Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production

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.

In vitro fermentation reveals an interplay relationship between oat β-glucan and human gut Bacteroides and their potential role in regulating gut cytokines

Dietary oat β-glucan regulates the gut microbial composition and structure; however, the interplay relationship between oat β-glucan and the gut microbiota is unclear. In this study, we aim to investigate the interaction between oat β-glucan and human gut Bacteroides, a versatile carbohydrate utilizer, and explore the effect of their interaction on gut immunity homeostasis. The results of in vitro fermentation showed that oat β-glucan significantly increased the abundance of gut Bacteroides at the genus level. Then, Bacteroides strains were isolated from human gut microbiota and 9 strains of Bacteroides could grow on oat β-glucan and degrade oat β-glucan to reducing sugars. Notably, strains Bacteroides xylanisolvens Bac02 and Bacteroides koreensis Bac08 possessed the strongest degradation capacity towards oat β-glucan. Genome analysis and functional annotations suggested that B. xylanisolvens Bac02 and B. koreensis Bac08 contained abundant genes encoding glycoside hydrolases family 3 (GH3) and GH16, which might be responsible for β-glucan degradation. Moreover, cell experiments revealed that the metabolites from oat β-glucan fermentation by these 9 strains of Bacteroides could regulate the polarization of macrophages and maintain gut immunity homeostasis. Our study provides a novel insight into research on the interplay between dietary compounds and the gut microbiota.

Properties and functions of acylated starch with short-chain fatty acids: a comprehensive review

Short-chain fatty acids (SCFAs) are the primary energy source of colonic epithelial cells, but oral SCFAs are digested, absorbed, or degraded before reaching the colon. The acylated starch with SCFAs can be fermented and release specific SCFAs under the action of colonic intestinal microbiota. This review first introduces the preparation method, reaction mechanism, and substitution factors. Second, the structure, physical and chemical properties, in vitro function, and mechanism of acylated starch were expounded. Finally, the application of acylated starch in foods is introduced, and its safety is evaluated, providing a basis for the further development of acylated starch-based foods. The acylated starch obtained by different acylation types and preparation methods is different in particle, molecular, and crystal structures, leading to changes in the function and physicochemical properties. Meanwhile, acylated starch has the functional potential of targeted delivery of SCFAs to the colon, which can increase SCFAs in feces and intestine, selectively regulate the intestinal microbiota, and produce a prebiotic effect conducive to host health. The safety of acetylated starch has been supported by relevant studies, which have been widely used in various food fields and have great potential in the food industry.

Gut microbiota signatures of vulnerability to food addiction in mice and humans

OBJECTIVE

Food addiction is a multifactorial disorder characterised by a loss of control over food intake that may promote obesity and alter gut microbiota composition. We have investigated the potential involvement of the gut microbiota in the mechanisms underlying food addiction.

DESIGN

We used the Yale Food Addiction Scale (YFAS) 2.0 criteria to classify extreme food addiction in mouse and human subpopulations to identify gut microbiota signatures associated with vulnerability to this disorder.

RESULTS

Both animal and human cohorts showed important similarities in the gut microbiota signatures linked to food addiction. The signatures suggested possible non-beneficial effects of bacteria belonging to the Proteobacteria phylum and potential protective effects of Actinobacteria against the development of food addiction in both cohorts of humans and mice. A decreased relative abundance of the species Blautia wexlerae was observed in addicted humans and of Blautia genus in addicted mice. Administration of the non-digestible carbohydrates, lactulose and rhamnose, known to favour Blautia growth, led to increased relative abundance of Blautia in mice faeces in parallel with dramatic improvements in food addiction. A similar improvement was revealed after oral administration of Blautia wexlerae as a beneficial microbe.

CONCLUSION

By understanding the crosstalk between this behavioural alteration and gut microbiota, these findings constitute a step forward to future treatments for food addiction and related eating disorders.

Fecal microbiota transplantation: current challenges and future landscapes

SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.

Prevotella enterotype associates with diets supporting acidic faecal pH and production of propionic acid by microbiota

Metabolism of dietary fibres by colon microbiota plays an important role for human health. Personal data from a nutrition study (57 subjects) were analysed to elucidate quantitative associations between the diet, faecal microbiome, organic acid concentrations and pH. Ratios of the predominant acids acetate, butyrate and propionate ranged from 1:0.67:0.27 to 1:0.17:0.36. Pectin-rich diets resulted in higher faecal acetate concentrations. Negative correlation between faecal pH and BSS was observed. Higher faecal pH and lower acid concentrations were related to the higher abundance of amino acid degrading Clostridium, Odoribacter and Eubacterium coprostanoligenes, which are weak carbohydrate fermenting taxa. Propionic acid correlated especially to high abundance of Prevotella and low abundance of proteobacteria. The acetate to propionate ratio of the Prevotella enterotype was about half of that of the Bacteroides enterotype. Based on the results we suggest the measurement of faecal pH and organic acid composition for research and diagnostic purposes.

Why does increased microbial fermentation in the human colon shift toward butyrate?

The microbial community of the human large intestine mainly ferments dietary fiber to short chain fatty acids (SCFAs), which are efficiently absorbed by the host. The three major SCFAs (acetate, propionate, and butyrate) have different fates within the body and different effects on health. A recent analysis of 10 human volunteer studies established that the proportions of these SCFA in fecal samples significantly shifted towards butyrate as the overall concentration of SCFA increased. Butyrate plays a key role in gut health and is preferentially utilized as an energy source by the colonic epithelium. Here we discuss possible mechanisms that underlie this 'butyrate shift'; these include the selection for butyrate-producing bacteria within the microbiota by certain types of fiber, and the possibility of additional butyrate formation from lactate and acetate by metabolite cross-feeding. However, a crucial factor appears to be the pH in the proximal colon, which decreases as the SCFA concentrations increase. A mildly acidic pH has been shown to have an important impact on microbial competition and on the stoichiometry of butyrate production. Understanding these complex interactions has been greatly aided by the refinement of theoretical models of the colonic microbiota that assume a small number (10) of microbial functional groups (MFGs).

