Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production

Systematically-designed mixtures outperform single fibers for gut microbiota support

Dietary fiber interventions to modulate the gut microbiota have largely relied on isolated fibers or specific fiber sources. We hypothesized that fibers systematically blended could promote more health-related bacterial groups. Initially, pooled in vitro fecal fermentations were used to design dietary fiber mixtures to support complementary microbial groups related to health. Then, microbial responses were compared for the designed mixtures versus their single fiber components in vitro using fecal samples from a separate cohort of 10 healthy adults. The designed fiber mixtures outperformed individual fibers in supporting bacterial taxa across donors resulting in superior alpha diversity and unexpected higher SCFA production. Moreover, unique shifts in community structure and specific taxa were observed for fiber mixtures that were not observed for single fibers, suggesting a synergistic effect when certain fibers are put together. Fiber mixture responses were remarkably more consistent than individual fibers across donors in promoting several taxa, especially butyrate producers from the Clostridium cluster XIVa. This is the first demonstration of synergistic fiber interactions for superior support of a diverse group of important beneficial microbes consistent across people, and unexpectedly high SCFA production. Overall, harnessing the synergistic potential of designed fiber mixtures represents a promising and more efficacious avenue for future prebiotic development.

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample

Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE

Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable cardiometabolic benefits were observed independently of L. reuteri administration, several of which could be accurately predicted by baseline and diet-responsive microbiome features. The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies.

Development of a comprehensive food glycomic database and its application: Associations between dietary carbohydrates and insulin resistance

Carbohydrates are an integral part of a healthy diet. The molecular compositions of carbohydrates encompass a very broad range of unique structures with many being ill-defined. This vast structural complexity is distilled into vague categories such as total carbohydrates, sugars, starches, and soluble/insoluble fibers. Structural elucidation of the food glycome is until recently extremely slow and immensely challenging. Dietary carbohydrates, including monosaccharides, oligosaccharides, glycosidic linkages, and polysaccharides were determined for the most consumed foods in the US consisting of 250 common foods using a multiglycomic platform. The food glycome was then correlated with clinical data from the National Health and Nutrition Examination Survey (NHANES) consisting of dietary recalls from 13,550 adults to determine associations between dietary carbohydrates, their structural features and insulin resistance. Several features were more powerful predictors compared to traditional measures indicating the need for molecular fine-scale food carbohydrate data in guiding precision nutrition initiatives and clinical studies.

Predicting metabolite response to dietary intervention using deep learning

Due to highly personalized biological and lifestyle characteristics, different individuals may have different metabolite responses to specific foods and nutrients. In particular, the gut microbiota, a collection of trillions of microorganisms living in the gastrointestinal tract, is highly personalized and plays a key role in the metabolite responses to foods and nutrients. Accurately predicting metabolite responses to dietary interventions based on individuals' gut microbial compositions holds great promise for precision nutrition. Existing prediction methods are typically limited to traditional machine learning models. Deep learning methods dedicated to such tasks are still lacking. Here we develop a method McMLP (Metabolite response predictor using coupled Multilayer Perceptrons) to fill in this gap. We provide clear evidence that McMLP outperforms existing methods on both synthetic data generated by the microbial consumer-resource model and real data obtained from six dietary intervention studies. Furthermore, we perform sensitivity analysis of McMLP to infer the tripartite food-microbe-metabolite interactions, which are then validated using the ground-truth (or literature evidence) for synthetic (or real) data, respectively. The presented tool has the potential to inform the design of microbiota-based personalized dietary strategies to achieve precision nutrition.

Obesogenic cafeteria diet induces dynamic changes in gut microbiota, reduces myenteric neuron excitability, and impairs gut contraction in mice

The cafeteria diet (CAF) is a superior diet model in animal experiments compared with the conventional high-fat diet (HFD), effectively inducing obesity, metabolic disturbances, and multi-organ damage. Nevertheless, its impact on gut microbiota composition during the progression of obesity, along with its repercussions on the enteric nervous system (ENS) and gastrointestinal motility has not been completely elucidated. To gain more insight into the effects of CAF diet in the gut, C57BL/6 mice were fed with CAF or a standard diet for 2 or 8 wk. CAF-fed mice experienced weight gain, disturbed glucose metabolism, dysregulated expression of colonic IL-6, IL-22, TNFα, and TPH1, and altered colon morphology, starting at week 2. Fecal DNA was isolated and gut microbiota composition was monitored by sequencing the V3-V4 16S rRNA region. Sequence analysis revealed that Clostridia and Proteobacteria were specific biomarkers associated with CAF-feeding at week 2, while Bacteroides and Actinobacteria were prominent at week 8. In addition, the impact of CAF diet on ENS was investigated (week 8), where HuC/D+ neurons were measured and counted, and their biophysical properties were evaluated by patch clamp. Gut contractility was tested in whole-mount preparations. Myenteric neurons in CAF-fed mice exhibited reduced body size, incremented cell density, and decreased excitability. The amplitude and frequency of the rhythmic spontaneous contractions in the colon and ileum were affected by the CAF diet. Our findings demonstrate, for the first time, that CAF diet gradually changes the gut microbiota and promotes low-grade inflammation, impacting the functional properties of myenteric neurons and gut contractility in mice.NEW & NOTEWORTHY The gut microbiota changes gradually following the consumption of CAF diet. An increase in Clostridia and Proteobacteria is a hallmark of dysbiosis at the early onset of gut inflammation and obesity. The CAF diet was effective in inducing intestinal low-grade inflammation and alterations in myenteric neuronal excitability in mice. CAF diet is a reliable strategy to study the interplay between gut dysbiosis and low-grade inflammation, in addition to the mechanisms underlying gastrointestinal dysmotility associated with obesity.

Classifying compounds as prebiotics - scientific perspectives and recommendations

Microbiomes provide key contributions to health and potentially important therapeutic targets. Conceived nearly 30 years ago, the prebiotic concept posits that targeted modulation of host microbial communities through the provision of selectively utilized growth substrates provides an effective approach to improving health. Although the basic tenets of this concept remain the same, it is timely to address certain challenges pertaining to prebiotics, including establishing that prebiotic-induced microbiota modulation causes the health outcome, determining which members within a complex microbial community directly utilize specific substrates in vivo and when those microbial effects sufficiently satisfy selectivity requirements, and clarification of the scientific principles on which the term 'prebiotic' is predicated to inspire proper use. In this Expert Recommendation, we provide a framework for the classification of compounds as prebiotics. We discuss ecological principles by which substrates modulate microbiomes and methodologies useful for characterizing such changes. We then propose statistical approaches that can be used to establish causal links between selective effects on the microbiome and health effects on the host, which can help address existing challenges. We use this information to provide the minimum criteria needed to classify compounds as prebiotics. Furthermore, communications to consumers and regulatory approaches to prebiotics worldwide are discussed.

RG-I pectic polysaccharides and hesperidin synergistically modulate gut microbiota: An in vitro study targeting the proportional relationship

In this study, we investigated how different proportions blends of Rhamnogalacturonan-I pectic polysaccharides and hesperidin impact the gut microbiota and metabolites using an in vitro simulated digestion and fermentation model. The results indicated that both of them could modulate the gut microbiota and produce beneficial metabolites. However, their blends in particular proportions (such as 1:1) exhibited remarkable synergistic effects on modulating the intestinal microenvironment, surpassing the effects observed with individual components. Specifically, these blends could benefit the host by increasing short-chain fatty acids production (such as acetate), improving hesperidin bioavailability, producing more metabolites (such as hesperetin, phenolic acids), and promoting the growth of beneficial bacteria. This synergistic and additive effect was inseparable from the role of gut microbiota. Certain beneficial bacteria, such as Blautia, Faecalibacterium, and Prevotella, exhibited strong preferences for those blends, thereby contributing to host health through participating in carbohydrate and flavonoid metabolism.

