Dietary Fiber and the Human Gut Microbiota: Application of Evidence Mapping Methodology

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.

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.

Dietary Fiber in Inflammatory Bowel Disease: Are We Ready to Change the Paradigm?

Accumulating evidence from pre-clinical and clinical studies demonstrate the benefit of dietary fibers for inflammatory bowel disease (IBD). However, the majority of patients avoid or limit their consumption to manage their symptoms during the active and remission phases, although limited research supports these long-term dietary habits. Although recent evidence-based dietary guidelines highlight the importance of promoting an adequate intake of dietary fiber in IBD patients, intervention trials have not yet clearly clarified the quality and quantity of dietary fiber that should be consumed to be equally tolerated by and provide benefit for patients with IBD. This narrative review describes dietary fibers and their characteristics, analyzes the real-word studies on the impact of dietary fiber consumption in IBD in different clinical settings, and concludes with potential future directions in fiber research, focusing on the real-world needs of characterizing the consumption of fiber-rich foods and promoting their adequate intake.

Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers

Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.

Exploring the Role of Inulin in Targeting the Gut Microbiota: An Innovative Strategy for Alleviating Colonic Fibrosis Induced By Irradiation

The use of radiation therapy to treat pelvic and abdominal cancers can lead to the development of either acute or chronic radiation enteropathy. Radiation-induced chronic colonic fibrosis is a common gastrointestinal disorder resulting from the above radiation therapy. In this study, we establish the efficacy of inulin supplements in safeguarding against colonic fibrosis caused by irradiation therapy. Studies have demonstrated that inulin supplements enhance the proliferation of bacteria responsible to produce short-chain fatty acids (SCFAs) and elevate the levels of SCFAs in feces. In a mouse model of chronic radiation enteropathy, the transplantation of gut microbiota and its metabolites from feces of inulin-treated mice were found to reduce colonic fibrosis in validation experiments. Administering inulin-derived metabolites from gut microbiota led to a notable decrease in the expression of genes linked to fibrosis and collagen production in mouse embryonic fibroblast cell line NIH/3T3. In the cell line, inulin-derived metabolites also suppressed the expression of genes linked to the extracellular matrix synthesis pathway. The results indicate a novel and practical approach to safeguarding against chronic radiation-induced colonic fibrosis.

A host-microbial metabolite interaction gut-on-a-chip model of the adult human intestine demonstrates beneficial effects upon inulin treatment of gut microbiome

Background: The gut and its microbiome have a major impact on many aspects of health and are therefore also an attractive target for drug- or food-based therapies. Here, we report on the added value of combining a microbiome screening model, the i-screen, with fresh intestinal tissue explants in a microfluidic gut-on-a-chip model, the Intestinal Explant Barrier Chip (IEBC). Methods: Adult human gut microbiome (fecal pool of 6 healthy donors) was cultured anaerobically in the i-screen platform for 24 h, without and with exposure to 4 mg/mL inulin. The i-screen cell-free culture supernatant was subsequently applied to the luminal side of adult human colon tissue explants (n = 3 donors), fixed in the IEBC, for 24 h and effects were evaluated. Results: The supplementation of the media with inulin promoted the growth of Anaerostipes, Bifidobacterium, Blautia, and Collinsella in the in vitro i-screen, and triggered an elevated production of butyrate by the microbiota. Human colon tissue exposed to inulin-treated i-screen cell-free culture supernatant or control i-screen cell-free culture supernatant with added short-chain fatty acids (SCFAs) showed improved tissue barrier integrity measured by a 28.2%-34.2% reduction in FITC-dextran 4000 (FD4) leakage and 1.3 times lower transport of antipyrine. Furthermore, the release of pro-inflammatory cytokines IL-1β, IL-6, IL-8, and TNF-α was reduced under these circumstances. Gene expression profiles confirmed these findings, but showed more profound effects for inulin-treated supernatant compared to SCFA-supplemented supernatant. Conclusion: The combination of i-screen and IEBC facilitates the study of complex intestinal processes such as host-microbial metabolite interaction and gut health.

Food sources of fiber and micronutrients of concern among infants and young children in Lebanon: a national cross-sectional study

BACKGROUND

Intakes of fiber, iron, zinc, calcium, vitamin D, vitamin A, and folate were shown to be low in a substantial proportion of infants and children in Lebanon. The study aims to identify the top food sources of fiber, iron, zinc, calcium, vitamin D, vitamin A, and folate amongst infants and young children in Lebanon and to evaluate the evolution of food sources of these nutrients from the beginning of the complementary feeding journey up until the age of 47.9 months.