Characteristics of exopolysaccharides from Paecilomyces hepiali and their simulated digestion and fermentation in vitro by human intestinal microbiota

The metabolic process of polysaccharides in gastrointestinal digestions and the effects of the resulting carbohydrates on the composition of gut microbes are important to explore their prebiotic properties. Therefore, the purpose of this study was to investigate the simulated digestion and fecal fermentation in vitro of three fractions (PHEPSs-1, PHEPSs-2 and PHEPSs-3) purified from the crude exopolysaccharides of Paecilomyces hepiali HN1 (PHEPSs) and to explore the potential prebiotic mechanisms. The three purified fractions were characterized by HPLC, UV, FT-IR, SEM and AFM, and they were all of galactoglucomannan family with molecular weight of 178, 232 and 119 kDa, respectively. They could resist the simulated gastrointestinal digestions, but they were metabolized in fecal fermentation in vitro. Furthermore, the mannose in PHEPSs showed a higher utilization rate than that of glucose or galactose. The proliferation effects of PHEPSs on Bifidobacterium and Lactobacillus were weaker significantly than those of fructooligosaccharides before 12 h of fecal fermentation, but stronger after 24 h of fecal fermentation. Meanwhile, higher levels of short-chain fatty acids were found in PHEPSs groups when the fecal fermentation extended to 36 h. Therefore, PHEPSs are expected to have a potent gut healthy activity and can be explored as functional food ingredients.

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic voluntary morphine

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance which could be influenced by differences in microbiota, and yet no study has capitalized upon this natural variation to identify specific features linked to tolerance. We leveraged this natural variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar and predictive morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained differences in the development in tolerance. Mice that did not develop tolerance also maintained a higher abundance of taxa capable of producing the short-chain fatty acid (SCFA) butyrate, known to bolster intestinal barriers, suppress inflammation, and promote neuronal homeostasis. Furthermore, dietary butyrate supplementation significantly reduced the development of tolerance. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

In Vitro Fermentation Shows Polyphenol and Fiber Blends Have an Additive Beneficial Effect on Gut Microbiota States

Polyphenols and fermentable fibers have shown favorable effects on gut microbiota composition and metabolic function. However, few studies have investigated whether combining multiple fermentable fibers or polyphenols may have additive beneficial effects on gut microbial states. Here, an in vitro fermentation model, seeded with human stool combined from 30 healthy volunteers, was supplemented with blends of polyphenols (PP), dietary fibers (FB), or their combination (PPFB) to determine influence on gut bacteria growth dynamics and select metabolite changes. PP and FB blends independently led to significant increases in the absolute abundance of select beneficial taxa, namely Ruminococcus bromii, Bifidobacterium spp., Lactobacillus spp., and Dorea spp. Total short-chain fatty acid concentrations, relative to non-supplemented control (F), increased significantly with PPFB and FB supplementation but not PP. Indole and ammonia concentrations decreased with FB and PPFB supplementation but not PP alone while increased antioxidant capacity was only evident with both PP and PPFB supplementation. These findings demonstrated that, while the independent blends displayed selective positive impacts on gut states, the combination of both blends provided an additive effect. The work outlines the potential of mixed substrate blends to elicit a broader positive influence on gut microbial composition and function to build resiliency toward dysbiosis.

Dietary Fiber in Inflammatory Bowel Disease: Are We Ready to Change the Paradigm?

Accumulating evidence from pre-clinical and clinical studies demonstrate the benefit of dietary fibers for inflammatory bowel disease (IBD). However, the majority of patients avoid or limit their consumption to manage their symptoms during the active and remission phases, although limited research supports these long-term dietary habits. Although recent evidence-based dietary guidelines highlight the importance of promoting an adequate intake of dietary fiber in IBD patients, intervention trials have not yet clearly clarified the quality and quantity of dietary fiber that should be consumed to be equally tolerated by and provide benefit for patients with IBD. This narrative review describes dietary fibers and their characteristics, analyzes the real-word studies on the impact of dietary fiber consumption in IBD in different clinical settings, and concludes with potential future directions in fiber research, focusing on the real-world needs of characterizing the consumption of fiber-rich foods and promoting their adequate intake.

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

BACKGROUND

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. However, there is still only limited knowledge on how the GM activity and metabolite production in the gastrointestinal tract could be influenced by pH and the pH gradient increases along the colon.

RESULTS

Here we investigate the effect of pH gradients corresponding to levels typically found in the colon on GM composition and metabolite production using substrates inulin, lactose, galactooligosaccharides (GOS), and fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) for each fecal inoculum and found that colonic pH gradients significantly influenced in vitro simulated GM structure, but the influence of fecal donor and substrate was more pronounced. Low pH regimes strongly influenced GM with the decreased relative abundance of Bacteroides spp. and increased Bifidobacterium spp. Higher in vitro simulated colonic pH promoted the production of SCFAs in a donor- and substrate-dependent manner. The butyrate producer Butyricimonas was enriched at higher pH conditions, where also butyrate production was increased for inulin. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae also increased at higher colonic pH, which was accompanied by increased production of propionate with GOS and FOS as substrates.

CONCLUSIONS

Together, our results show that colonic substrates such as dietary fibres influence GM composition and metabolite production, not only by being selectively utilized by specific microbes, but also because of their SCFA production, which in turn also influences colonic pH and overall GM composition and activity. Our work provides details about the effect of the gradients of rising pH from the proximal to distal colon on fermenting dietary substrates in vitro and highlights the importance of considering pH in GM research.

