The important role of the gut microbiome in maintaining human health has necessitated a better understanding of the temporal dynamics of intestinal microbial communities as well as the host and environmental factors driving these dynamics. Genetics, mode of birth, infant feeding patterns, antibiotic usage, sanitary living conditions and long term dietary habits contribute to shaping the composition of the gut microbiome. This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly. The infant gut microbiota is characterized by a high degree of instability, only reaching a state similar to that of adults by 2–3 years of age; consistent with the establishment of a varied solid food diet. The diet-related factors influencing the development of the infant gut microbiome include whether the child is breast or formula-fed as well as how and when solid foods are introduced. In contrast to the infant gut, the adult gut microbiome is resilient to large shifts in community structure. Several studies have shown that dietary changes induce transient fluctuations in the adult microbiome, sometimes in as little as 24 h; however, the microbial community rapidly returns to its stable state. Current knowledge of how long-term dietary habits shape the gut microbiome is limited by the lack of long-term feeding studies coupled with temporal gut microbiota characterization. However, long-term weight loss studies have been shown to alter the ratio of the Bacteroidetes and Firmicutes, the two major bacterial phyla residing in the human gastrointestinal tract. With aging, diet-related factors such as malnutrition are associated with microbiome shifts, although the cause and effect relationship between these factors has not been established. Increased pharmaceutical usage is also more prevalent in the elderly and can contribute to reduced gut microbiota stability and diversity. Foods containing prebiotic oligosaccharide components that nurture beneficial commensals in the gut community and probiotic supplements are being explored as interventions to manipulate the gut microbiome, potentially improving health status.

Background Oral microbial therapy has been studied as an intervention for a range of gastrointestinal disorders. Though research suggests that microbial exposure may affect the gastrointestinal system, motility, and host immunity in a pediatric population, data have been inconsistent, with most prior studies being in neither a randomized nor placebo-controlled setting. The aim of this randomized, placebo-controlled study was to evaluate the efficacy of a synbiotic on increasing weekly bowel movements (WBMs) in constipated children. Methods Sixty-four children (3–17 years of age) were randomized to receive a synbiotic (n = 33) comprising mixed-chain length oligosaccharides and nine microbial strains, or placebo (n = 31) for 84 days. Stool microbiota was analyzed on samples collected at baseline and completion. The primary outcome was a change from baseline of WBMs in the treatment group compared to placebo. Results Treatment increased (p < 0.05) the number of WBMs in children with low baseline WBMs, despite broadly distinctive baseline microbiome signatures. Sequencing revealed that low baseline microbial richness in the treatment group significantly anticipated improvements in constipation (p = 0.00074). Conclusions These findings suggest the potential for (i) multi-species-synbiotic interventions to improve digestive health in a pediatric population and (ii) bioinformatics-based methods to predict response to microbial interventions in children. Impact Synbiotic microbial treatment improved the number of spontaneous weekly bowel movements in children compared to placebo. Intervention induced an increased abundance of bifidobacteria in children, compared to placebo. All administered probiotic species were enriched in the gut microbiome of the intervention group compared to placebo. Baseline microbial richness demonstrated potential as a predictive biomarker for response to intervention.

Objectives While increasing fruit and vegetable (FV) intake is a near-universal recommendation for improved health outcomes, information on dietary FV amount and diversity impact on health biomarkers is scarce. FV are a major dietary source of gut microbiota (GM) accessible carbohydrates and phytochemicals, however, most studies have focused on single food items or their extracted components, with few holistic studies available. Here, two separate randomized dietary interventions were used to assess the impact of low vs high FV intake and low vs high botanical diversity on GM profiles in healthy adults. We hypothesized that increasing FV would result in beneficial modulations to GM with further increases benefits in those consuming FV from diverse botanical families. Methods Study 1 was a crossover design with, 11 males randomized to starting diets of low FV (L) or high FV (H) over 9 days. Stool samples were obtained at day 0, 3, 6 and 9 of each treatment period. In Study 2, 21 individuals were provided a low FV (L) lead-in diet for 4 days and then randomly assigned to a high FV diet with either low (LB; 11 families) or high botanical diversity (HB; 24 families) for an additional 4 days. Stool was collected at baseline, and after each diet intervention. GM was analyzed using 16S rRNA sequencing performed on an Illumina MiSeq. The Mothur pipeline was used for preliminary data analysis, followed by statistical analyses in PAST. Results In Study 1, the L treatment resulted in minimal microbiota alterations, while a significant increase in Bacteroidetes and decrease in Firmicutes (which peaked at day 6) was observed in the H group. Intriguingly, the L group experienced a short-term increase in Bifidobacterium and Lactobacillus, and both treatments incurred significant increases in Bacteroides and Akkermansia and a decline of Faecalibacterium. In study 2 the transition from low to high FV resulted in similar trends than in Study 1. However, the HB treatment resulted in a more diverse GM, characterized by increased relative abundances of beneficial Firmicutes (Lachnospiraceae, Faecalibacterium and Clostridium XIVa). Conclusions Our results suggest that both amounts of FV consumed and botanical diversity modulate the GM. Determining better FV combinations from a GM perspective thus appears as a possible task for future research. Funding Sources Colorado Agriculture Experiment Station.