METHODS

A national cross-sectional survey was conducted in 2012 as part of the "Early Life Nutrition and Health in Lebanon" project using stratified cluster sampling. Dietary intakes for infants and young children aged 6-47.9 months (n = 763) were assessed using 24- Hour Dietary Recall. Food items were categorized into food groups and the percent contribution of each food group to nutrient intakes was determined to identify the top food sources of fiber and selected micronutrients for three age groups: 6-11.9 m (infants), 12-23.9 m (toddlers), and 24-47.9 m (preschoolers).

RESULTS

The top food source of fiber was vegetables among children aged 6-47.9 months. Among infants and toddlers, infant/young child formula was the main contributor to iron, zinc, calcium, vitamin D, vitamin A, and folate intakes. Baby cereals also contributed to around 14% of iron intakes among infants. Among preschoolers, meat and fish contributed to 13% of iron intakes and 29% of zinc intakes, while cow's milk was the major contributor of calcium (41%), vitamin D (81%) and vitamin A (25%) intakes. Sweetened beverages and sweet bakery were also ranked among the major food sources contributing to substantial intakes of key nutrients, including fiber, iron, zinc, calcium, vitamin A, and folate among infants, toddlers, and preschoolers.

CONCLUSIONS

In addition to milk sources, vegetables, beans and legumes, breads, meats, and rice and pasta, sweet bakery and sweetened beverages have contributed to intakes of key nutrients from early ages. This calls for implementing initiatives and designing approaches to support nutrition education and improve nutrient intakes in infancy and early childhood.

Role of Type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection

Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.

Gut microbiome: New perspectives for type 2 diabetes prevention and treatment

Type 2 diabetes mellitus (T2DM), which is distinguished by increased glucose levels in the bloodstream, is a metabolic disease with a rapidly increasing incidence worldwide. Nevertheless, the etiology and characteristics of the mechanism of T2DM remain unclear. Recently, abundant evidence has indicated that the intestinal microbiota is crucially involved in the initiation and progression of T2DM. The gut microbiome, the largest microecosystem, engages in material and energy metabolism in the human body. In this review, we concentrated on the correlation between the gut flora and T2DM. Meanwhile, we summarized the pathogenesis involving the intestinal flora in T2DM, as well as therapeutic approaches aimed at modulating the gut microbiota for the management of T2DM. Through the analysis presented here, we draw attention to further exploration of these research directions.

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

Background

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 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 2564 fecal samples from 538 subjects across all interventions.

Results

Short-term increases in dietary fiber consumption resulted in highly consistent gut microbiome responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (versus 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 (increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

Conclusions

Our study is an example of the power of synthesizing and reanalyzing 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 as well as the particular taxa that respond to increased fiber.

Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans

Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of <0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.

Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans

Next generation amplicon sequencing has created a plethora of data from human microbiomes. The accessibility to this scientific data and its corresponding metadata is important for its reuse, to allow for new discoveries, verification of published results, and serving as path for reproducibility. Dietary fiber consumption has been associated with a variety of health benefits that are thought to be mediated by gut microbiota. To enable direct comparisons of the response of the gut microbiome to fiber, we obtained 16S rRNA sequencing data and its corresponding metadata from 11 fiber intervention studies for a total of 2,368 samples. We provide curated and pre-processed genetic data and common metadata for comparison across the different studies.

Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs

Background

Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut microbiome, microbial functions, and metabolite profiles post dietary interventions have been underexplored. How long these outcomes require to reach a steady-state, how they relate to one another, and their impact on host physiological changes are largely unknown. To address these unknowns, we collected longitudinal fecal samples following an abrupt dietary change in healthy adult beagles (n = 12, age: 5.16 ± 0.87 year, BW: 13.37 ± 0.68 kg) using a crossover design. All dogs were fed a kibble diet (control) from d1-14, and then fed that same diet supplemented with fiber (HFD) or a protein-rich canned diet (CD) from d15-27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for metabolite and microbiome assessment. Fecal microbial diversity and composition, metabolite profiles, and microbial functions dramatically diverged and stabilized within a few days (2 d for metabolites; 6 d for microbiota) after dietary interventions. Fecal acetate, propionate, and total short-chain fatty acids increased after change to HFD, while fecal isobutyrate, isovalerate, total branched-chain fatty acids, phenol, and indole increased after dogs consumed CD. Relative abundance of ~ 100 bacterial species mainly belonging to the Firmicutes, Proteobacteria, and Actinobacteria phyla increased in HFD. These shifts in gut microbiome diversity and composition were accompanied by functional changes. Transition to HFD led to increases in the relative abundance of KEGG orthology (KO) terms related to starch and sucrose metabolism, fatty acid biosynthesis, and amino sugar and nucleotide sugar metabolism, while transition to CD resulted in increased relative abundance of KO terms pertaining to inositol phosphate metabolism and sulfur metabolism. Significant associations among fecal microbial taxa, KO terms, and metabolites were observed, allowing for high-accuracy prediction of diet group by random forest analysis.