Prevention of high-fat-diet-induced obesity in mice by soluble dietary fiber from fermented and unfermented millet bran

Obesity-related diabetes, cardiovascular disease, and hypertension pose many risks to human health. Thus, mice on a high-fat diet were gavaged with millet bran (unfermented/fermented) soluble dietary fiber (RSDF/FSDF, 500 mg·kg-1) for 10 weeks in current research, and then evaluated the various biological indicators. These findings revealed that RSDF and FSDF supplements could prevent fat synthesis by inhibiting sterol regulatory element-binding protein-1c gene expression. The RSDF supplements can also accelerate fat catabolism through enhanced the mRNA expression levels of adipose triglyceride lipase and peroxisome proliferator-activated receptor α. FSDF supplements can prevent obesity by decreasing 3-hydroxy-3-methyl-glutaryl-CoA reductase expression and increasing cholesterol 7α-hydroxylase expression. Moreover, FSDF also controls obesity development by lowering total cholesterol and low-density lipoprotein cholesterol levels in the blood, triglyceride, total cholesterol, and bile acid levels in the liver. Notably, FSDF supplements can promote Bacteroides and Prevotella propagation; excretive propionic acid binds to free fatty acid receptor 2/3 and then stimulates intestinal epithelial cells to generate glucagon-like-peptide-1 and peptide YY, which can reduce food and energy intake and ultimately prevent obesity. All evidence suggests that FSDF supplements play a crucial role in preventing obesity.

Local and Systemic Effects of Bioactive Food Ingredients: Is There a Role for Functional Foods to Prime the Gut for Resilience?

Scientific advancements in understanding the impact of bioactive components in foods on the gut microbiota and wider physiology create opportunities for designing targeted functional foods. The selection of bioactive ingredients with potential local or systemic effects holds promise for influencing overall well-being. An abundance of studies demonstrate that gut microbiota show compositional changes that correlate age and disease. However, navigating this field, especially for non-experts, remains challenging, given the abundance of bioactive ingredients with varying levels of scientific substantiation. This narrative review addresses the current knowledge on the potential impact of the gut microbiota on host health, emphasizing gut microbiota resilience. It explores evidence related to the extensive gut health benefits of popular dietary components and bioactive ingredients, such as phytochemicals, fermented greens, fibres, prebiotics, probiotics, and postbiotics. Importantly, this review distinguishes between the potential local and systemic effects of both popular and emerging ingredients. Additionally, it highlights how dietary hormesis promotes gut microbiota resilience, fostering better adaptation to stress-a hallmark of health. By integrating examples of bioactives, this review provides insights to guide the design of evidence-based functional foods aimed at priming the gut for resilience.

The molecular mechanism of polysaccharides in combating major depressive disorder: A comprehensive review

Major depressive disorder (MDD) is a complex psychiatric condition with diverse etiological factors. Typical pathological features include decreased cerebral cortex, subcortical structures, and grey matter volumes, as well as monoamine transmitter dysregulation. Although medications exist to treat MDD, unmet needs persist due to limited efficacy, induced side effects, and relapse upon drug withdrawal. Polysaccharides offer promising new therapies for MDD, demonstrating antidepressant effects with minimal side effects and multiple targets. These include neurotransmitter, neurotrophin, neuroinflammation, hypothalamic-pituitary-adrenal axis, mitochondrial function, oxidative stress, and intestinal flora regulation. This review explores the latest advancements in understanding the pharmacological actions and mechanisms of polysaccharides in treating major depression. We discuss the impact of polysaccharides' diverse structures and properties on their pharmacological actions, aiming to inspire new research directions and facilitate the discovery of novel anti-depressive drugs.

Modulation of Designed Gut Bacterial Communities by Prebiotics and the Impact of Their Metabolites on Intestinal Cells

The impact of prebiotics on human health is associated with their capacity to modulate microbiota, improving beneficial microbiota-host interactions. Herein, the prebiotic potential of microbial-fructo-oligosaccharides (microbial-FOSs) produced by a co-culture of Aspergillus ibericus plus Saccharomyces cerevisiae was evaluated on seven- and nine-strain bacterial consortia (7SC and 9SC, respectively), designed to represent the human gut microbiota. The 7SC was composed of Bacteroides dorei, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium longum, Escherichia coli, Lactobacillus acidophilus, and Lactobacillus rhamnosus. The 9SC also comprised the aforementioned bacteria, with the addition of Bacteroides thetaiotaomicron and Roseburia faecis. The effect of microbial-FOSs on the metabolic activity of intestinal Caco-2/HT29-MTX-E12 co-culture was also assessed. The results showed that microbial-FOS selectively promoted the growth of probiotic bacteria and completely suppressed the growth of E. coli. The microbial-FOSs promoted the highest production rates of lactate and total short-chain fatty acids (SCFA) as compared to the commercial prebiotic Frutalose® OFP. Butyrate was only produced in the 9SC consortium, which included the R. faecis-a butyrate-producing bacteria. The inclusion of this bacteria plus another Bacteroides in the 9SC promoted a greater metabolic activity in the Caco-2/HT29-MTX-E12 co-culture. The microbial-FOSs showed potential as promising prebiotics as they selectively promote the growth of probiotic bacteria, producing high concentrations of SCFA, and stimulating the metabolic activity of gut cells.

Habitual consumption of high-fibre bread fortified with bean hulls increased plasma indole-3-propionic concentration and decreased putrescine and deoxycholic acid faecal concentrations in healthy volunteers

Only 6 to 8 % of the UK adults meet the daily recommendation for dietary fibre. Fava bean processing lead to vast amounts of high-fibre by-products such as hulls. Bean hull fortified bread was formulated to increase and diversify dietary fibre while reducing waste. This study assessed the bean hull: suitability as a source of dietary fibre; the systemic and microbial metabolism of its components and postprandial events following bean hull bread rolls. Nine healthy participants (53·9 ± 16·7 years) were recruited for a randomised controlled crossover study attending two 3 days intervention sessions, involving the consumption of two bread rolls per day (control or bean hull rolls). Blood and faecal samples were collected before and after each session and analysed for systemic and microbial metabolites of bread roll components using targeted LC-MS/MS and GC analysis. Satiety, gut hormones, glucose, insulin and gastric emptying biomarkers were also measured. Two bean hull rolls provided over 85 % of the daily recommendation for dietary fibre; but despite being a rich source of plant metabolites (P = 0·04 v. control bread), these had poor systemic bioavailability. Consumption of bean hull rolls for 3 days significantly increased plasma concentration of indole-3-propionic acid (P = 0·009) and decreased faecal concentration of putrescine (P = 0·035) and deoxycholic acid (P = 0·046). However, it had no effect on postprandial plasma gut hormones, bacterial composition and faecal short chain fatty acids amount. Therefore, bean hulls require further processing to improve their bioactives systemic availability and fibre fermentation.

