Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber

Structure and degradation dynamics of dietary pectin

Pectin, a complex dietary fiber, constitutes a key structural component of the cell walls of numerous edible plant products. It is resistant to digestion by human enzymes and undergoes depolymerization and saccharification in the gastrointestinal tract through the action of carbohydrate-active enzymes (CAZymes) produced by gut microbiota. This enzymatic breakdown generates intermediate structural fragments, which are subsequently converted into pectin oligosaccharides (POS) and monosaccharides. POS exhibit prebiotic properties and have demonstrated potential health benefits, including anti-carcinogenic effects, mucoadhesive capabilities, and the promotion of beneficial gut bacterial growth. However, the current understanding of the molecular structure of pectin and its degradation dynamics remains fragmented within the literature, impeding progress in dietary fiber intervention research and the development of personalized nutrition approaches. This review aims to provide a comprehensive overview of the structural features of pectin and the intricate breakdown mechanisms orchestrated by CAZymes. It underscores the complex architecture of pectin that influences its breakdown dynamics and specifies the enzymatic requirements for the cleavage of its diverse structural components. These insights complement our accompanying review on the structure-function relationships between pectin and the human gut microbiota, previously published in this journal.

Review of the Relationships Between Human Gut Microbiome, Diet, and Obesity

Obesity is a complex disease that increases the risk of other pathologies. Its prevention and long-term weight loss maintenance are problematic. Gut microbiome is considered a potential obesity modulator. The objective of the present study was to summarize recent findings regarding the relationships between obesity, gut microbiota, and diet (vegetable/animal proteins, high-fat diets, restriction of carbohydrates), with an emphasis on dietary fiber and resistant starch. The composition of the human gut microbiome and the methods of its quantification are described. Products of the gut microbiome metabolism, such as short-chain fatty acids and secondary bile acids, and their effects on the gut microbiota, intestinal barrier function and immune homeostasis are discussed in the context of obesity. The importance of dietary fiber and resistant starch is emphasized as far as effects of the host diet on the composition and function of the gut microbiome are concerned. The complex relationships between human gut microbiome and obesity are finally summarized.

Exploring the gut microbiome and head and neck cancer interplay

The gut microbiome, a complex community of microorganisms residing in the gastrointestinal tract, plays a crucial role in maintaining human health and influencing disease outcomes. Recent advancements in sequencing technologies have revealed the intricate relationship between gut microbiota and various health conditions. This review explores the impact of gut microbiome dysbiosis on immune function, chronic inflammation, and cancer progression. Dysbiosis, characterized by an imbalance in microbial populations, can lead to immune dysfunction, creating a pro-inflammatory environment conducive to tumorigenesis. Gut microbiome metabolites, such as short-chain fatty acids and bile acids, also play a significant role in modulating these processes. The interplay between these factors contributes to the development and progression of HNC. Furthermore, this review highlights the potential of therapeutic interventions targeting the gut microbiome, including probiotics, prebiotics, and dietary modifications, to restore microbial balance and mitigate cancer risk. Understanding the mechanisms by which the gut microbiome influences HNC can provide valuable insights into novel preventive and therapeutic strategies. Future research should focus on elucidating the specific microbial taxa and metabolites involved in HNC, as well as the impact of lifestyle factors such as diet, alcohol consumption, and oral hygiene on the gut microbiome. By leveraging the growing knowledge of the gut microbiome, it may be possible to develop personalized approaches to cancer prevention and treatment, ultimately improving patient outcomes.

Bifidogenic Effect of Human Milk Oligosaccharides on Pediatric IBD Fecal Microbiota

The prevalence of pediatric inflammatory bowel disease (pIBD) has been increasing over the last two decades. Yet, treatment strategies are still limited, in part due to the multifactorial nature of the disease and the complex interplay between genetic, environmental, dietary, immune, and gut microbial factors in its etiology. With their direct and indirect anti-inflammatory properties, human milk oligosaccharides (HMOs) are a promising treatment and management strategy for IBD. However, to date there are no insights into how HMOs may affect pIBD microbiota. Here, we compared the effects of 2'fucosyllactose (2'FL), difucosyllactose (DFL), 3'sialyllactose (3'SL), and blends thereof with fructooligosaccharide (FOS) on microbiota functionality (short- and branched-chain fatty acids, pH, and gas production) and composition (quantitative shallow shotgun sequencing) using fecal material from eight different pediatric Crohn's disease patients inoculated in the SIFR® technology. In general, all HMO treatments significantly increased total short-chain fatty acid production when compared with FOS, despite equal gas production. We found that 2'FL, either alone or in combination with DFL and 3'SL, exhibited a strong acetogenic and propiogenic effect, and 3'SL an acetogenic effect that surpassed the effects observed with FOS. No differences in overall community diversity between HMO- and FOS-treated pIBD microbiota were observed. There was, however, a stronger bifidogenic effect of 2'FL, 3'SL, 2'FL/DFL, and 2'FL/DFL + 3'SL when compared with FOS. In general, 3'SL and HMO blends enriched a broader species profile, including taxa with potentially anti-inflammatory properties, such as Faecalibacterium prausnitzii and Blautia species. This study suggests HMOs as a promising strategy to beneficially alter the gut microbial profile in pIBD.