Targeting gut microbiota by starch molecular size and chain-length distribution to produce various short-chain fatty acids

The detailed relationships among starch fine molecular structures, gut microbiota, and short-chain fatty acids (SCFAs) are not fully understood. We hypothesized that specific starch molecular size and chain-length distribution are favored by gut bacteria for the secretion of SCFAs. To investigate this, different types of starches with diverse molecular size and chain-length distributions (e.g., amylose content ranging from about 1 % to 38 %) were subjected to in vitro fermentation with human fecal inocula. Tapioca and waxy maize starches were notably more effective at producing acetate and propionate compared to lentil, wheat, and pea starches (p < 0.05). Correlation analysis revealed, for the first time, that the number of amylose chains with a degree of polymerization between 500 and 5000 was positively correlated with the abundance of Bacteroides_coprocola_DSM_17136 and Bacteroides_plebeius, possibly relating to the higher production of acetate and propionate. These results indicate that starches with certain fine molecular structures could be used to target gut bacteria to produce various types of SCFAs, thereby amplifying beneficial effects on human health.

Advances in understanding dietary fiber: Classification, structural characterization, modification, and gut microbiome interactions

Gut microbiota and their metabolites profoundly impact host physiology. Targeted modulation of gut microbiota has been a long-term interest in the scientific community. Numerous studies have investigated the feasibility of utilizing dietary fibers (DFs) to modulate gut microbiota and promote the production of health-beneficial bacterial metabolites. However, the complexity of fiber structures, microbiota composition, and their dynamic interactions have hindered the precise prediction of the impact of DF on the gut microbiome. We address this issue with a new perspective, focusing on the inherent chemical and structural complexity of DFs and their interaction with gut microbiota. The chemical and structural complexity of fibers was thoroughly elaborated, encompassing the fibers' molecular composition, polymorphism, mesoscopic structures, porosity, and particle size. Advanced characterization techniques to investigate fiber structural properties were discussed. Additionally, we examined the interactions between DFs and gut microbiota. Finally, we summarized processing techniques to modify fiber structures for improving the fermentability of DF by gut microbiota. The structure of fibers, such as their crystallinity, porosity, degree of branching, and pore wettability, significantly impacts their interactions with gut microbiota. These structural differences also substantially affect fiber's fermentability and capability to modulate the composition of gut microbiota. Conventional approaches are not capable of investigating complex fiber properties and their influences on the gut microbiome; therefore, it is of the essence to involve advanced material characterization techniques and artificial intelligence to unveil more comprehensive information on this topic.

Comparison of diet and exercise on cardiometabolic factors in young adults with overweight/obesity: multiomics analysis and gut microbiota prediction, a randomized controlled trial

The optimal strategy for improving cardiometabolic factors (CMFs) in young obese individuals through diet and exercise remains unclear, as do the potential mechanisms. We conducted an 8-week randomized controlled trial to compare the effects of different interventions in youth with overweight/obesity. Gut microbes and serum metabolites were examined to identify regulating mechanisms. A total of 129 undergraduates were randomly assigned to fiber-rich (FR) diet, rope-skipping (RS), combined FR-RS and control groups. The results showed that single interventions were as effective as combined interventions in improving weight, waist circumference, body fat, and lipid profile compared with control group. Notably, the FR group further reduced low-density lipoprotein (LDL-C) and uric acid (UA) (all p < 0.05). Mediation analysis revealed four gut microbiota-metabolite-host axes in improving CMFs. Additionally, we used machine learning algorithms to further predict individual responses based on baseline gut microbiota composition, with specific microbial genera guiding targeted intervention selection. In conclusion, FR diet and/or RS were effective in improving CMFs, with the FR diet particular effectiveness in reducing LDL-C and UA levels. These benefits may drive by gut microbiome-metabolite-host interactions. Moreover, the predictability of gut microbiota composition supports making targeted decisions in selecting interventions. Trial Registration: NCT04834687.

The role of the gut microbiota and the nicotinate/nicotinamide pathway in rotenone-induced neurotoxicity

Rotenone is a natural compound from plants. It is widely used in pesticides because of highly toxic to insects and fish. However, lots of research has reported that rotenone has neurotoxic effects in humans. It is confirmed there is a correlation between rotenone exposure and Parkinson's disease (PD). Therefore, the role of gut microbiota and related metabolic pathways was investigated in rotenone-induced neurotoxicity. The results showed that the abundance of gut microbiota changed significantly. The differential metabolites were enriched in the nicotinate and nicotinamide metabolism pathways, which had the greatest impact on the entire metabolic system. The contents of acetic acid and butyric acid in intestinal tissues decreased significantly. Additionally, Interleukin-6 (IL-6), Tumor necrosis factor alpha (TNF-α) and vasoactive intestinal peptide (VIP) were significantly up-regulated, while gastrin (GAS) and Ghrelin were significantly down-regulated. Expression of intestinal tight junction protein was significantly reduced. Moreover, nicotinamide adenine dinucleotide (NAD+), a the product of the nicotinate/nicotinamide pathways, decreased significantly. And the expression levels of nicotinamide phosphoribosyl transferase (NAMPT) and Solute Carrier Family 25 Member 51 (SLC25A51) also reduced significantly. Therefore, gut microbiota was influenced obviously in rats exposed to rotenone, leading to a decrease of acetic acid and butyric acid contents, which might in turn affect the change of intestinal barrier permeability and induce inflammatory reactions. Meanwhile, the nicotinate/nicotinamide metabolic pathways might play an important role in rats exposed to rotenone.

Morphological, physicochemical, and pasting properties of pre-gelatinized starch prepared by high-pressure homogenizer: A comparative study on starches from different resources

Pre-gelatinized starch, a physically modified starch known for its ability to swell in cold water, has wide applications across various industries. This study assesses the feasibility of high-pressure homogenization (HPH) in producing pre-gelatinized starches and compares their morphological, physicochemical, and pasting properties from different sources. Starches from eleven sources, including mung bean, pea, wheat, sweet potato, cassava, corn, non-waxy rice, waxy rice, chickpea, lentil, and chestnut, were processed using HPH at 150 MPa for three cycles. The resulting pre-gelatinized starch granules exhibited disrupted surface structures, increased water absorption and solubility, decreased crystallinity, and altered gelatinization temperatures. Results showed that waxy rice pre-gelatinized starch had the highest degree of pre-gelatinization (90.27%) and water absorption index (61.95%), while chestnut pre-gelatinized starch had the highest water solubility index (21.58%) and lentil pre-gelatinized starch demonstrated the highest gel strength (2178.00 g). X-ray diffraction analysis revealed a significant reduction in crystallinity, with values ranging from 13.96% to 18.29%. Additionally, the study observed variations in pasting properties, with cassava pre-gelatinized starch exhibiting the highest peak viscosity (5458 cP), trough viscosity (3864 cP), and final viscosity (6536 cP). These findings indicate that HPH is an effective method for producing pre-gelatinized starch with enhanced functional properties, enriching the scientific understanding of pre-gelatinized starches from different sources and promoting their application in the food industry and other sectors.

