Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome

Dietary fiber: Still alive

Dietary fiber (DF) was established as a key dietary constituent some decades ago, as were some of its mechanisms of action and health effects. Although there is consolidated evidence on many features regarding DF, at the same time there are still many aspects to be explored in the field, e.g., deeper explorations of the contribution of phenolic compounds linked to cell walls to the biological activities of DF, or of the relevance of the gut-brain axis. At the same time, increasing DF intake should be seen as a major public health problem since worldwide intakes are quite far from recommendations. The awareness of this fact by public bodies should lead, among others, to the assessment of effective strategies for promoting DF intake among general population or specific groups; and to consider potential regulatory modifications in order to clarify several aspects potentially misleading for consumers.

Incidence of Urinary Infections and Behavioral Risk Factors

This evaluation of the impact of behavioral risk factors on the incidence of urinary infections was based on a questionnaire in which 1103 respondents, predominantly women (883), participated. From the statistical processing of the data, it was observed that 598 of the respondents were of normal weight; the rest, more than half, were underweight or overweight (χ2 = 32.46, p < 0.001), with male respondents being predominantly overweight or obese (169 out of a total of 220). Most of the respondents were young (χ2 = 15.45, p < 0.001), under the age of 45 (840). According to the processed data, it was found that respondents in the age group of 26-35 years showed the greatest vulnerability to recurrent urinary infections, while the age group of 18-25 years recorded the highest number of responses related to the rare presence or even absence of episodes of urinary infections. A body weight-related vulnerability was also noted among the respondents; the majority of obese people declared that they face frequent episodes of urinary infections. Regarding diet quality, 210 respondents reported an adherence to an unhealthy diet, 620 to a moderately healthy diet, and 273 to a healthy diet. Of the respondents who adhered to a healthy diet, 223 were women (χ2 = 2.55, p = 0.279). There was a close connection between diet quality and the frequency of urinary infections: from the statistical processing of the data, it was observed that the highest percentage of respondents who rarely (57.14%) or never got urinary infections (29.30%) were among those who adhered to a healthy diet, and the highest percentage of those who declared that they often got urinary infections were among those with increased adherence to an unhealthy diet (χ2 = 13.46, p = 0.036). The results of this study highlight a strong impact of obesity, reduced consumption of fruit and vegetables, and sedentary lifestyle on the risk of recurring urinary infections.

Dry beans (Phaseolus vulgaris L.) modulate the kinetics of lipid digestion in vitro: Impact of the bean matrix and processing

The lipid-lowering effect of dry beans and their impact on lipid and cholesterol metabolism have been established. This study investigates the underlying mechanisms of this effect and explore how the structural integrity of processed beans influences their ability to modulate lipolysis using the INFOGEST static in vitro digestion model. Dietary fiber (DF) fractions were found to decrease lipolysis by increasing the digesta viscosity, leading to depletion-flocculation and/or coalescence of lipid droplets. Bean flours exhibited a more pronounced reduction in lipolysis compared to DF. Furthermore, different levels of bean structural integrity showed varying effects on modulating lipolysis, with medium-sized bean particles demonstrating a stronger reduction. Hydrothermal treatment compromised the ability of beans to modulate lipid digestion, while hydrostatic-pressure treatment (600 MPa/5min) enhanced the effect. These findings highlight that the lipid-lowering effect of beans is not solely attributed to DF but also to the overall bean matrix, which can be manipulated through processing techniques.

Reproducible microbiome composition signatures of anxiety and depressive symptoms

The gut microbiome is a significant contributor to mental health, with growing evidence linking its composition to anxiety and depressive disorders. Gut microbiome composition is associated with signs of anxiety and depression both in clinically diagnosed mood disorders and subclinically in the general population and may be influenced by dietary fibre intake and the presence of chronic pain. We provide an update of current evidence on the role of gut microbiome composition in depressive and anxiety disorders or symptoms by reviewing available studies. Analysing data from three independent cohorts (osteoarthritis 1 (OA1); n = 46, osteoarthritis 2 (OA2); n = 58, and healthy controls (CON); n = 67), we identified microbial composition signatures of anxiety and depressive symptoms at genus level and cross-validated our findings performing meta-analyses of our results with results from previously published studies. The genera Bifidobacterium (fixed-effect beta (95% CI) = -0.22 (-0.34, -0.10), p = 3.90e-04) and Lachnospiraceae NK4A136 group (fixed-effect beta (95% CI) = -0.09 (-0.13, -0.05), p = 2.53e-06) were found to be the best predictors of anxiety and depressive symptoms, respectively, across our three cohorts and published literature taking into account demographic and lifestyle covariates, such as fibre intake. The association with anxiety was robust in accounting for heterogeneity between cohorts and supports previous observations of the potential prophylactic effect of Bifidobacterium against anxiety symptoms.