The Impact of Yoyo Dieting and Resistant Starch on Weight Loss and Gut Microbiome in C57Bl/6 Mice

Cyclic weight loss and subsequent regain after dieting and non-dieting periods, a phenomenon termed yoyo dieting, places individuals at greater risk of metabolic complications and alters gut microbiome composition. Resistant starch (RS) improves gut health and systemic metabolism. This study aimed to investigate the effect of yoyo dieting and RS on the metabolism and gut microbiome. C57BL/6 mice were assigned to 6 diets for 20 weeks, including control, high fat (HF), yoyo (alternating HF and control diets every 5 weeks), control with RS, HF with RS, and yoyo with RS. Metabolic outcomes and microbiota profiling using 16S rRNA sequencing were examined. Yoyo dieting resulted in short-term weight loss, which led to improved liver health and insulin tolerance but also a greater rate of weight gain compared to continuous HF feeding, as well as a different microbiota profile that was in an intermediate configuration between the control and HF states. Mice fed HF and yoyo diets supplemented with RS gained less weight than those fed without RS. RS supplementation in yoyo mice appeared to shift the gut microbiota composition closer to the control state. In conclusion, yoyo dieting leads to obesity relapse, and increased RS intake reduces weight gain and might help prevent rapid weight regain via gut microbiome restoration.

The pectin metabolizing capacity of the human gut microbiota

The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.

Polyphenol-Rich Aronia melanocarpa Fruit Beneficially Impact Cholesterol, Glucose, and Serum and Gut Metabolites: A Randomized Clinical Trial

Polyphenol-rich Aronia fruits have great potential as a functional food with anti-inflammatory, hypolipidemic, and hypoglycemic biologic activities. However, clinical intervention trials investigating the impact of Aronia fruit consumption on human health are limited. A randomized, controlled, double-blinded, parallel intervention trial was conducted using 14 human subjects who ingested either 0 mL or 100 mL of Aronia juice daily for 30 days. Anthropometric measurements, fasting, and postprandial measures of glucose and lipid metabolism and inflammation, 16S rRNA fecal microbial composition data, and mass spectrometry-acquired serum and fecal metabolomic data were collected before and after the intervention period. Data were analyzed using general linear models, ANOVA, and t-tests. Daily consumption of Aronia prevented a rise in cholesterol levels (β = -0.50, p = 0.03) and reduced postprandial glucose (β = -3.03, p < 0.01). No difference in microbial community composition by condition was identified at any taxonomic level, but a decrease (β = -18.2, p = 0.04) in microbial richness with Aronia was detected. Serum and fecal metabolomic profiles indicated shifts associated with central carbon and lipid metabolism and decreases in pro-inflammatory metabolites. Our study further informs the development of polyphenol-based dietary strategies to lower metabolic disease risk.

A double-blind intervention trial in healthy women demonstrates the beneficial impact on Bifidobacterium with low dosages of prebiotic galacto-oligosaccharides

Introduction

Galacto-oligosaccharides (GOS) are well-substantiated prebiotic substrates. Multiple studies have demonstrated a positive impact of GOS on gut microbiota composition and activity, so-far mainly related to Bifidobacterium. However, data on the beneficial impact at lower dosages in a healthy female population are limited. The primary aim of the current study was to reveal the effect of low dosages (1.3 and 2.0 g) of GOS on fecal Bifidobacterium abundance in healthy women. Other outcomes included the effect of low dosage of GOS on overall fecal microbiota composition and on self-perceived GI comfort, sleep quality and mental wellbeing.

Method

Eighty-eight healthy women (42-70 years, BMI 18.7-30 kg/m2) were included in this randomized, parallel, double-blind study of 6 weeks. The participants were stratified for fiber intake, BMI and age and randomized to consume either 1.3 or 2.0 g of GOS per day for 3 weeks after a control period of 3 weeks without any intervention. Fecal samples were collected for shotgun metagenomics sequencing at the start (t = -3) and end (t = 0) of the control period and at the end of the intervention period (t = 3). Self-perceived gut comfort, sleep quality, and mental wellbeing were assessed weekly. Hierarchical clustering of principal components was applied to data collected from study participants.

