Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022].

The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.

Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity.

PURPOSE: We aimed to assess whether total daily physical activity (PA), PA intensities, sedentary time (ST), and prolonged ST are associated with differences in the gut microbiota composition or short-chain fatty acid (SCFA) profile of adults with overweight or obesity. METHODS: Cross-sectional associations between total daily PA (counts per minute), PA intensities (light and moderate-to-vigorous (MVPA)), ST, prolonged ST, and fecal microbiota composition were assessed in adults ( n = 124) between 25 and 45 yr of age with body mass index ≥25 kg·m -2 . Fecal microbiota composition was assessed with 16S rRNA gene sequencing. Daily PA and ST were measured with a hip-worn ActiGraph wGT3X-BT accelerometer. RESULTS: Daily PA volume and intensity were positively associated with relative abundance of Faecalibacterium ( P = 0.04) and negatively associated with the abundances of Alistipes , Parabacteroides , and Gemmiger ( P = 0.003-0.04) as well as the concentrations of acetate, butyrate, and total SCFA (all P = 0.04). Conversely, ST was negatively associated with abundance of Faecalibacterium but positively associated with the abundances of taxa, including Ruminococcaceae, Parabacteroides , Alistipes , and Gemmiger . Clustering of participants based on whether they met PA recommendations suggested that SCFA profiles differed between individuals who did and did not meet PA recommendations. K-means clustering based on percent of time spent in MVPA and ST also identified differences in fecal microbiota composition between cluster 1 (lower MVPA, higher ST) and cluster 2 (higher MVPA, lower ST), including a higher abundance of Alistipes in cluster 1. CONCLUSIONS: The current analysis suggests a beneficial association of daily PA on the fecal microbiota and a negative association of ST, particularly with respect to the associations of these variables with the genera Faecalibacterium , a butyrate-producing taxon.

The Prebiotic Potential of Inulin-Type Fructans: A Systematic Review.

Inulin-type fructans (ITF), including short-chain fructooligosaccharides (scFOS), oligofructose, and inulin, are commonly used fibers that are widely regarded as prebiotic for their ability to be selectively utilized by the intestinal microbiota to confer a health benefit. However, to our knowledge the literature thus far lacks a thorough discussion of the evidence from human clinical trials for the prebiotic effect of ITF, including beneficial effects on intestinal microbiota composition and intestinal and extraintestinal processes (e.g., glucose homeostasis, lipids, mineral absorption and bone health, appetite and satiety, inflammation and immune function, and body composition). Additionally, there has been a lack of discussion regarding aspects such as the effect of ITF chain length on its intestinal and extraintestinal effects. The overall objective of this systematic review was to summarize the prebiotic potential of ITF based on the results of human clinical trials in healthy adult populations. Evidence from studies included in the current review suggest that ITF have a prebiotic effect on the intestinal microbiota, promoting the abundances of Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii. Beneficial health effects reported following ITF intake include improved intestinal barrier function, improved laxation, increased insulin sensitivity, decreased triglycerides and an improved lipid profile, increased absorption of calcium and magnesium, and increased satiety. Although there is some evidence for differing effects of ITF based on chain length, the lack of direct comparisons and detailed descriptions of physicochemical properties limits the ability to draw conclusions from human clinical studies. Future research should focus on elucidating the mechanisms by which the intestinal microbiota mediates or modifies the effects of ITF on human health and the contribution of individual factors such as age and metabolic health to the movement toward personalization of prebiotic applications.

Resistant starch wheat increases PYY and decreases GIP but has no effect on self-reported perceptions of satiety.

Dietary fiber has numerous health benefits, such as increasing satiety, and is regularly included in healthy dietary recommendations. However, different types and sources of fiber vary in their chemical properties and biological effects. This double-blind, randomized, placebo-controlled, crossover study investigated the effects of resistant starch type 2 (RS2) from wheat on self-reported perceptions of satiety and associated gut hormones in 30 healthy adults ages 40-65 years of age. Participants consumed rolls made using either RS2-enriched wheat flour or a wild-type flour for one week before a test day during which they ate a mixed meal containing the same roll type. Both self-reported perceptions of satiety and plasma concentrations of gut hormones were measured following the meal to assess whether the RS2-enriched wheat enhanced satiety and suppressed hunger for a longer period than the control wheat. Exploratory analysis indicated that fasting and peak concentration of peptide YY3-36 (PYY3-36; qfast = 0.02, qpeak = 0.02) increased, while peak concentration and iAUC of glucose-dependent insulinotropic peptide (GIP; qpeak < 0.001, qiAUC < 0.001) decreased after ingesting RS2-enriched wheat. However, self-reported perceptions of hunger or fullness using visual analog scales (VAS) did not differ following the test meal.