Could tolerance to DNA be broken in the gut in systemic lupus erythematosus?

The bacteria in the human colon outnumber the total number of nucleated cells in the human body by approximately 10:1. The DNA that the bacteria contain is enriched around 20-fold in immune stimulatory CpG motifs compared to the DNA of host cells. In addition, this DNA can have alternative more immunogeneic DNA structures and it may be presented to the immune system alongside other proinflammatory bacterial innate ligands such as LPS. To ensure that this immunostimulatory combination is not pathogenic, the luminal boundary of host tissues in the human gastrointestinal tract is protected by cells secreting bactericides together with the secreted enzyme DNASE1L3 that can break down bacterial DNA. Cells with RNA encoding DNASE1L3 are particularly abundant in the gut-associated lymphoid tissue where bacteria are specifically sampled into the body, alongside B cells noted for their T independent function. Importantly, individuals with loss of function mutations in DNASE1L3 develop anti-DNA antibodies and lupus symptoms. In this review, we explore the possibility that a perfect storm might break tolerance to DNA: when bacterial DNA from microbiota that is not digested by DNASE1L3 directly encounters B cells that are not necessarily restricted by T cell dependence.

Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine

Understanding the etiological complexity of diseases requires identifying biomarkers longitudinally associated with specific phenotypes. Advanced sequencing tools generate dynamic microbiome data, providing insights into microbial community functions and their impact on health. This review aims to explore the current roles and future visionary endeavors of dynamic methods for integrating longitudinal microbiome multi-omics data in personalized and precision medicine. This work seeks to synthesize existing research, propose best practices, and highlight innovative techniques. The development and application of advanced dynamic methods, including the unified analytical frameworks and deep learning tools in artificial intelligence, are critically examined. Aggregating data on microbes, metabolites, genes, and other entities offers profound insights into the interactions among microorganisms, host physiology, and external stimuli. Despite progress, the absence of gold standards for validating analytical protocols and data resources of various longitudinal multi-omics studies remains a significant challenge. The interdependence of workflow steps critically affects overall outcomes. This work provides a comprehensive roadmap for best practices, addressing current challenges with advanced dynamic methods. The review underscores the biological effects of clinical, experimental, and analytical protocol settings on outcomes. Establishing consensus on dynamic microbiome inter-studies and advancing reliable analytical protocols are pivotal for the future of personalized and precision medicine.

Exploring a maize-derived dietary fiber-phenolic acid complex with prebiotic effects

The structural, functional, and prebiotic properties of three maize-derived cell wall dietary fiber-phenolic acid complexes (CWDFPC1, CWDFPC2, and CWDFPC3) were investigated. The results showed that all three CWDFPCs had similar proximate composition and XRD pattern (type I). However, there were significant differences in the phytochemical profiles of their phenolic compounds (PC). Although the testa was the primary source of bound PC (BPC) in all three CWDFPCs, CWDFPC2 had the highest BPC content (15.41 mg GAE/g) and exhibited the greatest antioxidant activity in vitro (DPPH and ABTS assays). The water holding capacity of CWDFPC1 (6.53 g/g) and CWDFPC3 (6.86 g/g) was higher than CWDFPC2 (4.84 g/g), and three CWDFPCs had similar nitrite ion adsorption capacity, bile adsorption capacity, and cation-exchange capacity. After 48 h of in vitro fecal fermentation, CWDFPC2 produced more short-chain fatty acids (46.33 mM) compared to CWDFPC1 and CWDFPC3 (40.26 mM and 44.20 mM, respectively).

Consumption of resistant potato starch produces changes in gut microbiota that correlate with improvements in abnormal bowel symptoms: a secondary analysis of a clinical trial

BACKGROUND

Studies have linked a lack of dietary fibre, including resistant starch (RS), to disease-associated changes in intestinal bacteria. Healthy people often report abnormal bowel symptoms (ABS), including bloating, constipation, abdominal pain, and diarrhea, however, connections between these symptoms and the gut microbiota are poorly understood. Determining correlations between ABS and taxonomic groups may provide predictive value for using prebiotics to mitigate ABS in combination with stool microbiome testing.

METHODS

Post hoc analysis of a three-arm randomized, double-blind, placebo-controlled clinical trial evaluating the effects of 3.5 g and 7 g resistant potato starch (RPS) doses or placebo was conducted. The study population (n = 70) were healthy adults aged 18-69 years old living in and around Guelph, ON. Participants evaluated their stools using the Bristol Stool Chart and also recorded any ABS daily. The presence of ABS was compared between treatment arms at baseline and changes in ABS were compared within treatment arms over 1- and 4-week periods. Pearson correlation analysis was used to identify significant relationships between changes in ABS and changes in bacterial taxa.

RESULTS

Abdominal pain, belching, bloating, constipation, diarrhea, gas, and feeling unwell were reported by participants at low levels at baseline. Neither RPS nor placebo had significant effects on mean ABS scores. However, we identified positive correlations between treatment-dependent changes in symptoms and changes in Granulicatella, Haemophilus, Lachnospira, Olsenella, Papillibacter, Turicibacter, unclassified Enterobacteriaceae, unclassified Fusobacteriaceae, unclassified Pasteurellaceae, and unclassified Gammaproteobacteria. We also identified negative correlations between treatment-dependent changes in symptoms and changes in Anaerotruncus, Dorea, RFN20, Victivallis, unclassified Coriobacteriaceae, and unclassified Oxalobacteraceae. These Pearson correlations were significant after correction for repeated testing. The mean relative abundance of these taxa did not change in response to treatment. Finally, macronutrient intake was unaffected by RPS or placebo treatments.

CONCLUSION

Changes in ABS can be positively or negatively correlated with changes in specific gut microbiota, creating opportunities for personalized microbiome-targeted interventions to resolve ABS.

TRIAL REGISTRATION

The trial was registered at ClinicalTrials.gov (NCT05242913) on February 16, 2022.

The impact of a prebiotic-rich diet and/or probiotic supplements on human cognition: Secondary outcomes from the 'Gut Feelings' randomised controlled trial

BACKGROUND

Emerging evidence indicates that gut microbiota-targeted interventions may lead to improvements in cognition. We assessed whether a prebiotic-rich dietary intervention, probiotic supplement, or synbiotic combination of both would improve human cognition, as part of the 'Gut Feelings' trial.

METHODS

An 8-week, 2 × 2 factorial randomised controlled trial was conducted on 118 adults with low mood and potential for dietary improvement. Treatment arms: (1) probiotic supplement and diet-as-usual (probiotic group); (2) high-prebiotic diet and placebo supplement (prebiotic diet group); (3) probiotic supplement and high-prebiotic diet (synbiotic group); and (4) placebo supplement and diet-as-usual (placebo group). At baseline and 8-weeks, the Cogstate Brief Battery was administered, testing processing speed, attention, visual learning, and working memory. Data were analysed using Bayesian linear regression.

RESULTS

We found weak evidence that the probiotic improved working memory (Cohen's d = -0.32, 95% CI: -0.67, 0.03; posterior probability [post. prob] of benefit: 96%). For the other treatments, there was little or no evidence of cognitive improvement. We found weak evidence that the prebiotic diet impaired processing speed (d = 0.25, 95% CI: -0.02, 0.51; post. prob of harm: 97%). There was little indication of a synergistic interaction between the probiotic and prebiotic diet.