Results

The relative abundance of Bifidobacterium in feces increased significantly after 3 weeks of daily consumption of both 1.3 g (p < 0.01) and 2.0 g GOS (p < 0.01). This was accompanied by a significant shift in the overall microbiota composition for the dosage of 2.0 g GOS (p < 0.01). Participants that showed a larger increase in Bifidobacterium in the intervention period compared to the change in Bifidobacterium in the control period, defined as responders, showed a significant overall difference in initial fecal microbiota composition as compared to non-responders (p = 0.04) and a trend towards lower baseline levels of Bifidobacterium in responders (p = 0.10).

Conclusion

Daily consumption of a low dose of GOS can lead to an increase in the relative abundance of Bifidobacterium in feces of healthy women. Additionally, with 2.0 g GOS, the enrichment of Bifidobacterium is accompanied with a shift in the overall microbiota composition.Clinical trial registration: clinicaltrials.gov, identifier NCT05762965.

The gut microbiome and dietary metabolites in the treatment of renal cell carcinoma

The gut microbiome is interlinked with renal cell carcinoma (RCC) and its response to systemic treatment. Mounting data suggests that certain elements of the gut microbiome may correlate with improved outcomes. New generation sequencing techniques and advanced bioinformatic data curation are accelerating the investigation of specific markers and metabolites that could predict treatment response. A variety of new therapeutic strategies, such as fecal microbiota transplantation, probiotic supplements, and dietary interventions, are currently being developed to modify the gut microbiome and improve anticancer therapies in patients with RCC. This review discusses the preliminary evidence indicating the role of the microbiome in cancer treatment, the techniques and tools necessary for its proper study and some of the current forms with which the microbiome can be modulated to improve patient outcomes.

Bifidobacterium longum subsp. longum BG-L47 boosts growth and activity of Limosilactobacillus reuteri DSM 17938 and its extracellular membrane vesicles

The aim of this study was to identify a Bifidobacterium strain that improves the performance of Limosilactobacillus reuteri DSM 17938. Initial tests showed that Bifidobacterium longum subsp. longum strains boosted the growth of DSM 17938 during in vivo-like conditions. Further characterization revealed that one of the strains, BG-L47, had better bile and acid tolerance compared to BG-L48, as well as mucus adhesion compared to both BG-L48 and the control strain BB536. BG-L47 also had the capacity to metabolize a broad range of carbohydrates and sugar alcohols. Mapping of glycoside hydrolase (GH) genes of BG-L47 and BB536 revealed many GHs associated with plant-fiber utilization. However, BG-L47 had a broader phenotypic fiber utilization capacity. In addition, B. longum subsp. longum cells boosted the bioactivity of extracellular membrane vesicles (MV) produced by L. reuteri DSM 17938 during co-cultivation. Secreted 5'-nucleotidase (5'NT), an enzyme that converts AMP into the signal molecule adenosine, was increased in MV boosted by BG-L47. The MV exerted an improved antagonistic effect on the pain receptor transient receptor potential vanilloid 1 (TRPV1) and increased the expression of the immune development markers IL-6 and IL-1ß in a peripheral blood mononuclear cell (PBMC) model. Finally, the safety of BG-L47 was evaluated both by genome safety assessment and in a human safety study. Microbiota analysis showed that the treatment did not induce significant changes in the composition. In conclusion, B. longum subsp. longum BG-L47 has favorable physiological properties, can boost the in vitro activity of L. reuteri DSM 17938, and is safe for consumption, making it a candidate for further evaluation in probiotic studies.

IMPORTANCE

By using probiotics that contain a combination of strains with synergistic properties, the likelihood of achieving beneficial interactions with the host can increase. In this study, we first performed a broad screening of Bifidobacterium longum subsp. longum strains in terms of synergistic potential and physiological properties. We identified a superior strain, BG-L47, with favorable characteristics and potential to boost the activity of the known probiotic strain Limosilactobacillus reuteri DSM 17938. Furthermore, we demonstrated that BG-L47 is safe for consumption in a human randomized clinical study and by performing a genome safety assessment. This work illustrates that bacteria-bacteria interactions differ at the strain level and further provides a strategy for finding and selecting companion strains of probiotics.

Short-term dietary fiber interventions produce consistent gut microbiome responses across studies

The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

IMPORTANCE

Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.