Roles of Short-Chain Fatty Acids in Inflammatory Bowel Disease

The gut microbiome is a diverse bacterial community in the human gastrointestinal tract that plays important roles in a variety of biological processes. Short-chain fatty acids (SCFA) are produced through fermentation of dietary fiber. Certain microbes in the gut are responsible for producing SCFAs such as acetate, propionate and butyrate. An imbalance in gut microbiome diversity can lead to metabolic disorders and inflammation-related diseases. Changes in SCFA levels and associated microbiota were observed in IBD, suggesting an association between SCFAs and disease. The gut microbiota and SCFAs affect reactive oxygen species (ROS) associated with IBD. Gut microbes and SCFAs are closely related to IBD, and it is important to study them further.

The Effect of Mushroom Dietary Fiber on the Gut Microbiota and Related Health Benefits: A Review

Mushroom dietary fiber is a type of bioactive macromolecule derived from the mycelia, fruiting bodies, or sclerotia of edible or medicinal fungi. The use of mushroom dietary fiber as a prebiotic has recently gained significant attention for providing health benefits to the host by promoting the growth of beneficial microorganisms; therefore, mushroom dietary fiber has promising prospects for application in the functional food industry and in drug development. This review summarizes methods for the preparation and modification of mushroom dietary fiber, its degradation and metabolism in the intestine, its impact on the gut microbiota community, and the generation of short-chain fatty acids (SCFAs); this review also systematically summarizes the beneficial effects of mushroom dietary fiber on host health. Overall, this review aims to provide theoretical guidance and a fresh perspective for the prebiotic application of mushroom dietary fiber in the development of new functional foods and drugs.

Dietary fiber - a scoping review for Nordic Nutrition Recommendations 2023

Dietary fiber is a term crudely defined as carbohydrates (CHOs) that escape digestion and uptake in the small intestine. Lignin, which is not a CHO, is also a part of the dietary fiber definition. Dietary fibers come in different sizes and forms, with a variety of combinations of monomeric units. Health authorities worldwide have for many years recommended a diet rich in dietary fibers based on consistent findings that dietary fibers are associated with reduced incidences of major non-communicable diseases, including obesity, type 2 diabetes, cardiovascular disease, and colorectal cancer. Most fibers come from common edible foods from the plant kingdom, but fibers are also found in food additives, supplements, and breast milk. The recommended intake in Nordic Nutrition Recommendations 2012 (NNR2012) is 25 g/d for women and 35 g/d for men, whereas the actual intake is significantly lower, ranging from 16 g/d to 22 g/d in women and 18 g/d to 26 g/d in men. New studies since NNR2012 confirm the current view that dietary fiber is beneficial for health, advocating intakes of at least 25 g/day.

The role of intestinal microbes on intestinal barrier function and host immunity from a metabolite perspective

The gut is colonized by many commensal microorganisms, and the diversity and metabolic patterns of microorganisms profoundly influence the intestinal health. These microbial imbalances can lead to disorders such as inflammatory bowel disease (IBD). Microorganisms produce byproducts that act as signaling molecules, triggering the immune system in the gut mucosa and controlling inflammation. For example, metabolites like short-chain fatty acids (SCFA) and secondary bile acids can release inflammatory-mediated signals by binding to specific receptors. These metabolites indirectly affect host health and intestinal immunity by interacting with the intestinal epithelial and mucosal immune cells. Moreover, Tryptophan-derived metabolites also play a role in governing the immune response by binding to aromatic hydrocarbon receptors (AHR) located on the intestinal mucosa, enhancing the intestinal epithelial barrier. Dietary-derived indoles, which are synthetic precursors of AHR ligands, work together with SCFA and secondary bile acids to reduce stress on the intestinal epithelium and regulate inflammation. This review highlights the interaction between gut microbial metabolites and the intestinal immune system, as well as the crosstalk of dietary fiber intake in improving the host microbial metabolism and its beneficial effects on the organism.

The Alteration of the Gut Microbiome during Ramadan Offers a Novel Perspective on Ramadan Fasting: A Pilot Study

An intermittent fasting regimen is widely perceived to lead to various beneficial health effects, including weight loss, the alleviation of insulin resistance, and the restructuring of a healthy gut microbiome. Because it shares certain commonalities with this dietary intervention, Ramadan fasting is sometimes misinterpreted as intermittent fasting, even though there are clear distinctions between these two regimens. The main purpose of this study is to verify whether Ramadan fasting drives the same beneficial effects as intermittent fasting by monitoring alterations in the gut microbiota. We conducted a study involving 20 Muslim individuals who were practicing Ramadan rituals and assessed the composition of their gut microbiomes during the 4-week period of Ramadan and the subsequent 8-week period post-Ramadan. Fecal microbiome analysis was conducted, and short-chain fatty acids (SCFAs) were assessed using liquid-chromatography-mass spectrometry. The observed decrease in the levels of SCFAs and beneficial bacteria during Ramadan, along with the increased microbial diversity post-Ramadan, suggests that the daily diet during Ramadan may not provide adequate nutrients to maintain robust gut microbiota. Additionally, the notable disparities in the functional genes detected through the metagenomic analysis and the strong correlation between Lactobacillus and SCFAs provide further support for our hypothesis.