CONCLUSION

We found suggestive evidence of a probiotic-induced improvement in working memory, and prebiotic-induced impairment in processing speed. However, the evidence remains inconclusive regarding any cognitive benefit or harm induced by the probiotic, prebiotic diet, or synbiotic treatments. Larger intervention studies are recommended, with inclusion of neuroimaging or electrophysiology measures.Trial Registration: Australian New Zealand Clinical Trials Registry (ACTRN12617000795392; registered 31 May 2017).

Propionic Acid Impact on Multiple Sclerosis: Evidence and Challenges

Accumulating evidence suggests that multiple sclerosis (MS) is an environmentally influenced disorder with contributions from life-time exposure to factors including Epstein-Barr virus infection or shifts in microbiome, diet and lifestyle. One suggested factor is a deficiency in propionic acid, a short-chain fatty acid produced by gut bacteria that may contribute to the disease pathology both in animal models and in human cases of MS. Propionate appears to exert beneficial effects on the immune, peripheral and central nervous systems of people with MS (pwMS), showing immunoregulatory, neuroprotective and neurogenerative effects. These functions are crucial, given that MS is characterized by immune-mediated damage of myelin in the central nervous system. Accordingly, propionate supplementation or a modulated increase in its levels through the microbiome and diet may help counteract the pro-inflammatory state in MS by directly regulating immune system and/or by decreasing permeability of gut barrier and blood-brain barrier. This could potentially improve outcomes when used with immune-modulating therapy. However, while its broad effects are promising, further large clinical trials are necessary to evaluate its efficacy and safety in pwMS and clarify its role as a complementary therapeutic strategy. This review provides a comprehensive analysis of the evidence, challenges and limitations concerning propionic acid supplementation in MS.

Gut microbiota modulates depressive-like behaviors induced by chronic ethanol exposure through short-chain fatty acids

BACKGROUND

Chronic ethanol exposure (CEE) is recognized as an important risk factor for depression, and the gut-brain axis has emerged as a key mechanism underlying chronic ethanol exposure-induced anxiety and depression-like behaviors. Short-chain fatty acids (SCFAs), which are the key metabolites generated by gut microbiota from insoluble dietary fiber, exert protective roles on the central nervous system, including the reduction of neuroinflammation. However, the link between gut microbial disturbances caused by chronic ethanol exposure, production of SCFAs, and anxiety and depression-like behaviors remains unclear.

METHODS

Initially, a 90-day chronic ethanol exposure model was established, followed by fecal microbiota transplantation model, which was supplemented with SCFAs via gavage. Anxiety and depression-like behaviors were determined by open field test, forced swim test, and elevated plus-maze. Serum and intestinal SCFAs levels were quantified using GC-MS. Changes in related indicators, including the intestinal barrier, intestinal inflammation, neuroinflammation, neurotrophy, and nerve damage, were detected using Western blotting, immunofluorescence, and Nissl staining.

RESULTS

Chronic ethanol exposure disrupted with gut microbial homeostasis, reduced the production of SCFAs, and led to anxiety and depression-like behaviors. Recipient mice transplanted with fecal microbiota that had been affected by chronic ethanol exposure exhibited impaired intestinal structure and function, low levels of SCFAs, intestinal inflammation, activation of neuroinflammation, a compromised blood-brain barrier, neurotrophic defects, alterations in the GABA system, anxiety and depression-like behaviors. Notably, the negative effects observed in these recipient mice were significantly alleviated through the supplementation of SCFAs.

CONCLUSION

SCFAs not only mitigate damage to intestinal structure and function but also alleviate various lesions in the central nervous system, such as neuroinflammation, and reduce anxiety and depression-like behaviors, which were triggered by transplantation with fecal microbiota that had been affected by chronic ethanol exposure, adding more support that SCFAs serve as a bridge between the gut and the brain.

The interplay between diet and the gut microbiome: implications for health and disease

Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies.

Cassava (Manihot esculenta) Brazilian cultivars have different chemical compositions, present prebiotic potential, and beneficial effects on the colonic microbiota of celiac individuals

The purpose of this study was to investigate the potential prebiotic properties of cassava cultivars from Northeast [Doce mel and Ourinho (OUR)] and South [Baiana, and IPR-Upira (UPI)] of Brazil in in vitro fermentation systems. The cultivars were evaluated for their chemical composition, and, then, two cultivars were selected (OUR and UPI) and subjected to in vitro gastrointestinal digestion to assess the effects on probiotics Lacticaseibacillus casei, Lactobacillus acidophilus, and Bifidobacterium animalis growth, metabolic activity, and prebiotic activity scores. Finally, the impact of cassava cultivars on the fecal microbiota of celiac individuals was evaluated using the 16S rRNA gene. Cassava cultivars have variable amounts of fiber, resistant starch, fructooligosaccharides (FOS), organic acids, phenolic compounds, and sugars, with OUR and UPI cultivars standing out. OUR and UPI cultivars contributed to the increase in the proliferation rates of L. casei (0.04-0.19), L. acidophilus (0.34-0.27), and B. animalis (0.10-0.03), resulting in more significant effects than FOS, an established prebiotic compound. Also, the positive scores of prebiotic activities with probiotic strains indicate OUR and UPI's ability to stimulate beneficial bacteria while limiting enteric competitors selectively. In addition, OUR and UPI promoted increased relative abundance of Bifidobacteriaceae, Enterococcaceae, and Lactobacillaceae in the fecal microbiota of celiac individuals while decreased Lachnospirales, Bacteroidales, and Oscillospirales. The results show that cassava cultivars caused beneficial changes in the composition and metabolic activity of the human intestinal microbiota of celiacs. OUR and UPI cultivars from the Northeast and South of Brazil could be considered potential prebiotic ingredients for use in the formulation of functional foods and dietary supplements.

Rethinking the classification of non-digestible carbohydrates: Perspectives from the gut microbiome

Clarification is required when the term "carbohydrate" is used interchangeably with "saccharide" and "glycan." Carbohydrate classification based on human digestive enzyme activities brings clarity to the energy supply function of digestible sugars and starch. However, categorizing structurally diverse non-digestible carbohydrates (NDCs) to make dietary intake recommendations for health promotion remains elusive. In this review, we present a summary of the strengths and weaknesses of the traditional dichotomic classifications of carbohydrates, which were introduced by food chemists, nutritionists, and microbiologists. In parallel, we discuss the current consensus on commonly used terms for NDCs such as "dietary fiber," "prebiotics," and "fermentable glycans" and highlight their inherent differences from the perspectives of gut microbiome. Moreover, we provide a historical perspective on the development of novel concepts such as microbiota-accessible carbohydrates, microbiota-directed fiber, targeted prebiotics, and glycobiome. Crucially, these novel concepts proposed by multidisciplinary scholars help to distinguish the interactions between diverse NDCs and the gut microbiome. In summary, the term NDCs created based on the inability of human digestive enzymes fails to denote their interactions with gut microbiome. Considering that the gut microbiome possesses sophisticated enzyme systems to harvest diverse NDCs, the subclassification of NDCs should be realigned to their metabolism by various gut microbes, particularly health-promoting microbes. Such rigorous categorizations facilitate the development of microbiome-targeted therapeutic strategies by incorporating specific types of NDCs.