Dietary Oncopharmacognosy as a Crosswalk between Precision Oncology and Precision Nutrition

While diet and nutrition are modifiable risk factors for many chronic and infectious diseases, their role in cancer prevention and control remains under investigation. The lack of clarity of some diet-cancer relationships reflects the ongoing debate about the relative contribution of genetic factors, environmental exposures, and replicative errors in stem cell division as determinate drivers of cancer risk. In addition, dietary guidance has often been based upon research assuming that the effects of diet and nutrition on carcinogenesis would be uniform across populations and for various tumor types arising in a specific organ, i.e., that one size fits all. Herein, we present a paradigm for investigating precision dietary patterns that leverages the approaches that led to successful small-molecule inhibitors in cancer treatment, namely understanding the pharmacokinetics and pharmacodynamics of small molecules for targeting carcinogenic mechanisms. We challenge the scientific community to refine the paradigm presented and to conduct proof-in-concept experiments that integrate existing knowledge (drug development, natural products, and the food metabolome) with developments in artificial intelligence to design and then test dietary patterns predicted to elicit drug-like effects on target tissues for cancer prevention and control. We refer to this precision approach as dietary oncopharmacognosy and envision it as the crosswalk between the currently defined fields of precision oncology and precision nutrition with the goal of reducing cancer deaths.

Short Photoperiod-Dependent Enrichment of Akkermansia spec. as the Major Change in the Intestinal Microbiome of Djungarian Hamsters (Phodopus sungorus)

The Djungarian hamster (Phodopus sungorus) is a prominent model organism for seasonal acclimatization, showing drastic whole-body physiological adjustments to an energetically challenging environment, which are considered to also involve the gut microbiome. Fecal samples of hamsters in long photoperiod and again after twelve weeks in short photoperiod were analyzed by 16S-rRNA sequencing to evaluate seasonal changes in the respective gut microbiomes. In both photoperiods, the overall composition was stable in the major superordinate phyla of the microbiota, with distinct and delicate changes of abundance in phyla representing each <1% of all. Elusimicrobia, Tenericutes, and Verrucomicrobia were exclusively present in short photoperiod hamsters. In contrast to Elusimicrobium and Aneroplasma as representatives of Elusimicrobia and Tenericutes, Akkermansia muciniphila is a prominent gut microbiome inhabitant well described as important in the health context of animals and humans, including neurodegenerative diseases and obesity. Since diet was not changed, Akkermansia enrichment appears to be a direct consequence of short photoperiod acclimation. Future research will investigate whether the Djungarian hamster intestinal microbiome is responsible for or responsive to seasonal acclimation, focusing on probiotic supplementation.

Does Alteration of the Microbiome Cause Diverticular Disease?

The role of the microbiome in influencing the development and course of human disease is increasingly understood and appreciated. In diverticular disease, the microbiome presents an intriguing potential link between the disease and its long-established risk factors, dietary fiber and industrialization. However, current data have yet to demonstrate a clear link between specific alterations in the microbiome and diverticular disease. The largest study of diverticulosis is negative and studies of diverticulitis are small and heterogeneous. Although multiple disease-specific hurdles exist, the early state of the current research and the many un- or underexplored clinical phenotypes present a significant opportunity for investigators to improve our knowledge of this common and incompletely understood disease.

Natural Products in Precision Oncology: Plant-Based Small Molecule Inhibitors of Protein Kinases for Cancer Chemoprevention

Striking progress is being made in cancer treatment by using small molecule inhibitors of specific protein kinases that are products of genes recognized as drivers for a specific type of cancer. However, the cost of newly developed drugs is high, and these pharmaceuticals are neither affordable nor accessible in most parts of the world. Accordingly, this narrative review aims to probe how these recent successes in cancer treatment can be reverse-engineered into affordable and accessible approaches for the global community. This challenge is addressed through the lens of cancer chemoprevention, defined as using pharmacological agents of natural or synthetic origin to impede, arrest, or reverse carcinogenesis at any stage in the disease process. In this regard, prevention refers to reducing cancer-related deaths. Recognizing the clinical successes and limitations of protein kinase inhibitor treatment strategies, the disciplines of pharmacognosy and chemotaxonomy are juxtaposed with current efforts to exploit the cancer kinome to describe a conceptual framework for developing a natural product-based approach for precision oncology.

Moderate intakes of soluble corn fibre or inulin do not cause gastrointestinal discomfort and are well tolerated in healthy children

We investigated the gastrointestinal (GI) tolerance of soluble corn fibre (SCF) compared with inulin in children 3-9 years old. SCF (3-8 g/d for 10d) was tolerated as well as inulin: no differences were identified in stool frequency and consistency, proportion of subjects with at least one loose stool or reporting symptoms during bowel movement. Compared to inulin, 6 g/d of SCF lowered gas severity in children aged 3-5 years old. No differences were noted for alpha and beta diversity, relative abundance of Bacteroidota, Firmicutes, Ruminococcaceae, or the Firmicutes to Bacteroidota ratio. Relative abundance of some specific strains (i.e. Anaerostipes, Bifidobacterium, Fusicatenibacter, Parabacteroides) varied depending on the fibre type and dose level. Fortification at a level of 6-8 g/d of SCF and/or inulin could help addressing the fibre gap without any GI discomfort.