Water-Insoluble Polysaccharide Extracted from Poria cocos Alleviates Antibiotic-Associated Diarrhea Based on Regulating the Gut Microbiota in Mice

Antibiotics are very effective in treating a variety of bacterial infections, while clinical overuse of antibiotics can lead to diseases such as antibiotic-associated diarrhea. Numerous studies have shown that natural polysaccharides can be used as prebiotics to alleviate antibiotic-associated diarrhea (AAD). Poria cocos is a medicinal and edible mushroom widely used for thousands of years in China, and our former study demonstrated that water-insoluble polysaccharide (PCY) has the potential prebiotic function. Therefore, we simulated the digestion and fermentation of PCY using feces from volunteers, and then administered it to C57BL/6 mice with AAD to study its effects on the gut microbiota and metabolites. The results indicated that PCY effectively alleviated the symptoms of AAD in mice, restored the intestinal barrier function, improved the content of short-chain fatty acids (SCFAs), decreased the level of inflammatory cytokines, and changed the structure of gut microbiota by increasing the relative abundance of norank_f__Muribaculaceae and unclassified_f__Lachnospiraceae, and decreasing that of Escherichia-Shigella, Staphylococcus and Acinetobacter. This study further demonstrated that PCY is an effective functional prebiotic for improving AAD disease, and provided a new avenue and insight for developing PCY as a functional food or prebiotic for alleviating gastrointestinal diseases.

Human microbiome myths and misconceptions

Over the past two decades, interest in human microbiome research has increased exponentially. Regrettably, this increased activity has brought with it a degree of hype and misinformation, which can undermine progress and public confidence in the research. Here we highlight selected human microbiome myths and misconceptions that lack a solid evidence base. By presenting these examples, we hope to draw increased attention to the implications of inaccurate dogma becoming embedded in the literature, and the importance of acknowledging nuance when describing the complex human microbiome.

Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study

Introduction

The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults.

Methods

Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing.

Results and Discussion

The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.

Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome

SCOPE

Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood.

METHODS AND RESULTS

Metabolite production and microbial populations are tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gives rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure.

CONCLUSION

Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.

The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases

The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.

In vitro digestion models for the design of safe and nutritious foods

Responsible development of future foods requires in depth understanding of food digestion in the human body based on robust research models, ranging from in vitro models to randomized controlled human trials. This chapter overviews fundamental aspects of food digestion, namely bioaccessibility and bioavailability, and models mirroring gastric, intestinal, and colonic conditions. Second, the chapter demonstrates the potential of in vitro digestion models to help screen adverse effects of food additives, such as Titanium dioxide or carrageenan, or underpin the determinants of macro- and micronutrient digestion in different strata of the population, for example digestion of emulsions. Such efforts support rationalized design of functional foods, such as infant formulae, cheese, cereals and biscuits which are validated in vivo or in randomized controlled trials.

Utilization of dietary mixed-linkage β-glucans by the Firmicute Blautia producta

The β-glucans are structurally varied, naturally occurring components of the cell walls and storage materials of a variety of plant and microbial species. In the human diet, mixed-linkage glucans [MLG - β-(1,3/4)-glucans] influence the gut microbiome and the host immune system. Although consumed daily, the molecular mechanism by which human gut Gram-positive bacteria utilize MLG largely remains unknown. In this study, we used Blautia producta ATCC 27340 as a model organism to develop understanding of MLG utilization. B. producta encodes a gene locus comprising a multi-modular cell-anchored endo-glucanase (BpGH16_MLG), an ABC transporter, and a glycoside phosphorylase (BpGH94_MLG) for utilizing MLG, as evidenced by the up-regulation of expression of the enzyme- and solute binding protein (SBP)-encoding genes in this cluster when the organism is grown on MLG. We determined that recombinant BpGH16_MLG cleaved various types of β-glucan, generating oligosaccharides suitable for cellular uptake by B. producta. Cytoplasmic digestion of these oligosaccharides is then performed by recombinant BpGH94_MLG and β-glucosidases (BpGH3-AR8_MLG and BpGH3-X62_MLG). Using targeted deletion, we demonstrated BpSBP_MLG is essential for B. producta growth on barley β-glucan. Furthermore, we revealed that beneficial bacteria, such as Roseburia faecis JCM 17581^T, Bifidobacterium pseudocatenulatum JCM 1200T, Bifidobacterium adolescentis JCM 1275T, and Bifidobacterium bifidum JCM 1254, can also utilize oligosaccharides resulting from the action of BpGH16_MLG. Disentangling the β-glucan utilizing capability of B. producta provides a rational basis on which to consider the probiotic potential of this class of organism.

In Vitro Ileal Fermentation is Affected More by the Fiber Source Fermented than the Ileal Microbial Composition in Growing Pigs

Background

The fermentation of undigested material in the ileum is quantitatively important. However, the respective contributions of the microbial composition and the substrate to ileal fermentation are unclear.

Objective

This aim was to investigate the contribution of microbial composition and fiber source to in vitro ileal fermentation outcomes.

Methods

Thirteen ileal cannulated female pigs (Landrace/Large White; 9-wk-old; 30.5 kg body weight) were given diets containing black beans, wheat bread, chickpeas, peanuts, pigeon peas, sorghum, or wheat bran as the sole protein source for 7 d (100 g protein/kg dry matter diet). On day 7, ileal digesta were collected and stored at -80°C for microbial analysis and in vitro fermentation. For each diet, a pooled ileal inoculum was prepared to ferment different fiber sources (cellulose, pectin, arabinogalactan, inulin, fructooligosaccharides, and resistant starch) for 2 h at 37°C. Organic matter fermentability and organic acid production were determined following in vitro fermentation. Data were analyzed using a 2-way ANOVA (inoculum × fiber).

Results

Forty-five percent of the identified genera in the digesta differed across diets. For instance, the number of Lactococcus was 115-fold greater (P ≤ 0.05) in the digesta of pigs fed the pigeon pea diet than for pigs fed the wheat bran diet. For both in vitro organic matter fermentability and organic acid production, there were significant (P ≤ 0.05) interactions between the inoculum and the fiber source. For instance, pectin and resistant starch resulted in 1.6- to 31-fold more (P ≤ 0.05) lactic acid production when fermented by the pigeon pea inoculum than other inocula. For specific fiber sources, statistically significant correlations were found between the number of bacteria from certain members of the ileal microbial community and fermentation outcomes.