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.

Fueling Gut Microbes: A Review of the Interaction between Diet, Exercise, and the Gut Microbiota in Athletes.

The athlete's goal is to optimize their performance. Towards this end, nutrition has been used to improve the health of athletes' brains, bones, muscles, and cardiovascular system. However, recent research suggests that the gut and its resident microbiota may also play a role in athlete health and performance. Therefore, athletes should consider dietary strategies in the context of their potential effects on the gut microbiota, including the impact of sports-centric dietary strategies (e.g., protein supplements, carbohydrate loading) on the gut microbiota as well as the effects of gut-centric dietary strategies (e.g., probiotics, prebiotics) on performance. This review provides an overview of the interaction between diet, exercise, and the gut microbiota, focusing on dietary strategies that may impact both the gut microbiota and athletic performance. Current evidence suggests that the gut microbiota could, in theory, contribute to the effects of dietary intake on athletic performance by influencing microbial metabolite production, gastrointestinal physiology, and immune modulation. Common dietary strategies such as high protein and simple carbohydrate intake, low fiber intake, and food avoidance may adversely impact the gut microbiota and, in turn, performance. Conversely, intake of adequate dietary fiber, a variety of protein sources, and emphasis on unsaturated fats, especially omega-3 (É·-3) fatty acids, in addition to consumption of prebiotics, probiotics, and synbiotics, have shown promising results in optimizing athlete health and performance. Ultimately, while this is an emerging and promising area of research, more studies are needed that incorporate, control, and manipulate all 3 of these elements (i.e., diet, exercise, and gut microbiome) to provide recommendations for athletes on how to "fuel their microbes."

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.

Higher protein intake during resistance training does not potentiate strength, but modulates gut microbiota, in middle-aged adults: a randomized control trial.

Protein intake above the recommended dietary allowance (RDA) and resistance training are known anabolic stimuli to support healthy aging. Specifically, protein supplementation after resistance exercise and nightly are strategies to maximize utilization of protein intake above the RDA in healthy adults. As such, the primary objective was to examine the efficacy of protein supplementation and nutritional counseling resulting in either moderate (MOD: ∼1.0 g·kg-1·day-1) or higher (HIGH: ∼1.6 g·kg-1·day-1) protein intake during resistance training on strength (one-repetition maximum, 1-RM; isokinetic and isometric peak torque) in healthy middle-aged adults. Exploratory analyses include diet-exercise effects on lean body mass (LBM), clinical biomarkers, gut microbiota, and diet composition. In all, 50 middle-aged adults (age: 50 ± 8 yr, BMI: 27.2 ± 4.1 kg/m2) were randomized to either MOD or HIGH protein intake during a 10-wk resistance training program (3 × wk). Participants received dietary counseling and consumed either 15 g (MOD) or 30 g (HIGH) of protein from lean beef in the immediate postexercise period and each evening. Maximal strength (1-RM) for all upper and lower body exercises significantly increased with no effect of protein intake (P < 0.050). There was a main effect of time for LBM (P < 0.005). Cardiovascular, renal, or glycemic biomarkers were not affected by the intervention. Gut microbiota were associated with several health outcomes (P < 0.050). In conclusion, higher protein intake above moderate amounts does not potentiate resistance training adaptations in previously untrained middle-aged adults. This trial was registered at clinicaltrials.gov as NCT03029975.NEW & NOTEWORTHY Our research evaluates the efficacy of higher in comparison with moderate animal-based protein intake on resistance exercise training-induced muscle strength, clinical biomarkers, and gut microbiota in middle-aged adults through a dietary counseling-controlled intervention. Higher protein intake did not potentiate training adaptations, nor did the intervention effect disease biomarkers. Both diet and exercise modified gut microbiota composition. Collectively, moderate amounts of high-quality, animal-based protein is sufficient to promote resistance exercise adaptations at the onset of aging.

Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi.