Dietary contributors to fermentable carbohydrate intake in healthy American college students

OBJECTIVE

The study explored food items that contribute most toward increased fermentable carbohydrate (FC) intake and its association with diet quality in college students.

METHOD

This cross-sectional study included 571 consented college students (≥18 years) with reported energy intakes (500-3500 kcal/day for women; 800-4000 kcal/day for men). FC intake and healthy eating index-2015 (HEI-2015) scores were assessed by diet history questionnaire-II. Data were analyzed by unadjusted bivariate linear regression and Pearson correlation tests.

RESULTS

The mean intakes of total FC (β = 1.24; 95% Confidence Interval: 1.02, 1.47) significantly predicted HEI-2015 scores. Positive correlations were found between FC intake and red and orange vegetables (r = 0.62), whole fruits (r = 0.63), and dark green vegetables (r = 0.58). Conclusions: Higher FC intake was associated with higher diet quality; vegetables and fruits are primary contributors to FC content. Efforts are required to promote these food items to improve diet quality and FC intake to shape eating choices in college students.

In Vitro Colonic Fermentation Profiles and Microbial Responses of Cellulose Derivatives with Different Colloidal States

Although cellulose derivatives are widely applied in the food industry, the effects of their structural properties on colonic health is unknown. Here, four types of cellulose derivatives, including microcrystalline cellulose (MCC), TEMPO-oxidized nanofibrillated cellulose (TOCNF), TEMPO-oxidized nanocrystalline cellulose (TOCNC), and carboxymethyl cellulose (CMC) were selected to investigate their in vitro fermentation profiles. TOCNF exhibited the highest production of total short-chain fatty acids (SCFAs), followed by TOCNC. The results suggested that reduced particle size and increased aspect ratio improved the fermentability of insoluble cellulose derivatives. MCC and CMC were barely fermented with similar total SCFAs production as the blank. 16S rRNA sequencing revealed that the fermentation of cellulose derivatives resulted in divergent microbial community structures. Moreover, Bacteroides cellulosilyticus showed high specificity to utilize TOCNF and TOCNC. The findings demonstrated that the colloidal states of cellulose derivatives, such as size and solubility, were important factors governing microbial community composition and metabolites.

Valuing the Diversity of Research Methods to Advance Nutrition Science

The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.

Rethinking healthy eating in light of the gut microbiome

Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.

Dietary macronutrients and the gut microbiome: a precision nutrition approach to improve cardiometabolic health

Accumulating evidence indicates that the gut microbiome is an important regulator of body weight, glucose and lipid metabolism, and inflammatory processes, and may thereby play a key role in the aetiology of obesity, insulin resistance and type 2 diabetes. Interindividual responsiveness to specific dietary interventions may be partially determined by differences in baseline gut microbiota composition and functionality between individuals with distinct metabolic phenotypes. However, the relationship between an individual's diet, gut microbiome and host metabolic phenotype is multidirectional and complex, yielding a challenge for practical implementation of targeted dietary guidelines. In this review, we discuss the latest research describing interactions between dietary composition, the gut microbiome and host metabolism. Furthermore, we describe how this knowledge can be integrated to develop precision-based nutritional strategies to improve bodyweight control and metabolic health in humans. Specifically, we will address that (1) insight in the role of the baseline gut microbial and metabolic phenotype in dietary intervention response may provide leads for precision-based nutritional strategies; that (2) the balance between carbohydrate and protein fermentation by the gut microbiota, as well as the site of fermentation in the colon, seems important determinants of host metabolism; and that (3) 'big data', including multiple omics and advanced modelling, are of undeniable importance in predicting (non-)response to dietary interventions. Clearly, detailed metabolic and microbial phenotyping in humans is necessary to better understand the link between diet, the gut microbiome and host metabolism, which is required to develop targeted dietary strategies and guidelines for different subgroups of the population.

Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice

Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea, and emerging evidence has linked dietary components with CDI pathogenesis, suggesting that dietary modulation may be an effective strategy for prevention. Here, we show that mice fed a high-fat/low-fiber “Western-type” diet (WD) had dramatically increased mortality in a murine model of antibiotic-induced CDI compared to a low-fat/low-fiber (LF/LF) diet and standard mouse chow controls. We found that the WD had a pro- C. difficile bile acid composition that was driven in part by higher levels of primary bile acids that are produced to digest fat, and a lower level of secondary bile acids that are produced by the gut microbiome. This lack of secondary bile acids was associated with a greater disturbance to the gut microbiome with antibiotics in both the WD and LF/LF diet compared to mouse chow. Mice fed the WD also had the highest level of toxin TcdA just prior to the onset of mortality, but not of TcdB or increased inflammation. These findings indicate that dietary intervention to decrease fat may complement previously proposed dietary intervention strategies to prevent CDI in high-risk individuals.