Background: Oral microbial therapy has been studied as an intervention for a range of gastrointestinal and immunological disorders. Though emerging research suggests microbial exposure may intimately affect the gastrointestinal system, motility, and host immunity in a pediatric population, data has been inconsistent and variable, with the majority of prior studies conducted in neither a randomized nor placebo-controlled setting. The aim of this placebo-controlled study was to evaluate efficacy of a synbiotic (a prebiotic and rationally-defined microbial consortia) on increasing weekly bowel movement frequency in constipated children. Methods: Sixty-four children (3-17 years of age) were randomized to receive a synbiotic composition (n=33) comprised of mixed-chain length, prebiotic oligosaccharides and nine microbial strains or placebo (n=31) for 84 days. Stool microbiota was analyzed using shotgun metagenomic sequencing on samples collected at baseline (T1) and completion (T2). The primary outcome was change from baseline of Weekly Bowel Movements (WBMs) in children compared to placebo. Results: Treatment with a multi-strain synbiotic significantly (p < 0.05) increased the number of WBMs in children with low bowel movement frequency (< 4 WBMs and < 5 WBMs), irrespective of broadly distinctive microbiome signatures at baseline. Metagenomic shotgun sequencing revealed that low baseline microbial richness in the treatment group significantly anticipated improvements in constipation (p = 0.00074). Conclusions: These findings suggest the potential for (i) multi-species synbiotic interventions to improve digestive health in a pediatric population and (ii) bioinformatics-based methods to predict response to microbial interventions in children. Impact: Synbiotic microbial treatment exerted functional improvements in the number of spontaneous Weekly Bowel Movements in children compared to placebo. Intervention induced a significant bifidogenic effect in children compared to placebo. All administered probiotic species were enriched in the gut microbiome of the intervention group compared to placebo. Baseline microbial richness demonstrated potential as a predictive biomarker for response to intervention.

Modern diets typically contain dramatically lower fiber content compared to traditional hunter-gatherer and agrarian diets, and this trend is paralleled by an enhanced frequency of chronic diseases. Despite national nutrition policy and education instructing Americans on the beneficial health value of increasing daily fiber consumption, a 'fiber gap' still persistently exists. Fortification of product groups frequently consumed by a large proportion of society provides an attractive strategy to close this 'fiber gap' and may have the potential to concomitantly reverse the detrimental health effects exacerbated by our modern diets. Besides prebiotic fibers, products can contain several other functional components, such as botanicals. However, the vast majority of studies have investigated functional components in isolation. For instance, preferential fermentation of specific prebiotic fibers by bifidobacteria has been clearly established, both in terms of their increased abundance in the gut microbiome and the elevated levels of beneficial metabolites, including short chain fatty acids (SCFAs) produced directly (acetate) or through interactions with other microbiota members (resulting in butyrate and propionate production). The impact of other components present in functional product blends on this bifidogenic effect are largely unexplored. Here, we investigated the fiber and botanical blends included in OLIPOP, a functional soda, in an in vitro gut fermentation model. Our data revealed that the blend of inulins and resistant dextrins promoted growth of bifidobacteria across gut microbiota from four donors, even those with small initial populations. In addition, botanicals interacted with fiber fermentation in donor-specific ways, in some cases strongly enhancing fermentation rate and production of SCFAs. Our data suggest that botanicals can modify the rate and microbial and metabolic fates of prebiotic fiber fermentation, and suggest that future studies should examine such interactions in greater detail.