Recent developments in enzymatic preparation, physicochemical properties, bioactivity, and application of resistant starch type III from staple food grains

Resistant starch (RS) was classified into five types and referred to the starch that cannot be digested and absorbed by the small intestine of healthy human beings. Among them, RS3 has received a lot of attention from researchers because of its good functional properties and greater application prospects. Meanwhile, the enzymatic method is widely used in the preparation of RS3 because of its high efficiency and environmental protection. α-Amylase and pullulanase as the main enzymes can effectively improve the yield of RS3. The physical properties of RS3 have an excellent potential for application in improving food crispness, texture and producing low glycemic index (GI) foods. It is more valuable because it has biological activities such as inducing apoptosis in tumor cells, lowering intestinal pH, and regulating blood glucose, etc. This paper summarized the current research progress of RS3 from different staple food grains, including current applications of enzymes commonly used in the preparation of RS3, physical properties and biological activities of RS3, and the application of RS3 in different areas to provide a theoretical basis for future research on RS3 as well as further development and applications based on the market requirement.

Examining the healthy human microbiome concept

Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a 'healthy' human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome-health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.

Ketogenic Diet: A Review of Composition Diversity, Mechanism of Action and Clinical Application

The ketogenic diet (KD) is a special high-fat, very low-carbohydrate diet with the amount of protein adjusted to one's requirements. By lowering the supply of carbohydrates, this diet induces a considerable change in metabolism (of protein and fat) and increases the production of ketone bodies. The purpose of this article is to review the diversity of composition, mechanism of action, clinical application and risk associated with the KD. In the last decade, more and more results of the diet's effects on obesity, diabetes and neurological disorders, among other examples have appeared. The beneficial effects of the KD on neurological diseases are related to the reconstruction of myelin sheaths of neurons, reduction of neuron inflammation, decreased production of reactive oxygen species, support of dopamine production, repair of damaged mitochondria and formation of new ones. Minimizing the intake of carbohydrates results in the reduced absorption of simple sugars, thereby decreasing blood glucose levels and fluctuations of glycaemia in diabetes. Studies on obesity indicate an advantage of the KD over other diets in terms of weight loss. This may be due to the upregulation of the biological activity of appetite-controlling hormones, or to decreased lipogenesis, intensified lipolysis and increased metabolic costs of gluconeogenesis. However, it is important to be aware of the side effects of the KD. These include disorders of the digestive system as well as headaches, irritability, fatigue, the occurrence of vitamin and mineral deficiencies and worsened lipid profile. Further studies aimed to determine long-term effects of the KD are required.

The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer

Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.

The human gut metacommunity as a conceptual aid in the development of precision medicine

Human gut microbiomes (microbiotas) are highly individualistic in taxonomic composition but nevertheless are functionally similar. Thus, collectively, they comprise a "metacommunity." In ecological terminology, the assembly of human gut microbiomes is influenced by four processes: selection, speciation, drift, and dispersal. As a result of fortuitous events associated with these processes, individual microbiomes are taxonomically "tailor-made" for each host. However, functionally they are "off-the-shelf" because of similar functional outputs resulting from metabolic redundancy developed in host-microbe symbiosis. Because of this, future microbiological and molecular studies of microbiomes should emphasize the metabolic interplay that drives the human gut metacommunity and that results in these similar functional outputs. This knowledge will support the development of remedies for specific functional dysbioses and hence provide practical examples of precision medicine.

Resistant Potato Starch Supplementation Reduces Serum Free Fatty Acid Levels and Influences Bile Acid Metabolism

Background: Resistant starches, such as high-amylose maize starch and resistant potato starch (RPS), have prebiotic effects that are linked to improved metabolism at >15 g/day, but the effects at lower doses have not been reported. Methods: We performed an exploratory post hoc analysis of free fatty acids (FFAs), bile acids (BAs), and ketone bodies in serum previously collected from a randomized, double-blind, placebo-controlled clinical trial evaluating the effects of one- and four-week consumption of 3.5 g/day RPS versus a placebo using two-way ANOVA adjusted by pFDR. Associations between week 4 changes in FFAs, BAs, and ketone bodies were assessed by Pearson's correlations. Results: RPS consumption reduced total FFAs relative to the placebo, including multiple unsaturated FFAs and octanedioic acid, with reductions in taurine- and glycine-conjugated secondary BAs also detected (q < 0.05). No changes in ketone bodies were observed (q > 0.05). Changes in 7-ketodeoxycholic acid (r = -0.595) and glycolithocholic acid (r = -0.471) were inversely correlated with treatment-induced reductions in FFAs for RPS but not the placebo, suggesting the effects were from the prebiotic. Shifts in β-hydroxybutyrate were further correlated with FFA changes in both treatments (q < 0.05). Conclusions: These findings demonstrate that low doses of RPS positively influence fatty acid metabolism in humans, reducing circulating levels of FFA and conjugated BAs.

Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese

It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days), Clostridia_UCG-014, RF39 (at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.IMPORTANCELow dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.

Orange Cookies with Type-4 Resistant Starch: Physical, Nutritional, and Sensorial Characteristics as Evaluated by Patients with Irritable Bowel Syndrome

A low-fermentable oligo-, di-, monosaccharide and polyol (low-FODMAP) diet for patients with irritable bowel syndrome (IBS) should include an adequate fiber source. Our aim was to formulate orange cookies using maize flour and type-4 resistant starch (RS4) from maize and to evaluate their properties and sensorial attributes by IBS patients. We prepared two formulations: 37.7% RS4 and 14.7% maize flour and a control with normal maize starch (MS) instead of RS4. We added orange juice and zest instead of water and evaluated their properties. The viscosity, water absorption capacity, and solubility were lower for RS4 than for MS. The width, thickness, L* and a* values of both cookies were comparable (p > 0.05), although RS4-C had a decreased b* value and higher hardness (90.6 vs. 80.1 N). The nutrient content was similar between RS4-C and MS-C, but the glycemic index of RS4-C was 63 compared to 95 of MS-C. According to IBS patients, the appearance, taste, hardness, overall quality, and perception of healthiness and nutritional value of both types of cookies were similarly high (p > 0.05). Panelists recommend the cookies. Therefore, RS4 cookies could be further investigated for their ability to improve bowel habits and re-equilibrate the microbiota of IBS patients.

Modulating butyric acid-producing bacterial community abundance and structure in the intestine of immunocompromised mice with neutral polysaccharides extracted from Codonopsis pilosula

Codonopsis pilosula, an important medicinal and edible plant in traditional Chinese medicine, is used widely as a tonifying herb for various immunodeficiency diseases. A neutral polysaccharide (CPPs-D1N1) was purified from C. pilosula, composed of fructose and glucose in a molar ratio of 97.28:2.72, with an average molecular weight of 5.985 kDa. Structural analysis revealed a backbone composed of →1)-β-D-Fruf-(2 → units with some β-D-Fruf-(2 → linkages. In a murine immunosuppression model induced by cyclophosphamide injection, oral treatment with C. pilosula polysaccharide was administered, investigating changes in gut microbiota during therapy. The polysaccharide modulated serum immunoglobulins (Ig-G, Ig-M), cytokines (IL-2, IL-6, TNFα), and spleen and thymus indices in immunodeficient mice. Additionally, functional gene primer sequencing enrichment methods revealed alterations in abundance, diversity, and structure of butyrate-producing bacterial populations in the gut, with primary differential genera identified as Butyribacter, Rumanococcus, Dysosmobacter, and Ruseburia. This study provides in vivo evidence supporting the beneficial effects of C. pilosula polysaccharide oral therapy in improving gut microbiota, particularly butyrate-producing bacteria, during treatment of immunosuppressive diseases.