Best Practices for Probiotic Research in Athletic and Physically Active Populations: Guidance for Future Randomized Controlled Trials

Probiotic supplementation, traditionally used for the prevention or treatment of a variety of disease indications, is now recognized in a variety of population groups including athletes and those physically active for improving general health and performance. However, experimental and clinical trials with probiotics commonly suffer from design flaws and different outcome measures, making comparison and synthesis of conclusions difficult. Here we review current randomized controlled trials (RCTs) using probiotics for performance improvement, prevention of common illnesses, or general health, in a specific target population (athletes and those physically active). Future RCTs should address the key elements of (1) properly defining and characterizing a probiotic intervention, (2) study design factors, (3) study population characteristics, and (4) outcome measures, that will allow valid conclusions to be drawn. Careful evaluation and implementation of these elements should yield improved trials, which will better facilitate the generation of evidence-based probiotic supplementation recommendations for athletes and physically active individuals.

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response

Gut bacteria modulate the response to immune checkpoint blockade (ICB) treatment in cancer, but the effect of diet and supplements on this interaction is not well studied. We assessed fecal microbiota profiles, dietary habits, and commercially available probiotic supplement use in melanoma patients and performed parallel preclinical studies. Higher dietary fiber was associated with significantly improved progression-free survival in 128 patients on ICB, with the most pronounced benefit observed in patients with sufficient dietary fiber intake and no probiotic use. Findings were recapitulated in preclinical models, which demonstrated impaired treatment response to anti–programmed cell death 1 (anti–PD-1)–based therapy in mice receiving a low-fiber diet or probiotics, with a lower frequency of interferon-γ–positive cytotoxic T cells in the tumor microenvironment. Together, these data have clinical implications for patients receiving ICB for cancer.

Changes in Quantity and Sources of Dietary Fiber from Adopting Healthy Low-Fat vs. Healthy Low-Carb Weight Loss Diets: Secondary Analysis of DIETFITS Weight Loss Diet Study

The daily intake of dietary fiber is well below the recommended levels in the US. The effect of adopting a low-fat vs. a low-carbohydrate weight loss diet on fiber intake is of interest but not well-documented, especially when both approaches promote high-quality food choices. The objective of this paper is to compare the quantity and sources of dietary fiber between a healthy low-fat (HLF) vs. healthy low-carbohydrate (HLC) diet group when consumed over 12 months in a weight loss diet study. In this secondary analysis of the Diet Intervention Examining The Factors Interacting with Treatment Success (DIETFITS) study, the amount and sources of dietary fiber were examined in generally healthy adults, 18-50 years of age, Body Mass Index (BMI) 28-40 kg/m², randomized to HLF or HLC for 12 months, who had available 24-h recalls at 0 (n = 609), 3 (n = 549), 6 (n = 491), and 12 (n = 449) months. The dietary intake was estimated by the Nutrition Data System for Research (NDS-R). The sources of fiber were determined for the major food groups. Significantly more total dietary fiber was consumed by HLF at every post-randomization time point, and, at 12 m, was 23.04 ± 9.43 g vs. 18.61 ± 8.12 g for HLF vs. HLC, respectively, p < 0.0001. In both diet groups at 12 months, the highest amount of dietary fiber came from non-starchy vegetables (4.13 ± 3.05 g and 5.13 ± 3.59 g). The other primary sources of fiber at 12 months for the HLF group were from whole grains (3.90 ± 3.13 g) and fruits (3.40 ± 2.87 g), and, for the HLC group, were from plant protein and fat sources, such as nuts and seeds, their butters, and avocados (2.64 ± 2.64 g). In the DIETFITS study, the difference in the total fiber intake for the HLF vs. HLC groups was more modest than expected. The HLC group consumed reasonably high amounts of fiber from high-protein and high fat plant-based sources.

Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study

BACKGROUND

One mechanism that can explain the link between processed meat consumption and colorectal cancer (CRC) is the production of carcinogenic N-nitroso compounds (NOCs) in the gastrointestinal tract. Oral and gut microbes metabolize ingested proteins (a source of secondary and tertiary amines and amides) and can reduce nitrate to nitrite, generating potentially carcinogenic NOCs.

OBJECTIVE

We evaluated whether nitrate/nitrite in processed meat or water influences the fecal or salivary microbiota.

