fat addition also did not impact on cytokines induced by LPS. Under high fat conditions, numbers of bifidobacteria significantly increased by B. coagulans or B-GOS. In addition, B. coagulans or B-GOS significantly suppressed TNF-α production induced by LPS. Under high fat conditions, both B. coagulans and B-GOS led to potentially beneficial effects by targeting specific bacterial groups and modulating immune markers.

SummaryBackground Prebiotics have been shown to reduce abdominal symptoms in patients with functional gut disorders, despite that they are fermented by colonic bacteria and may induce gas-related symptoms. Aim To investigate changes in the metabolic activity of gut microbiota induced by a recognised prebiotic. Methods Healthy subjects (n = 20) were given a prebiotic (2.8 g/day HOST-G904, HOST Therabiomics, Jersey, Channel Islands) for 3 weeks. During 3-day periods immediately before, at the beginning and at the end of the administration subjects were put on a standard diet (low fibre diet supplemented with one portion of high fibre foods) and the following outcomes were measured: (i) number of daytime gas evacuations for 2 days by means of an event marker; (ii) volume of gas evacuated via a rectal tube during 4 h after a test meal; and (iii) microbiota composition by faecal Illumina MiSeq sequencing. Results At the beginning of administration, HOST-G904 significantly increased the number of daily anal gas evacuations (18 ± 2 vs. 12 ± 1 pre-administration; P < 0.001) and the volume of gas evacuated after the test meal (236 ± 23 mL vs. 160 ± 17 mL pre-administration; P = 0.006). However, after 3 weeks of administration, these effects diminished (11 ± 2 daily evacuations, 169 ± 23 mL gas evacuation). At day 21, relative abundance of butyrate producers (Lachnospiraceae) correlated inversely with the volume of gas evacuated (r = −0.52; P = 0.02). Conclusion The availability of substrates induces an adaptation of the colonic microbiota activity in bacterial metabolism, which produces less gas and associated issues. Clinical trials.gov NCT02618239.

Globally a new trend is developing that recommends avoidance of nondigestible, rapidly fermentable carbohydrates, also referred to as FODMAPs. This trend includes the publication of "free from" books and articles and the launch of diet programs and specialty foods. In this article we present information to help in making appropriate dietary recommendations.

© 2019, Springer Nature Limited. Probiotics and prebiotics are microbiota-management tools for improving host health. They target gastrointestinal effects via the gut, although direct application to other sites such as the oral cavity, vaginal tract and skin is being explored. Here, we describe gut-derived effects in humans. In the past decade, research on the gut microbiome has rapidly accumulated and has been accompanied by increased interest in probiotics and prebiotics as a means to modulate the gut microbiota. Given the importance of these approaches for public health, it is timely to reiterate factual and supporting information on their clinical application and use. In this Review, we discuss scientific evidence on probiotics and prebiotics, including mechanistic insights into health effects. Strains of Lactobacillus, Bifidobacterium and Saccharomyces have a long history of safe and effective use as probiotics, but Roseburia spp., Akkermansia spp., Propionibacterium spp. and Faecalibacterium spp. show promise for the future. For prebiotics, glucans and fructans are well proven, and evidence is building on the prebiotic effects of other substances (for example, oligomers of mannose, glucose, xylose, pectin, starches, human milk and polyphenols).

Synbiotic supplements contain pre- and probiotics and are used to modulate gut microbiota composition. This study aimed to investigate effects of two synbiotic mixtures on human faecal bacteria in vitro. Short chain fructooligosaccharides (FOS) (1% w/v) combined with either Bifidobacterium lactis Bb12 or Bifidobacterium lactis HN019 (106 colony-forming units (CFU)/mL)] were added to pH-controlled anaerobic batch cultures inoculated with human faeces. Maltodextrin (1% w/v), FOS (1% w/v) and the probiotic strains were also tested individually. Effects on bacteria, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were assessed over 48 h. With maltodextrin, FOS and the synbiotic mixtures, there was a significant increase in total bacteria and bifidobacteria numbers, compared to the negative control or probiotics alone. Increases in Atopobium cluster and Clostridium coccoides-Eubacterium rectale group occurred with FOS and maltodextrin, respectively. Additionally, maltodextrin, FOS and synbiotics resulted in a greater production of acetate and butyrate (SCFAs) compared to the negative control and probiotics alone, whereas concentrations of iso-valerate (BCFA) were lower with these treatments. In conclusion, synbiotic-induced in vitro bacterial changes and changes in SCFAs concentrations were not different from those observed with FOS alone. These data suggest that metabolic effects of these synbiotics are largely driven by the prebiotic component.