Understanding the role of the human gut microbiome in overweight and obesity

The gut microbiome may be related to the prevalence of overweight and obesity, but high interindividual variability of the human microbiome complicates our understanding. Obesity often occurs concomitantly with micronutrient deficiencies that impair energy metabolism. Microbiota composition is affected by diet. Host-microbiota interactions are bidirectional. We propose three pathways whereby these interactions may modulate the gut microbiome and obesity: (1) ingested compounds or derivatives affecting small intestinal transit, endogenous secretions, digestion, absorption, microbiome balance, and gut barrier function directly affect host metabolism; (2) substrate availability affecting colonic microbial composition and contact with the gut barrier; and (3) microbial end products affecting host metabolism. The quantity/concentration, duration, and/or frequency (circadian rhythm) of changes in these pathways can alter the gut microbiome, disrupt the gut barrier, alter host immunity, and increase the risk of and progression to overweight and obesity. Host-specific characteristics (e.g., genetic variations) may further affect individual sensitivity and/or resilience to diet- and microbiome-associated perturbations in the colonic environment. In this narrative review, the effects of selected interventions, including fecal microbiota transplantation, dietary calorie restriction, dietary fibers and prebiotics, probiotics and synbiotics, vitamins, minerals, and fatty acids, on the gut microbiome, body weight, and/or adiposity are summarized to help identify mechanisms of action and research opportunities.

Role of short-chain fatty acids in host physiology

Short-chain fatty acids (SCFAs) are major metabolites produced by the gut microbiota through the fermentation of dietary fiber, and they have garnered significant attention due to their close association with host health. As important mediators between the gut microbiota and the host, SCFAs serve as energy substrates for intestinal epithelial cells and maintain homeostasis in host immune and energy metabolism by influencing host epigenetics, activating G protein-coupled receptors, and inhibiting pathogenic microbial infections. This review provides a comprehensive summary of SCFAs synthesis and metabolism and offering an overview of the latest research progress on their roles in protecting gut health, enhancing energy metabolism, mitigating diseases such as cancer, obesity, and diabetes, modulating the gut-brain axis and gut-lung axis, and promoting bone health.

Dietary fibre and metabolic health: A clinical primer

Dietary fibres consist of a heterogeneous group of carbohydrate polymers which resist digestion by human gastrointestinal enzymes. Consumption of dietary fibre has been linked with innumerable health benefits encompassing the foundational pillars of metabolic health from obesity to hypertension, dyslipidaemia, and type 2 diabetes mellitus (T2DM), with many of these benefits linked with metabolites produced by the fermentation of fibre by gut microbes [1]. The potential of dietary fibre to provide a safe and effective nonpharmacologic complementary tool with which to combat the evolving consequences of the obesity epidemic has recently garnered tremendous attention in both medical literature and lay media alike. HIGHLIGHTS: Consumption of dietary fibre has been linked with innumerable health benefits encompassing the foundational pillars of metabolic health with many of these benefits linked with metabolites produced by the fermentation of fibre by gut microbes At the present time clinicians are faced with an impossible task in which there is rapidly mounting evidence for dietary fibres advancing metabolic health, but little practical options for healthcare providers other than to simply recommend patients consume more fibre. Benefits of fibre intake may perhaps be maximised in an individual by matching specific fibre consumption with existing microbial functional characteristics If dietary fibres could be demonstrated to act as successful adjuncts to sustain or improve standard of care therapies or even alleviate common gastrointestinal side effects associated with current treatments, they would be an invaluable tool in our metabolic health armamentarium. Neither Dr. Madsen or I have any financial conflicts of interest pertinent to the contents of this manuscript.

Predicting metabolite response to dietary intervention using deep learning

Due to highly personalized biological and lifestyle characteristics, different individuals may have different metabolite responses to specific foods and nutrients. In particular, the gut microbiota, a collection of trillions of microorganisms living in the gastrointestinal tract, is highly personalized and plays a key role in the metabolite responses to foods and nutrients. Accurately predicting metabolite responses to dietary interventions based on individuals' gut microbial compositions holds great promise for precision nutrition. Existing prediction methods are typically limited to traditional machine learning models. Deep learning methods dedicated to such tasks are still lacking. Here we develop a method McMLP (Metabolite response predictor using coupled Multilayer Perceptrons) to fill in this gap. We provide clear evidence that McMLP outperforms existing methods on both synthetic data generated by the microbial consumer-resource model and real data obtained from six dietary intervention studies. Furthermore, we perform sensitivity analysis of McMLP to infer the tripartite food-microbe-metabolite interactions, which are then validated using the ground-truth (or literature evidence) for synthetic (or real) data, respectively. The presented tool has the potential to inform the design of microbiota-based personalized dietary strategies to achieve precision nutrition.

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.

Towards a personalized prediction, prevention and therapy of insomnia: gut microbiota profile can discriminate between paradoxical and objective insomnia in post-menopausal women

Background

Insomnia persists as a prevalent sleep disorder among middle-aged and older adults, significantly impacting quality of life and increasing susceptibility to age-related diseases. It is classified into objective insomnia (O-IN) and paradoxical insomnia (P-IN), where subjective and objective sleep assessments diverge. Current treatment regimens for both patient groups yield unsatisfactory outcomes. Consequently, investigating the neurophysiological distinctions between P-IN and O-IN is imperative for devising novel precision interventions aligned with primary prediction, targeted prevention, and personalized medicine (PPPM) principles.Working hypothesis and methodology.Given the emerging influence of gut microbiota (GM) on sleep physiology via the gut-brain axis, our study focused on characterizing the GM profiles of a well-characterized cohort of 96 Italian postmenopausal women, comprising 54 insomniac patients (18 O-IN and 36 P-IN) and 42 controls, through 16S rRNA amplicon sequencing. Associations were explored with general and clinical history, sleep patterns, stress, hematobiochemical parameters, and nutritional patterns.

Results

Distinctive GM profiles were unveiled between O-IN and P-IN patients. O-IN patients exhibited prominence in the Coriobacteriaceae family, including Collinsella and Adlercreutzia, along with Erysipelotrichaceae, Clostridium, and Pediococcus. Conversely, P-IN patients were mainly discriminated by Bacteroides, Staphylococcus, Carnobacterium, Pseudomonas, and respective families, along with Odoribacter.

Conclusions

These findings provide valuable insights into the microbiota-mediated mechanism of O-IN versus P-IN onset. GM profiling may thus serve as a tailored stratification criterion, enabling the identification of women at risk for specific insomnia subtypes and facilitating the development of integrated microbiota-based predictive diagnostics, targeted prevention, and personalized therapies, ultimately enhancing clinical effectiveness.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00369-1.