DESIGN

In this dietary intervention study, 63 volunteers consumed diets high in conventional processed meats for two weeks, switched to diets high in poultry for two weeks, and then consumed phytochemical-enriched conventional processed or low-nitrite processed meat diets for two weeks. During the intervention, they drank water with low nitrate concentrations and consumed a healthy diet with low antioxidants. Then the volunteers drank nitrate-enriched water for 1 week, in combination with one of the four different diets. We measured creatinine-adjusted urinary nitrate levels and characterized the oral and fecal microbiota using 16S rRNA amplicon sequencing.

RESULTS

Using linear mixed models, we found that, compared to baseline, urinary nitrate levels were reduced during the phytochemical-enriched low-nitrite meat diet (p-value = 0.009) and modestly during the poultry diet (p-value = 0.048). In contrast, urinary nitrate increased after 1-week of drinking nitrate-enriched water (p-value<10^-5). Nitrate-enriched water, but not processed meats with or without phytochemicals, altered the saliva microbial population (p-value ≤0.001), and significantly increased abundance of 8 bacterial taxa, especially genus Neisseria and other nitrate-reducing taxa. Meats, phytochemicals and nitrate-enriched water had no significant effects on saliva alpha diversity or any diversity parameter measured for the fecal microbiota.

CONCLUSION

These findings support the hypothesis that drinking high nitrate water increases oral nitrate-reducing bacteria, which likely results in increased NOC. However, meat nitrate/nitrite at the levels tested had no effect on either the gut or oral bacteria. CLINICALTRIALS.

GOV IDENTIFIER

NCT04138654.

Dietary fat and low fiber in purified diets differently impact the gut-liver axis to promote obesity-linked metabolic impairments

Selecting the most relevant control diet is of critical importance for metabolic and intestinal studies in animal models. Chow and LF-purified diet differentially impact metabolic and gut microbiome outcomes resulting in major changes in intestinal integrity in LF-fed animals which contributes to altering metabolic homeostasis. Dietary fat and low fiber both contribute to the deleterious metabolic effect of purified HF diets through both selective and overlapping mechanisms.

An Overview of Current Knowledge of the Gut Microbiota and Low-Calorie Sweeteners

This review provides an overview of the interrelationships among the diet, gut microbiota and health status, and then focuses specifically on published research assessing the relationship of low/no-calorie sweeteners (LNCS) to selected aspects of the gut microbiota. Microbiome research is expanding as new data on its role in health and disease vulnerability emerge. The gut microbiome affects health, digestion, and susceptibility to disease. In the last 10 years, investigations of LNCS effects on the gut microbiota have proliferated, though results are conflicting and are often confounded by differences in study design such as study diet, the form of the test article, dosage, and study population. Staying current on microbiome research and the role of dietary inputs, like LNCS, will allow healthcare and nutrition practitioners to provide evidenced-based guidance to the individuals they serve.

Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure

The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.

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

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

Resistant Starch Type 2 from Wheat Reduces Postprandial Glycemic Response with Concurrent Alterations in Gut Microbiota Composition

The majority of research on the physiological effects of dietary resistant starch type 2 (RS2) has focused on sources derived from high-amylose maize. In this study, we conduct a double-blind, randomized, placebo-controlled, crossover trial investigating the effects of RS2 from wheat on glycemic response, an important indicator of metabolic health, and the gut microbiota. Overall, consumption of RS2-enriched wheat rolls for one week resulted in reduced postprandial glucose and insulin responses relative to conventional wheat when participants were provided with a standard breakfast meal containing the respective treatment rolls (RS2-enriched or conventional wheat). This was accompanied by an increase in the proportions of bacterial taxa Ruminococcus and Gemmiger in the fecal contents, reflecting the composition in the distal intestine. Additionally, fasting breath hydrogen and methane were increased during RS2-enriched wheat consumption. However, although changes in fecal short-chain fatty acid (SCFA) concentrations were not significant between control and RS-enriched wheat roll consumption, butyrate and total SCFAs were positively correlated with relative abundance of Faecalibacterium, Ruminoccocus, Roseburia, and Barnesiellaceae. These effects show that RS2-enriched wheat consumption results in a reduction in postprandial glycemia, altered gut microbial composition, and increased fermentation activity relative to wild-type wheat.