An unhealthy gut microbial community may act as a barrier to improvement in growth and health outcomes in response to nutritional interventions. The objective of this analysis was to determine whether the infant microbiota modified the effects of a randomized controlled trial of lipid-based nutrient supplements (LNS) in Malawi on growth and inflammation at 12 and 18 months, respectively. We characterized baseline microbiota composition of fecal samples at 6 months of age (n = 506, prior to infant supplementation, which extended to 18 months) using 16S rRNA gene sequencing of the V4 region. Features of the gut microbiota previously identified as being involved in fatty acid or micronutrient metabolism or in outcomes relating to growth and inflammation, especially in children, were investigated. Prior to correction for multiple hypothesis testing, the effects of LNS on growth appeared to be modified by Clostridium (p-for-interaction = 0.02), Ruminococcus (p-for-interaction = 0.007), and Firmicutes (p-for-interaction = 0.04) and effects on inflammation appeared to be modified by Faecalibacterium (p-for-interaction = 0.03) and Streptococcus (p-for-interaction = 0.004). However, after correction for multiple hypothesis testing these findings were not statistically significant, suggesting that the gut microbiota did not alter the effect of LNS on infant growth and inflammation in this cohort.

The HDL lipidome is widely remodeled by fast food versus Mediterranean diet in 4 days.

INTRODUCTION: HDL is associated with increased longevity and protection from multiple chronic diseases. The major HDL protein ApoA-I has a half-life of about 4 days, however, the effects of diet on the composition of HDL particles at this time scale have not been studied. OBJECTIVES: The objective of this study is to investigate the short term dietary effect on HDL lipidomic composition. METHODS: In this randomized order cross-over study, ten healthy subjects consumed a Mediterranean (Med) and a fast food (FF) diet for 4 days, with a 4-day wash-out between treatments. Lipidomic composition was analyzed in isolated HDL fractions by an untargeted LC-MS method with 15 internal standards. RESULTS: HDL phosphatidylethanolamine (PE) content was increased by FF diet, and 41 out of 170 lipid species were differentially affected by diet. Saturated fatty acids (FAs) and odd chain FA were enriched after FF diet, while very-long chain FA and unsaturated FA were enriched after Med diet. The composition of phosphatidylcholine (PC), triacylglycerol (TG) and cholesteryl ester (CE) were significantly altered to reflect the FA composition of the diet whereas the composition of sphingomyelin (SM) and ceramides were generally unaffected. CONCLUSION: Results from this study indicate that the HDL lipidome is widely remodeled within 4 days of diet change and that certain lipid classes are more sensitive markers of diet whereas other lipid classes are better indicators of non-dietary factors.

The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results.

The gut microbiota is increasingly implicated in the health and metabolism of its human host. The host's diet is a major component influencing the composition and function of the gut microbiota, and mounting evidence suggests that the composition and function of the gut microbiota influence the host's metabolic response to diet. This effect of the gut microbiota on personalized dietary response is a growing focus of precision nutrition research and may inform the effort to tailor dietary advice to the individual. Because the gut microbiota has been shown to be malleable to some extent, it may also allow for therapeutic alterations of the gut microbiota in order to alter response to certain dietary components. This article is the second in a 2-part review of the current research in the field of precision nutrition incorporating the gut microbiota into studies investigating interindividual variability in response to diet. Part I reviews the methods used by researchers to design and carry out such studies as well as analyze the results subsequently obtained. Part II reviews the findings of these studies and discusses the gaps in our current knowledge and directions for future research. The studies reviewed provide the current understanding in this field of research and a foundation from which we may build, utilizing and expanding upon the methods and results they present to inform future studies.

The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models-Part I: Overview of Current Methods.

Health care is increasingly focused on health at the individual level. In the rapidly evolving field of precision nutrition, researchers aim to identify how genetics, epigenetics, and the microbiome interact to shape an individual's response to diet. With this understanding, personalized responses can be predicted and dietary advice can be tailored to the individual. With the integration of these complex sources of data, an important aspect of precision nutrition research is the methodology used for studying interindividual variability in response to diet. This article stands as the first in a 2-part review of current research investigating the contribution of the gut microbiota to interindividual variability in response to diet. Part I reviews the methods used by researchers to design and carry out such studies as well as the statistical and bioinformatic methods used to analyze results. Part II reviews the findings of these studies, discusses gaps in our current knowledge, and summarizes directions for future research. Taken together, these reviews summarize the current state of knowledge and provide a foundation for future research on the role of the gut microbiome in precision nutrition.

A Review of the Role of the Gut Microbiome in Personalized Sports Nutrition.

The gut microbiome is a key factor in determining inter-individual variability in response to diet. Thus, far, research in this area has focused on metabolic health outcomes such as obesity and type 2 diabetes. However, understanding the role of the gut microbiome in determining response to diet may also lead to improved personalization of sports nutrition for athletic performance. The gut microbiome has been shown to modify the effect of both diet and exercise, making it relevant to the athlete's pursuit of optimal performance. This area of research can benefit from recent developments in the general field of personalized nutrition and has the potential to expand our knowledge of the nexus between the gut microbiome, lifestyle, and individual physiology.