Journey of dietary fiber along the gastrointestinal tract: role of physical interactions, mucus, and biochemical transformations

Dietary fiber-rich foods have been associated with numerous health benefits, including a reduced risk of cardiovascular and metabolic diseases. Harnessing the potential to deliver positive health outcomes rests on our understanding of the underlying mechanisms that drive these associations. This review addresses data and concepts concerning plant-based food functionality by dissecting the cascade of physical and chemical digestive processes and interactions that underpin these physiological benefits. Functional transformations of dietary fiber along the gastrointestinal tract from the stages of oral processing and gastric emptying to intestinal digestion and colonic fermentation influence its capacity to modulate digestion, transit, and commensal microbiome. This analysis highlights the significance, limitations, and challenges in decoding the complex web of interactions to establish a coherent framework connecting specific fiber components' molecular and macroscale interactions across multiple length scales within the gastrointestinal tract. One critical area that requires closer examination is the interaction between fiber, mucus barrier, and the commensal microbiome when considering food structure design and personalized nutritional strategies for beneficial physiologic effects. Understanding the response of specific fibers, particularly concerning an individual's physiology, will offer the opportunity to exploit these functional characteristics to elicit specific, symptom-targeting effects or use fiber types as adjunctive therapies.

Microbiota-Short Chain Fatty Acid Relationships Underlie Clinical Heterogeneity and Identify Key Microbial Targets in Irritable Bowel Syndrome (IBS)

Background

Identifying microbial targets in irritable bowel syndrome (IBS) and other disorders of gut-brain interaction (DGBI) is challenging due to the dynamic nature of microbiota-metabolite-host interactions. SCFA are key microbial metabolites that modulate intestinal homeostasis and may influence IBS pathophysiology. We aimed to assess microbial features associated with short chain fatty acids (SCFA) and determine if features varied across IBS subtypes and endophenotypes. Among 96 participants who were screened, 71 completed the study. We conducted in-depth investigations of stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across clinical groups. To explore relationships between microbially-derived SCFA and IBS traits, we compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption.

Results

Overall stool microbiome composition and individual taxa abundances differed between clinical groups. Microbes-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that may drive subtype-specific microbially-mediated mechanisms. Strongest microbe-SCFA associations were observed in IBS-D and several SCFA-producing species surprisingly demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM.

Conclusion

Keystone taxa responsible for SCFA production differ according to IBS subtype and traits and the IBS microbiome is characterized by reduced functional redundancy. Differences in microbial substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS and other DGBI.

Evaluating the Effects of Corn Flour Product Consumption on Cardiometabolic Outcomes and the Gut Microbiota in Adults with Elevated Cholesterol: A Randomized Crossover

BACKGROUND

Consumption of whole grains is associated with a reduction in chronic diseases and offers benefits for cardiovascular health and metabolic regulation. The relationship between whole-grain corn and corn bran with the gut microbiota (GM) remains an area of growing interest, particularly regarding their influence on cardiometabolic health.

OBJECTIVES

To investigate the effects of different corn flours on cardiometabolic outcomes and GM changes in adults with elevated low-density lipoprotein cholesterol (LDL cholesterol) concentrations.

METHODS

In this crossover study, 36 adults with LDL cholesterol above 110 mg/dL consumed 48 g/d of 3 corn flour types for 4 wk: whole-grain corn meal, refined corn meal (RCM), and a blend of RCM and corn bran (RCM + B). We assessed the impact on cardiometabolic markers [LDL cholesterol, high-density lipoprotein cholesterol (HDL cholesterol), total cholesterol, and triglycerides)] and GM composition and estimated function. Statistical analyses included mixed-effects modeling and responder (>5% decrease in LDL cholesterol) analysis to evaluate changes in GM related to lipid profile improvements.

RESULTS

Of the 3 corn flour types, only RCM + B significantly decreased LDL cholesterol over time (-10.4 ± 3.6 mg/dL, P = 0.005) and marginally decreased total cholesterol (-9.2 ± 3.9 mg/dL, P = 0.072) over time. There were no significant effects on HDL cholesterol or triglyceride concentrations. No significant changes were observed in GM alpha diversity, whereas beta diversity metrics indicated individual variability. Two genera, unclassified Lachnospiraceae and Agathobaculum (Padj ≤ 0.096), differed significantly by treatment, but only Agathobaculum remained significantly elevated in the whole-grain corn meal, compared to RCM and RCM + B, after adjustment for multiple comparisons.

CONCLUSIONS

The type of corn flour, particularly RCM + B, notably influenced LDL cholesterol concentrations in adults with elevated LDL cholesterol. This study suggests that incorporating milled fractions (e.g., bran) of whole-grain corn with refined corn flour may be a viable alternative to supplementing manufactured grain products with isolated or synthetic fibers for improved metabolic health. This trial was registered at clinicaltrials.gov as NCT03967990.

The mechanisms in the gut microbiota regulation and type 2 diabetes therapeutic activity of resistant starches

Resistant starch (RS) can potentially prevent type 2 diabetes through the modulation of intestinal microbiota and microbial metabolites. Currently, it has been wildly noted that altering the intestinal microbial composition and short-chain fatty acids levels can achieve therapeutic effects, although the specific mechanisms were rarely elucidated. This review systematically explores the structural characteristics of different RS, analyzes the cross-feeding mechanism utilized by intestinal microbiota, and outlines the pathways and targets of butyrate, a primary microbial metabolite, for treating diabetes. Different RS types may have a unique impact on microbiota composition and their cross-feeding, thus exploring regulatory mechanisms of RS on diabetes through intestinal flora interaction and their metabolites could pave the way for more effective treatment outcomes for host health. Furthermore, by understanding the mechanisms of strain-level cross-feeding and metabolites of RS, precise dietary supplementation methods targeted at intestinal composition and metabolites can be achieved to improve T2DM.

Investigating the response of the butyrate production potential to major fibers in dietary intervention studies

Interventions involving dietary fibers are known to benefit host health. A leading contribution of gut microbiota is commonly recognized with production of short chain fatty acids (SCFA) suspected to play a key role. However, the detailed mechanisms are largely unknown, and apart from a well-described bifidogenic effect of some fibers, results for other bacterial taxa are often incongruent between studies. We performed pooled analyses of 16S rRNA gene data derived from intervention studies (n = 14) based on three fibers, namely, inulin-type fructans (ITF), resistant starch (RS), and arabinoxylan-oligosaccharides (AXOS), harmonizing the bioinformatics workflow to reveal taxa stimulated by those substrates, specifically focusing on the SCFA-production potential. The results showed an increased butyrate production potential after ITF (p < 0.05) and RS (p < 0.1) treatment via an increase in bacteria exhibiting the enzyme butyryl-CoA:acetate CoA-transferase (but) that was governed by Faecalibacterium, Anaerostipes (ITF) and Agathobacter (RS) respectively. AXOS did not promote an increase in butyrate producers, nor were pathways linked to propionate production stimulated by any intervention. A bifidogenic effect was observed for AXOS and ITF, which was only partly associated with the behavior of but-containing bacteria and largely represented a separate response. Low and high Ruminococcus abundances pre-intervention for ITF and RS, respectively, promoted an increase in but-containing taxa (p < 0.05) upon interventions, whereas initial Prevotella abundance was negatively associated with responses of butyrate producers for both fibers. Collectively, our data demonstrate targeted stimulation of specific taxa by individual fibers increasing the potential to synthesize butyrate, where gut microbiota composition pre-intervention strongly controlled outcomes.