Nutritional profile of rodent diets impacts experimental reproducibility in microbiome preclinical research

The lack of reproducibility of animal experimental results between laboratories, particularly in studies investigating the microbiota, has raised concern among the scientific community. Factors such as environment, stress and sex have been identified as contributors, whereas dietary composition has received less attention. This study firstly evaluated the use of commercially available rodent diets across research institutions, with 28 different diets reported by 45 survey respondents. Secondly, highly variable ingredient, FODMAP (Fermentable Oligo-, Di-, Mono-saccharides And Polyols) and gluten content was found between different commercially available rodent diets. Finally, 40 mice were randomized to four groups, each receiving a different commercially available rodent diet, and the dietary impact on cecal microbiota, short- and branched-chain fatty acid profiles was evaluated. The gut microbiota composition differed significantly between diets and sexes, with significantly different clusters in β-diversity. Total BCFA were highest (p = 0.01) and SCFA were lowest (p = 0.03) in mice fed a diet lower in FODMAPs and gluten. These results suggest that nutritional composition of commercially available rodent diets impact gut microbiota profiles and fermentation patterns, with major implications for the reproducibility of results across laboratories. However, further studies are required to elucidate the specific dietary factors driving these changes.

How Food Affects Colonization Resistance Against Enteropathogenic Bacteria

Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.

The Influence of Feed and Drinking Water on Terrestrial Animal Research and Study Replicability

For more than 50 years, the research community has made strides to better determine the nutrient requirements for many common laboratory animal species. This work has resulted in high-quality animal feeds that can optimize growth, maintenance, and reproduction in most species. We have a much better understanding of the role that individual nutrients play in physiological responses. Today, diet is often considered as an independent variable in experimental design, and specialized diet formulations for experimental purposes are widely used. In contrast, drinking water provided to laboratory animals has rarely been a consideration in experimental design except in studies of specific water-borne microbial or chemical contaminants. As we advance in the precision of scientific measurements, we are constantly discovering previously unrecognized sources of experimental variability. This is the nature of science. However, science is suffering from a lack of experimental reproducibility or replicability that undermines public trust. The issue of reproducibility/replicability is especially sensitive when laboratory animals are involved since we have the ethical responsibility to assure that laboratory animals are used wisely. One way to reduce problems with reproducibility/replicability is to have a strong understanding of potential sources of inherent variability in the system under study and to provide "…a clear, specific, and complete description of how the reported results were reached [1]." A primary intent of this review is to provide the reader with a high-level overview of some basic elements of laboratory animal nutrition, methods used in the manufacturing of feeds, sources of drinking water, and general methods of water purification. The goal is to provide background on contemporary issues regarding how diet and drinking water might serve as a source of extrinsic variability that can impact animal health, study design, and experimental outcomes and provide suggestions on how to mitigate these effects.

Effects of oats on gastrointestinal health as assessed by in vitro, animal, and human studies

Oats are uniquely nutritious, owing to their composition of bioactive compounds, lipids, and β-glucan. Scientific research has established that oats can improve diet quality, reduce cholesterol, regulate satiety, and protect against carcinogenesis in the colon; however, determining the effects of oats on gastrointestinal health and the gut microbiome is a newer, evolving area of research. To better understand the effects of oats on gastrointestinal health in humans, a literature review with predefined search criteria was conducted using the PubMed database and keywords for common gastrointestinal health outcomes. Moreover, to examine the gastrointestinal effects of oats across the scientific spectrum, a similar search strategy was executed to identify animal studies. In vitro studies were identified from the reference lists of human and animal studies. A total of 8 human studies, 19 animal studies, and 5 in vitro studies met the inclusion criteria for this review. The evidence in humans shows beneficial effects of oats on gastrointestinal health, with supportive evidence provided by in vitro and animal studies. The effective dose of oats varies by type, although an amount providing 2.5 to 2.9 g of β-glucan per day was shown to decrease fecal pH and alter fecal bacteria. For oat bran, 40 to 100 g/d was shown to increase fecal bacterial mass and short-chain fatty acids in humans. Differences in study design, methodology, and type of oats tested make valid comparisons difficult. The identification of best practices for the design of oat studies should be a priority in future research, as the findings will be useful for determining how oats influence specific indices of gastrointestinal health, including the composition of the human gut microbiome.

Adolescent dietary manipulations differentially affect gut microbiota composition and amygdala neuroimmune gene expression in male mice in adulthood

Adolescence is a critical developmental period that is characterised by growth spurts and specific neurobiological, neuroimmune and behavioural changes. In tandem the gut microbiota, which is a key player in the regulation of health and disease, is shaped during this time period. Diet is one of the most important regulators of microbiota composition. Thus, we hypothesised that dietary disturbances of the microbiota during this critical time window result in long-lasting changes in immunity, brain and behaviour. C57BL/6 male mice were exposed to either high fat diet or cafeteria diet during the adolescent period from postnatal day 28 to 49 and were tested for anxiety-related and social behaviour in adulthood. Our results show long-lasting effects of dietary interventions during the adolescent period on microbiota composition and the expression of genes related to neuroinflammation or neurotransmission. Interestingly, changes in myelination-related gene expression in the prefrontal cortex following high fat diet exposure were also observed. However, these effects did not translate into overt behavioural changes in adulthood. Taken together, these data highlight the importance of diet-microbiota interactions during the adolescent period in shaping specific outputs of the microbiota-gut-brain axis in later life.