Conclusions

Both the fiber source fermented and the ileal microbial composition of the growing pig affected in vitro fermentation; however, the effect of the fiber source was predominant.Curr Dev Nutr 2023;x:xx.

Fecal microbiota transplantation reduces mouse mortality from Listeria monocytogenes infection

Listeria monocytogenes (Lm) is a food bacterium with strong pathogenicity which causes infections via the gastrointestinal tract. Mechanisms by which gut microbiota (GM) resist microbial infections have received little attention. Eight-week-old mice were orally inoculated with wild-type Lm EGD-e and fecal microbiota transplantation (FMT) employed. GM richness and diversity of infected mice changed rapidly within 24h. Firmicutes class decreased and Bacteroidetes, Tenericutes and Ruminococcaceae increased significantly. Coprococcus, Blautia and Eubacterium also increased on the 3rd day post-infection. Moreover, GM transplanted from healthy mice reduced mortality of infected mice by approximately 32%. FMT treatment decreased production of TNFα, IFN-γ, IL-1β and IL-6 relative to PBS treatment. In summary, FMT has potential as a treatment against Lm infection and may be used for bacterial resistance management. Further work is required to elucidate the key GM effector molecules.

The modulatory effect of encapsulated bioactives and probiotics on gut microbiota: improving health status through functional food

The gut microbiota can be a determining factor of the health status of the host by its association with some diseases. It is known that dietary intake can modulate this microbiota through the consumption of compounds like essential oils, unsaturated fatty acids, non-digestible fiber, and probiotics, among others. However, these kinds of compounds can be damaged in the gastrointestinal tract as they pass through it to reach the intestine. This is due to the aggressive and changing conditions of this tract. For this reason, to guarantee that compounds arrive in the intestine at an adequate concentration to exert a modulatory effect on the gut microbiota, encapsulation should be sought. In this paper, we review the current research on compounds that modulate the gut microbiota, the encapsulation techniques used to protect the compounds through the gastrointestinal tract, in vitro models of this tract, and how these encapsulates interact with the gut microbiota. Finally, an overview of the regulatory status of these encapsulates is presented. The key findings are that prebiotics are the best modulators of gut microbiota fermentation metabolites. Also, probiotics promote an increase of beneficial gut microorganisms, which in some cases promotes their fermentation metabolites as well. Spray drying, freeze drying, and electrodynamics are notable encapsulation techniques that permit high encapsulation efficiency, high viability, and, together with wall materials, a high degree of protection against gastrointestinal conditions, allowing controlled release in the intestine and exerting a modulatory effect on gut microbiota.

Bridging preclinical and clinical gut microbiota research using the ex vivo SIFR® technology

Introduction

While modulation of the human adult gut microbiota is a trending strategy to improve health, the underlying mechanisms are poorly understood.

Methods

This study aimed to assess the predictive value of the ex vivo, reactor-based, high-throughput SIFR^® (Systemic Intestinal Fermentation Research) technology for clinical findings using three structurally different prebiotics [inulin (IN), resistant dextrin (RD) and 2'-fucosyllactose (2'FL)].

Results

The key finding was that data obtained within 1-2 days were predictive for clinical findings upon repeated prebiotic intake over weeks: among hundreds of microbes, IN stimulated Bifidobacteriaceae, RD boosted Parabacteroides distasonis, while 2'FL specifically increased Bifidobacterium adolescentis and Anaerobutyricum hallii. In line with metabolic capabilities of these taxa, specific SCFA (short-chain fatty acids) were produced thus providing insights that cannot be obtained in vivo where such metabolites are rapidly absorbed. Further, in contrast to using single or pooled fecal microbiota (approaches used to circumvent low throughput of conventional models), working with 6 individual fecal microbiota enabled correlations that support mechanistic insights. Moreover, quantitative sequencing removed the noise caused by markedly increased cell densities upon prebiotic treatment, thus allowing to even rectify conclusions of previous clinical trials related to the tentative selectivity by which prebiotics modulate the gut microbiota. Counterintuitively, not the high but rather the low selectivity of IN caused only a limited number of taxa to be significantly affected. Finally, while a mucosal microbiota (enriched with Lachnospiraceae) can be integrated, other technical aspects of the SIFR^® technology are a high technical reproducibility, and most importantly, a sustained similarity between the ex vivo and original in vivo microbiota.

Discussion

By accurately predicting in vivo results within days, the SIFR^® technology can help bridge the so-called "Valley of Death" between preclinical and clinical research. Facilitating development of test products with better understanding of their mode of action could dramatically increase success rate of microbiome modulating clinical trials.Graphical Abstract.

The waxy mutation in sorghum and other cereal grains reshapes the gut microbiome by reducing levels of multiple beneficial species

Waxy starches from cereal grains contain >90% amylopectin due to naturally occurring mutations that block amylose biosynthesis. Waxy starches have unique organoleptic characteristics (e.g. sticky rice) as well as desirable physicochemical properties for food processing. Using isogenic pairs of wild type sorghum lines and their waxy derivatives, we studied the effects of waxy starches in the whole grain context on the human gut microbiome. In vitro fermentations with human stool microbiomes show that beneficial taxonomic and metabolic signatures driven by grain from wild type parental lines are lost in fermentations of grain from the waxy derivatives and the beneficial signatures can be restored by addition of resistant starch. These undesirable effects are conserved in fermentations of waxy maize, wheat, rice and millet. We also demonstrate that humanized gnotobiotic mice fed low fiber diets supplemented with 20% grain from isogenic pairs of waxy vs. wild type parental sorghum have significant differences in microbiome composition and show increased weight gain. We conclude that the benefits of waxy starches on food functionality can have unintended tradeoff effects on the gut microbiome and host physiology that could be particularly relevant in human populations consuming large amounts of waxy grains.

Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability

It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.