Dual Regulation Mechanism of Obesity: DNA Methylation and Intestinal Flora

Obesity is a multifactorial chronic inflammatory metabolic disorder, with pathogenesis influenced by genetic and non-genetic factors such as environment and diet. Intestinal microbes and their metabolites play significant roles in the occurrence and development of obesity by regulating energy metabolism, inducing chronic inflammation, and impacting intestinal hormone secretion. Epigenetics, which involves the regulation of host gene expression without changing the nucleotide sequence, provides an exact direction for us to understand how the environment, lifestyle factors, and other risk factors contribute to obesity. DNA methylation, as the most common epigenetic modification, is involved in the pathogenesis of various metabolic diseases. The epigenetic modification of the host is induced or regulated by the intestinal microbiota and their metabolites, linking the dynamic interaction between the microbiota and the host genome. In this review, we examined recent advancements in research, focusing on the involvement of intestinal microbiota and DNA methylation in the etiology and progression of obesity, as well as potential interactions between the two factors, providing novel perspectives and avenues for further elucidating the pathogenesis, prevention, and treatment of obesity.

Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations

Fecal metabolites effectively discriminate inflammatory bowel disease (IBD) and show differential associations with diet. Metabolomics and AI-based models, including explainable AI (XAI), play crucial roles in understanding IBD. Using datasets from the UK Biobank and the Human Microbiome Project Phase II IBD Multi'omics Database (HMP2 IBDMDB), this study uses multiple machine learning (ML) classifiers and Shapley additive explanations (SHAP)-based XAI to prioritize plasma and fecal metabolites and analyze their diet correlations. Key findings include the identification of discriminative metabolites like glycoprotein acetyl and albumin in plasma, as well as nicotinic acid metabolites andurobilin in feces. Fecal metabolites provided a more robust disease predictor model (AUC [95%]: 0.93 [0.87-0.99]) compared to plasma metabolites (AUC [95%]: 0.74 [0.69-0.79]), with stronger and more group-differential diet-metabolite associations in feces. The study validates known metabolite associations and highlights the impact of IBD on the interplay between gut microbial metabolites and diet.

Resistant starch and tannic acid synergistically ameliorated dextran sulfate sodium-induced ulcerative colitis, particularly in the distal colon

We previously confirmed that tannic acid could delay the metabolism of resistant starch in vitro, which suggested that tannic acid might deliver resistant starch to the distal colon in vivo. Accordingly, co-supplementation of resistant starch and tannic acid might be beneficial for keeping the distal colon healthy. Thus, this study compared the effects of resistant starch, tannic acid and their mixtures on dextran sulfate sodium (DSS)-induced ulcerative colitis in mice. It was found that the mixtures had a more profound effect on ameliorating DSS-induced ulcerative colitis than resistant starch or tannic acid. In particular, the mixtures reversed the histology damage of the distal colon induced by DSS, while resistant starch or tannic acid alone did not. The mixtures also had a stronger ability to resist oxidative stress and inhibit inflammation in the distal colon. These results suggested that resistant starch and tannic acid synergistically alleviated DSS-induced ulcerative colitis, particularly in the distal colon. On the other hand, DSS decreased the production of short-chain fatty acids and induced significant microbial disorder, while the administration of resistant starch, tannic acid and their mixtures reversed the above shifts caused by DSS. In particular, the mixtures exhibited stronger prebiotic activity, as indicated by the microbial composition and production of short-chain fatty acids. Therefore, it was inferred that tannic acid delivered resistant starch to the distal colon of mice, and thus the mixtures had stronger prebiotic activity. As a result, the mixtures effectively alleviated ulcerative colitis in the whole colon.

The branching ratio of enzymatically synthesized α-glucans impacts microbiome and metabolic outcomes of in vitro fecal fermentation

The aim of this study was to evaluate the impacts of enzymatically synthesized α-glucans possessing α-1,4- and α-1,6-glucose linkages, and varying in branching ratio, on colonic microbiota composition and metabolic function. Four different α-glucans varying in branching ratio were synthesized by amylosucrase from Neisseria polysaccharea and glycogen branching enzyme from Rhodothermus obamensis. The branching ratios were found to range from 0 % to 2.8 % using GC/MS. In vitro fecal fermentation analyses (n = 8) revealed that the branching ratio dictates the short-chain fatty acid (SCFA) generation by fecal microbiota. Specifically, slightly branched (0.49 %) α-glucan resulted in generation of significantly (P < 0.05) higher amounts of propionate, compared to more-branched counterparts. In addition, the amount of butyrate generated from this α-glucan was statistically (P > 0.05) indistinguishable than those observed in resistant starches. 16S rRNA sequencing revealed that enzymatically synthesized α-glucans stimulated Lachnospiraceae and Ruminococcus related OTUs. Overall, the results demonstrated metabolic function of colonic microbiota can be manipulated by altering the branching ratio of enzymatically synthesized α-glucans, providing insights into specific structure-function relationships between dietary fibers and the colonic microbiome. Furthermore, the slightly branched α-glucans could be used as functional carbohydrates to stimulate the beneficial microbiota and SCFAs in the colon.

Dichotomous effect of dietary fiber in pediatrics: a narrative review of the health benefits and tolerance of fiber

Dietary fibers are associated with favorable gastrointestinal, immune, and metabolic health outcomes when consumed at sufficient levels. Despite the well-described benefits of dietary fibers, children and adolescents continue to fall short of daily recommended levels. This gap in fiber intake (i.e., "fiber gap") might increase the risk of developing early-onset pediatric obesity and obesity-related comorbidities such as type 2 diabetes mellitus into adulthood. The structure-dependent physicochemical properties of dietary fiber are diverse. Differences in solubility, viscosity, water-holding capacity, binding capability, bulking effect, and fermentability influence the physiological effects of dietary fibers that aid in regulating appetite, glycemic and lipidemic responses, and inflammation. Of growing interest is the fermentation of fibers by the gut microbiota, which yields both beneficial and less favorable end-products such as short-chain fatty acids (e.g., acetate, propionate, and butyrate) that impart metabolic and immunomodulatory properties, and gases (e.g., hydrogen, carbon dioxide, and methane) that cause gastrointestinal symptoms, respectively. This narrative review summarizes (1) the implications of fibers on the gut microbiota and the pathophysiology of pediatric obesity, (2) some factors that potentially contribute to the fiber gap with an emphasis on undesirable gastrointestinal symptoms, (3) some methods to alleviate fiber-induced symptoms, and (4) the therapeutic potential of whole foods and commonly marketed fiber supplements for improved health in pediatric obesity.

Beneficial Effects of Synbiotics on the Gut Microbiome in Individuals with Low Fiber Intake: Secondary Analysis of a Double-Blind, Randomized Controlled Trial

Insufficient dietary fiber intake can negatively affect the intestinal microbiome and, over time, may result in gut dysbiosis, thus potentially harming overall health. This randomized controlled trial aimed to improve the gut microbiome of individuals with low dietary fiber intake (<25 g/day) during a 7-week synbiotic intervention. The metabolically healthy male participants (n = 117, 32 ± 10 y, BMI 25.66 ± 3.1 kg/m2) were divided into two groups: one receiving a synbiotic supplement (Biotic Junior, MensSana AG, Forchtenberg, Germany) and the other a placebo, without altering their dietary habits or physical activity. These groups were further stratified by their dietary fiber intake into a low fiber group (LFG) and a high fiber group (HFG). Stool samples for microbiome analysis were collected before and after intervention. Statistical analysis was performed using linear mixed effects and partial least squares models. At baseline, the microbiomes of the LFG and HFG were partially separated. After seven weeks of intervention, the abundance of SCFA-producing microbes significantly increased in the LFG, which is known to improve gut health; however, this effect was less pronounced in the HFG. Beneficial effects on the gut microbiome in participants with low fiber intake may be achieved using synbiotics, demonstrating the importance of personalized synbiotics.