Diet and the gut microbiome: from hype to hypothesis

Microbiome research in the last two decades has delivered as a key finding that the human intestine hosts a unique and complex ecosystem with many variables affecting the composition of the microbiota and in turn its function in metabolism and immune defence. Hundreds of external (environmental) factors have meanwhile been identified as significantly associated with bacterial biomass and diversity and, amongst these, diet is considered as a key determinant of microbial populations. However, dietary intervention studies, including those with fermentable substrates that have bulk effects on bowel functions, have revealed only very minor effects on overall microbiome composition and usually show only a very few species changing in population size. What that means in the context of hundreds of different species coexisting in competition or mutualism in the human colon is far from understood. This review addresses some of the current limits in research on diet effects by taking anatomical and physiological features of the intestine into consideration. It also provides some recommendations on future human studies needed to assess how the diet influences the microbiome and associated effects on metabolic health.

Effect of whole-grain consumption on changes in fecal microbiota: a review of human intervention trials

Whole-grain (WG) consumption is known to have beneficial effects on human health. However, the influence of WGs on the microbiota is not well understood. To evaluate how WG intake modulates the gut microbiota composition, a literature review of human intervention studies was conducted. Whole grain, whether a mixed WG food or diet (n = 5) or specific WG intervention (WG wheat [n = 5], barley [n = 2], rye [n = 2] or rice, corn, or oats [n = 1 for each]), generally modified microbiota composition but did so inconsistently across measurements of microbial diversity and taxa. Interventions used both parallel and crossover designs and varied from single product substitutions to fully controlled diets with WG exposures of 3-12 weeks. The effect of amount of WG was difficult to capture due to variable reporting of WG. Methods used to measure microbiota varied in ability to resolve changes at different taxonomic levels, and comparisons of interventions using similar methods was lacking. Because many dietary components besides WGs alter gut microbiota, further research is needed, particularly in linking microbiota changes to health outcomes, and study design recommendations for future research on WGs and microbiota are warranted.

Conserved and variable responses of the gut microbiome to resistant starch type 2

Resistant starch type 2 (RS2), a dietary fiber comprised solely of glucose, has been extensively studied in clinical trials and animal models for its capacity to improve metabolic and systemic health. Because the health modulatory effects of RS2 and other dietary fibers are thought to occur through modification of the gut microbiome, those studies frequently include assessments of RS2-mediated changes to intestinal microbial composition and function. In this review, we identify the conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies. Consistent outcomes of RS2 interventions include reductions in bacterial α-diversity; increased production of lumenal short-chain fatty acids; and enrichment of Ruminococcus bromii, Bifidobacterium adolescentis, and other gut taxa. Different taxa are usually responsive in animal models, and many RS2-mediated changes to the gut microbiome vary within and between studies. The root causes for this variation are examined with regard to methodological and analytical differences, host genetics and age, species differences (eg, human, animal), health status, intervention dose and duration, and baseline microbial composition. The significant variation found for this single dietary compound highlights the challenges in targeting the gut microbiome to improve health with dietary interventions. This knowledge on RS2 also provides opportunities to improve the design of nutrition studies targeting the gut microbiome and to ultimately identify the precise mechanisms via which dietary fiber benefits human health.

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics

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.

Improving natural product research translation: From source to clinical trial

While great interest in health effects of natural product (NP) including dietary supplements and foods persists, promising preclinical NP research is not consistently translating into actionable clinical trial (CT) outcomes. Generally considered the gold standard for assessing safety and efficacy, CTs, especially phase III CTs, are costly and require rigorous planning to optimize the value of the information obtained. More effective bridging from NP research to CT was the goal of a September, 2018 transdisciplinary workshop. Participants emphasized that replicability and likelihood of successful translation depend on rigor in experimental design, interpretation, and reporting across the continuum of NP research. Discussions spanned good practices for NP characterization and quality control; use and interpretation of models (computational through in vivo) with strong clinical predictive validity; controls for experimental artefacts, especially for in vitro interrogation of bioactivity and mechanisms of action; rigorous assessment and interpretation of prior research; transparency in all reporting; and prioritization of research questions. Natural product clinical trials prioritized based on rigorous, convergent supporting data and current public health needs are most likely to be informative and ultimately affect public health. Thoughtful, coordinated implementation of these practices should enhance the knowledge gained from future NP research.

Advances in Nutrition Science and Integrative Physiology: Insights From Controlled Feeding Studies

Nutrition science is a highly impactful but contentious area of biomedical science. Establishing cause and effect relationships between the nutrients and/or diets we consume and the avoidance of or risk of disease is extremely challenging. As such, evidence-based nutrition is best served by considering the totality of evidence across multiple study types including nutritional epidemiological studies, randomized controlled trials of behavioral interventions, and controlled feeding studies. The purpose of the present review is to provide an overview for those conducting research outside of clinical nutrition on how controlled feeding studies can be used to gain insight into integrative physiology/metabolism as well as to inform dietary guidelines. We discuss the rationale, basic elements, and complexities of conducting controlled feeding studies and provide examples of contributions of controlled feeding studies to advances in nutrition science and integrative physiology. Our goal is to provide a resource for those wishing to leverage the experimental advantage provided by controlled feeding studies in their own research programs.