Soy isoflavone-specific biotransformation product S-equol in the colon: physiological functions, transformation mechanisms, and metabolic regulatory pathways

Epidemiological data suggest that regular intake of soy isoflavones may reduce the incidence of estrogen-dependent and aging-associated disorders. Equol is a metabolite of soy isoflavone (SI) produced by specific gut microbiota and has many beneficial effects on human health due to its higher biological activity compared to SI. However, only 1/3 to 1/2 of humans are able to produce equol in the body, which means that not many people can fully benefit from SI. This review summarizes the recent advances in equol research, focusing on the chemical properties, physiological functions, conversion mechanisms in vitro and vivo, and metabolic regulatory pathways affecting S-equol production. Advanced experimental designs and possible techniques in future research plan are also fully discussed. Furthermore, this review provides a fundamental basis for researchers in the field to understand individual differences in S-equol production, the efficiency of metabolic conversion of S-equol, and fermentation production of S-equol in vitro.

Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data

The bacteria-derived short-chain fatty acids (SCFAs) butyrate and propionate play important (distinct) roles in health and disease, and understanding the ecology of respective bacteria on a community-wide level is a top priority in microbiome research. Applying sequence data (metagenomics and 16S rRNA gene) to predict SCFAs production in vitro and in vivo, a clear split between butyrate- and propionate-forming bacteria was detected with only very few taxa exhibiting pathways for the production of both SCFAs. After in vitro growth of fecal communities from distinct donors (n = 8) on different substrates (n = 7), abundances of bacteria exhibiting pathways correlated with respective SCFA concentrations, in particular in the case of butyrate. For propionate, correlations were weaker, indicating that its production is less imprinted into the core metabolism compared with butyrate-forming bacteria. Longitudinal measurements in vivo (n = 5 time-points from 20 subjects) also revealed a correlation between abundances of pathway-carrying bacteria and concentrations of the two SCFAs. Additionally, lower bacterial cell concentrations, together with higher stool moisture, promoted overall bacterial activity (measured by flow cytometry and coverage patterns of metagenome-assembled genomes) that led to elevated SCFA concentrations with over-proportional levels of butyrate. Predictions on pathway abundances based on 16S rRNA gene data using our in-house database worked well, yielding similar results as metagenomic-based analyses. Our study indicates that stimulating growth of butyrate- and propionate-producing bacteria directly leads to more production of those compounds, which is governed by two functionally distinct bacterial groups facilitating the development of precision intervention strategies targeting either metabolite.

Reduced-particle size wheat bran and endoxylanase supplementation in broiler feed affect arabinoxylan hydrolysis and fermentation with broiler age differently

Since the caecal microbiota of young broilers are not yet able to ferment the dietary fibre (DF) fraction of the feed to a large extent, increasing the accessibility of DF substrates along the gastrointestinal tract is crucial to benefit from the health stimulating metabolic end-products (e.g. butyric acid) generated upon microbial DF fermentation. Therefore, the present study aimed to evaluate the potential of reduced-particle size wheat bran (RPS-WB) and endoxylanases as feed additives to stimulate arabinoxylan (AX) hydrolysis and fermentation along the hindgut of young broilers. To this end, RPS-WB and endoxylanase supplementation were evaluated in a 2 × 2 factorial design using a total of 256 male 1-d-old chicks (Ross 308). Broilers were assigned to 4 dietary treatments: a basal wheat-based diet with (1) no feed additives (control, CTRL), (2) an endoxylanase (XYL; Econase XT 25 at 0.10 g/kg diet), (3) 1% wheat bran with an average reduced particle size of 297 μm (RPS-WB) and (4) an endoxylanase and 1% RPS-WB (RPS-WB + XYL). Each dietary treatment was replicated 8 times and on d 10 and 28, respectively, 24 and 16 broilers per treatment group were euthanised to analyse AX degradation, short-chain fatty acid production and digesta viscosity in the ileum and caecum. Broilers receiving XYL in their diet showed increased AX solubilisation and fermentation at both d 10 and 28 compared to the CTRL group (P < 0.05). Adding RPS-WB to the diet stimulated wheat AX utilisation by the primary AX degraders in the caecum at 10 d of age compared to the CTRL group, as observed by the high AX digestibility coefficient for the RPS-WB supplemented group at this young age (P < 0.05). At 28 d, RPS-WB supplementation lowered body-weight gains but increased butyric acid concentrations compared to the XYL and CTRL group (P < 0.05). Although no synergistic effect for RPS-WB + XYL broilers was observed for AX hydrolysis and fermentation, these findings suggest that both additives can raise a dual benefit to the broiler as a butyrogenic effect and improved AX fermentation along the ileum and caecum were observed throughout the broiler's life.

Recent advances in developing butyrogenic functional foods to promote gut health

As one of the major short-chain fatty acids produced via microbial fermentation, butyrate serves as not only a preferred energy substrate but also an important signaling molecule. Butyrate concentrations in circulation, tissues, and gut luminal contents have important pathophysiological implications. The genetic capacity of butyrate biosynthesis by the gut microbiota is frequently compromised during aging and various disorders, such as inflammatory bowel disease, metabolic disorders and colorectal cancer. Substantial efforts have been made to identify potent butyrogenic substrates and butyrate-hyperproducing bacteria to compensate for butyrate deficiency. Interindividual butyrogenic responses exist, which are more strongly predicted by heterogeneity in the gut microbiota composition than by ingested prebiotic substrates. In this review, we catalog major food types rich in butyrogenic substrates. We also discuss the potential of butyrogenic foods with proven properties for promoting gut health and disease management using findings from clinical trials. Potential limitations and constraints in the current research are highlighted. We advocate a precise nutrition approach in designing future clinical trials by prescreening individuals for key gut microbial signatures when recruiting study volunteers. The information provided in this review will be conducive to the development of microbiota engineering approaches for enhancing the sustained production of butyrate.

Ecological memory of prior nutrient exposure in the human gut microbiome

Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an "ecological memory" of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual's habitual exposure to dietary fiber was associated with their gut microbiome's efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.