Lipid- and glucose-lowering effects of Rhamnan sulphate from Monostroma nitidum with altered gut microbiota in mice

Rhamnan sulphate (RS) is a sulphated polysaccharide found in green algae such as Monostroma nitidum that exhibits various biological functions, including anticoagulant, antitumour, antiviral, and anti-obesity properties. In our previous clinical trial, we demonstrated that RS intake improves constipation. However, no specific bacteria showed a significant (p < .05) change. Notably, these results were obtained after a short RS inoculation period of only 2 weeks. In the present study, to evaluate the long-term effects of RS on the gut microbiota, we orally administered RS to BALB/c mice for 11 weeks, analyzed their blood biochemical data, and performed 16s rRNA-sequencing. Oral administration of RS increased body weight with increased food intake, whereas plasma total cholesterol and fasting plasma glucose levels decreased. RS-fed mice showed lower fasting insulin levels (p < .1) and decreased homeostatic model assessment for insulin resistance (HOMA-IR, p < .0001), suggesting that RS improved insulin resistance. In the feces of mice, the amounts of acetic and propionic acids increased. In the gut microbiota, predictive metagenomic profiling using the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) revealed functional alterations in Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways in RS-fed mice. Corresponding to the blood glucose-lowering effect, the glycolysis and tricarboxylic acid (TCA) cycle pathways were activated. In addition, the Firmicutes/Bacteroides (F/B) ratio, which may be associated with various health outcomes, was also reduced. These results suggest that the blood glucose-lowering effect, improvement in insulin resistance, and lipid-lowering effect of RS may be due to changes in the intestinal microbiota.

Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions

The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed-efficient and non-efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat-soybean based diet (CTR) or a low-energy, high-fibre corn-sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet-dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short-chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.

Swapping White for High-Fibre Bread Increases Faecal Abundance of Short-Chain Fatty Acid-Producing Bacteria and Microbiome Diversity: A Randomized, Controlled, Decentralized Trial

A low-fibre diet leads to gut microbiota imbalance, characterized by low diversity and reduced ability to produce beneficial metabolites, such as short-chain fatty acids (SCFAs). This imbalance is associated with poor gastrointestinal and metabolic health. We aimed to determine whether one dietary change, substitution of white bread with high-fibre bread, improves gut microbiota diversity and SCFA-producing capability. Twenty-two healthy adults completed a two-phase randomized, cross-over trial. The participants consumed three slices of a high-fibre bread (Prebiotic Cape Seed Loaf with BARLEYmax®) or control white bread as part of their usual diet for 2 weeks, with the treatment periods separated by a 4-week washout. High-fibre bread consumption increased total dietary fibre intake to 40 g/d, which was double the amount of fibre consumed at baseline or during the white bread intervention. Compared to white bread, the high-fibre bread intervention resulted in higher faecal alpha diversity (Shannon, p = 0.014) and relative abundance of the Lachnospiracae ND3007 group (p < 0.001, FDR = 0.019) and tended to increase the butyrate-producing capability (p = 0.062). In conclusion, substituting white bread with a high-fibre bread improved the diversity of gut microbiota and specific microbes involved in SCFA production and may enhance the butyrate-producing capability of gut microbiota in healthy adults. These findings suggest that a single dietary change involving high-fibre bread provides a practical way for adults to exceed recommended dietary fibre intake levels that improve gut microbiota composition and support gastrointestinal and metabolic health.

The impact of a modified microbiota-accessible carbohydrate diet on gut microbiome and clinical symptoms in colorectal cancer patients following surgical resection

A high-fiber diet is widely recognized for its positive effects on the gut microbiome. However, the specific impact of a high-fiber diet on the gut microbiome and bowel habits of patients with colon cancer remains poorly understood. In this study, we aimed to assess the effects of a modified microbiota-accessible carbohydrate (mMAC) diet on gut microbiota composition and clinical symptoms in colon cancer patients who underwent surgical resection. To achieve this, we enrolled 40 patients in two groups: those who received adjuvant chemotherapy and those who did not. Fecal samples were collected before and after dietary interventions for microbial and metabolite analyses. Each group was randomized in a 1: 1 ratio to follow either a 3-week conventional diet followed by a 3-week mMAC diet, or the reverse sequence. Although there were no significant differences in the microbial diversity data before and after the mMAC diet in both the non-chemotherapy and chemotherapy groups, distinct differences in gut microbial composition were revealed after the mMAC diet. Specifically, the abundance of Prevotella, which is associated with high-fiber diets, was further elevated with increased concentrations of acetate and propionate after the mMAC diet. Additionally, patients who experienced improved diarrhea and constipation after the mMAC diet exhibited an enrichment of beneficial bacteria and notable changes in metabolites. In conclusion, this study provides valuable insights into the potential benefits of the mMAC diet, specifically its impact on the gut microbiome and clinical symptoms in postoperative colorectal cancer (CRC) patients. These findings emphasize the potential role of a high-fiber diet in influencing the gut microbiome, and the clinical symptoms warrant further investigation.