Dietary Fiber and Gut Microbiota in Renal Diets

Nutrition is crucial for the management of patients affected by chronic kidney disease (CKD) to slow down disease progression and to correct symptoms. The mainstay of the nutritional approach to renal patients is protein restriction coupled with adequate energy supply to prevent malnutrition. However, other aspects of renal diets, including fiber content, can be beneficial. This paper summarizes the latest literature on the role of different types of dietary fiber in CKD, with special attention to gut microbiota and the potential protective role of renal diets. Fibers have been identified based on aqueous solubility, but other features, such as viscosity, fermentability, and bulking effect in the colon should be considered. A proper amount of fiber should be recommended not only in the general population but also in CKD patients, to achieve an adequate composition and metabolism of gut microbiota and to reduce the risks connected with obesity, diabetes, and dyslipidemia.

Impact of dietary ingredients on the interpretation of various fecal parameters in rats fed inulin

In the present study, the influences of diets (i.e. chow and AIN-93 diets) on the interpretation of various fecal parameters including viable microbiota, moisture, weight, and short-chain fatty acids in rats fed different amounts of inulin (0.5–2 g/kg). Eight groups of rats (n = 8/group) were fed, for 4 weeks, chow or AIN-93 diets with or without inulin supplementation. Fecal samples were analyzed for different fecal parameters. After a 2-week adaptation, apparent differences in some fecal parameters were observed between the chow and AIN-93 diet groups. Throughout the 4-week intervention period, significantly (p < 0.05) higher Lactobacillus spp. counts, fecal moisture (~2.7-fold), and fecal weight (~5.8-fold) were observed with chow diet over AIN-93 diet. More specifically, significant elevations in the levels of Bifidobacterium spp., Lactobacillus spp., fecal moisture, and fecal weight could be observed at low-dose (0.5 g/kg) of inulin in chow diet groups, while most of these changes could merely be seen at medium-dose (1 g/kg) in AIN-93 diet groups. These results demonstrated that the choice of experimental diets would affect the comparison of fecal parameters as well as the interpretation of effective dosage of prebiotic in intestinal health assessments.

Microbial regulation of organismal energy homeostasis

The gut microbiome has emerged as a key regulator of host metabolism. Here we review the various mechanisms through which the gut microbiome influences the energy metabolism of its host, highlighting the complex interactions between gut microbes, their metabolites and host cells. Among the most important bacterial metabolites are short-chain fatty acids, which serve as a direct energy source for host cells, stimulate the production of gut hormones and act in the brain to regulate food intake. Other microbial metabolites affect systemic energy expenditure by influencing thermogenesis and adipose tissue browning. Both direct and indirect mechanisms of action are known for specific metabolites, such as bile acids, branched chain amino acids, indole propionic acid and endocannabinoids. We also discuss the roles of specific bacteria in the production of specific metabolites and explore how external factors, such as antibiotics and exercise, affect the microbiome and thereby energy homeostasis. Collectively, we present a large body of evidence supporting the concept that gut microbiota-based therapies can be used to modulate host metabolism, and we expect to see such approaches moving from bench to bedside in the near future.

Whole Fruits and Fruit Fiber Emerging Health Effects

Less than 10% of most Western populations consume adequate levels of whole fruits and dietary fiber with typical intake being about half of the recommended levels. Evidence of the beneficial health effects of consuming adequate levels of whole fruits has been steadily growing, especially regarding their bioactive fiber prebiotic effects and role in improved weight control, wellness and healthy aging. The primary aim of this narrative review article is to examine the increasing number of health benefits which are associated with the adequate intake of whole fruits, especially fruit fiber, throughout the human lifecycle. These potential health benefits include: protecting colonic gastrointestinal health (e.g., constipation, irritable bowel syndrome, inflammatory bowel diseases, and diverticular disease); promoting long-term weight management; reducing risk of cardiovascular disease, type 2 diabetes and metabolic syndrome; defending against colorectal and lung cancers; improving odds of successful aging; reducing the severity of asthma and chronic obstructive pulmonary disease; enhancing psychological well-being and lowering the risk of depression; contributing to higher bone mineral density in children and adults; reducing risk of seborrheic dermatitis; and helping to attenuate autism spectrum disorder severity. Low whole fruit intake represents a potentially more serious global population health threat than previously recognized, especially in light of the emerging research on whole fruit and fruit fiber health benefits.