Short-Chain Fatty Acid Receptors and Blood Pressure Regulation: Council on Hypertension Mid-Career Award for Research Excellence 2021

The gut microbiome influences host physiology and pathophysiology through several pathways, one of which is microbial production of chemical metabolites which interact with host signaling pathways. Short-chain fatty acids (SCFAs) are a class of gut microbial metabolites known to activate multiple signaling pathways in the host. Growing evidence indicates that the gut microbiome is linked to blood pressure, that SCFAs modulate blood pressure regulation, and that delivery of exogenous SCFAs lowers blood pressure. Given that hypertension is a key risk factor for cardiovascular disease, the examination of novel contributors to blood pressure regulation has the potential to lead to novel approaches or treatments. Thus, this review will discuss SCFAs with a focus on their host G protein-coupled receptors including GPR41 (G protein-coupled receptor 41), GPR43, and GPR109A, as well as OLFR78 (olfactory receptor 78) and OLFR558. This includes a discussion of the ligand profiles, G protein coupling, and tissue distribution of each receptor. We will also review phenotypes relevant to blood pressure regulation which have been reported to date for Gpr41, Gpr43, Gpr109a, and Olfr78 knockout mice. In addition, we will consider how SCFA signaling influences physiology at baseline, and, how SCFA signaling may contribute to blood pressure regulation in settings of hypertension. In sum, this review will integrate current knowledge regarding how SCFAs and their receptors regulate blood pressure.

Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome

Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome.

Diet affects the human gut microbiome, but studies linking crop genetics to seed traits that influence the human gut microbiome are lacking. Here, the authors develop an in vitro microbiome screening method and reveal the association between sorghum genes regulating condensed tannin biosynthesis and human gut microbiome.

The microbiota composition drives personalized nutrition: Gut microbes as predictive biomarkers for the success of weight loss diets

The investigation of the human gut microbiome during recent years has permitted us to understand its relevance for human health at a systemic level, making it possible to establish different functional axes (e.g., the gut-brain, gut-liver, and gut-lung axes), which support the organ-like status conferred to this microecological component of our body. The human gut microbiota is extremely variable but modifiable via diet, a fact that allows targeting of microbes through defined dietary strategies to uncover cost-effective therapies to minimize the burden of non-communicable diseases such as pandemic obesity and overweight and its metabolic comorbidities. Nevertheless, randomly controlled dietary interventions regularly exhibit low to moderate degrees of success in weight control, making their implementation difficult in clinical practice. Here, we review the predictive value of the baseline gut microbiota configurations to anticipate the success of dietary interventions aimed at weight loss, mostly based on caloric restriction regimes and oral fiber supplementation. This emergent research concept fits into precision medicine by considering different diet patterns and adopting the best one, based on the individual microbiota composition, to reach significant adiposity reduction and improve metabolic status. We review the results from this fresh perspective of investigation, taking into account studies released very recently. We also discuss some future outlooks in the field and potential pitfalls to overcome with the aim of gaining knowledge in the field and achieving breakthroughs in personalized nutrition.

Unhealthy Diets Induce Distinct and Regional Effects on Intestinal Inflammatory Signalling Pathways and Long-Lasting Metabolic Dysfunction in Rats

The intestinal epithelium is a principal site for environmental agents’ detection. Several inflammation- and stress-related signalling pathways have been identified as key players in these processes. However, it is still unclear how the chronic intake of inadequate nutrients triggers inflammatory signalling pathways in different intestinal regions. We aimed to evaluate the impact of unhealthy dietary patterns, starting at a younger age, and the association with metabolic dysfunction, intestinal inflammatory response, and obesity in adulthood. A rat model was used to evaluate the effects of the consumption of sugary beverages (HSD) and a Western diet (WD), composed of ultra-processed foods. Both diets showed a positive correlation with adiposity index, but a positive correlation was found between the HSD diet and the levels of blood glucose and triglycerides, whereas the WD diet correlated positively with triglyceride levels. Moreover, a distinct inflammatory response was associated with either the WD or HSD diets. The WD induced an increase in TLR2, TLR4, and nuclear factor-kappa B (NF-κB) intestinal gene expression, with higher levels in the colon and overexpression of the inducible nitric oxide synthase. In turn, the HSD diet induced activation of the TLR2-mediated NF-κB signalling pathway in the small intestine. Altogether, these findings support the concept that early intake of unhealthy foods and nutrients are a main exogenous signal for disturbances of intestinal immune mechanisms and in a region-specific manner, ultimately leading to obesity-related disorders in later life.

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.

Intrinsic dietary fibers and the gut microbiome: Rediscovering the benefits of the plant cell matrix for human health

Dietary fibers contribute to structure and storage reserves of plant foods and fundamentally impact human health, partly by involving the intestinal microbiota, notably in the colon. Considerable attention has been given to unraveling the interaction between fiber type and gut microbiota utilization, focusing mainly on single, purified fibers. Studying these fibers in isolation might give us insights into specific fiber effects, but neglects how dietary fibers are consumed daily and impact our digestive tract: as intrinsic structures that include the cell matrix and content of plant tissues. Like our ancestors we consume fibers that are entangled in a complex network of plants cell walls that further encapsulate and shield intra-cellular fibers, such as fructans and other components from immediate breakdown. Hence, the physiological behavior and consequent microbial breakdown of these intrinsic fibers differs from that of single, purified fibers, potentially entailing unexplored health effects. In this mini-review we explain the difference between intrinsic and isolated fibers and discuss their differential impact on digestion. Subsequently, we elaborate on how food processing influences intrinsic fiber structure and summarize available human intervention studies that used intrinsic fibers to assess gut microbiota modulation and related health outcomes. Finally, we explore current research gaps and consequences of the intrinsic plant tissue structure for future research. We postulate that instead of further processing our already (extensively) processed foods to create new products, we should minimize this processing and exploit the intrinsic health benefits that are associated with the original cell matrix of plant tissues.