Conclusions

Longitudinal sampling and a multi-modal approach to characterizing the gastrointestinal environment allowed us to demonstrate how drastically and quickly dietary changes impact the fecal microbiome and metabolite profiles of dogs following an abrupt dietary change and identify key microbe-metabolite relationships that allowed for treatment prediction.

Galacto-oligosaccharides and Xylo-oligosaccharides Affect Meat Flavor by Altering the Cecal Microbiome, Metabolome, and Transcriptome of Chickens

Studies have shown that prebiotics can affect meat quality; however, the underlying mechanisms remain poorly understood. This study aimed to investigate whether prebiotics affect the flavor of chicken meat via the gut microbiome and metabolome. The gut content was collected from chickens fed with or without prebiotics (galacto-oligosaccharides or xylo-oligosaccharides) and subjected to microbiome and metabolome analyses, whereas transcriptome sequencing was performed using chicken breast. Prebiotic supplementation yielded a slight improvement that was not statistically significant in the growth and production performance of chickens. Moreover, treatment with prebiotics promoted fat synthesis and starch hydrolysis, thus increasing meat flavor by enhancing lipase and α-amylase activity in the blood of broiler chickens. The prebiotics altered the proportions of microbiota in the gut at different levels, especially microbiota in the phyla Bacteroidetes and Firmicutes, such as members of the Alistipes, Bacteroides, and Faecalibacterium genera. Furthermore, the prebiotics altered the content of cecal metabolites related to flavor substances, including 8 types of lysophosphatidylcholine (lysoPC) and 4 types of amino acid. Differentially expressed genes (DEGs) induced by prebiotics were significantly involved in fatty acid accumulation processes, such as lipolysis in adipocytes and the adipocytokine signaling pathway. Changes in gut microbiota were correlated with metabolites, for example, Bacteroidetes and Firmicutes were positively and negatively correlated with lysoPC, respectively. Finally, DEGs interacted with cecal metabolites, especially meat-flavor-related amino acids and their derivatives. The findings of this study integrated and incorporated associations among the gut microbiota, metabolites, and transcriptome, which suggests that prebiotics affect the flavor of chicken meat.

The Pulsed Electric Field Assisted-Extraction Enhanced the Yield and the Physicochemical Properties of Soluble Dietary Fiber From Orange Peel

The study aimed to investigate the effects of pulsed electric field (PEF)-assisted extraction on the yield, physicochemical properties, and structure of soluble dietary fiber (SDF) from orange peel. The results showed that the optinal parameters of PEF assisted extraction SDF was temperature of 45^oC with the electric field intensity of 6.0 kV/cm, pulses number of 30, and time of 20min and SDF treated with PEF showed the higher water solubility, water-holding and oil-holding capacity, swelling capacity, emulsifying activity, emulsion stability, foam stability and higher binding capacity for Pb²⁺, As³⁺, Cu²⁺, and higher which resulted from the higher viscosity due to PEF treatment. Compared with the untreated orange peel, the SDF obtained with PEF exhibited stronger antioxidant activities, which was due to its smaller molecular weight (189 vs. 512 kDa). In addition, scanning electron micrograph images demonstrated that the surface of PEF-SDF was rough and collapsed. Overall, it was suggested that PEF treatment could improve the physicochemical properties of SDF from the orange peel and would be the potential extraction technology with high efficiency.

Bypassing the Gut-Lung Axis via Microbial Metabolites: Implications for Chronic Respiratory Diseases

The gut microbiome engages in constant interactions with the immune system, laying down the fundamentals of what we perceive as health or disease. The gut microbiota acts locally in the intestines and distally in other organs, such as the lungs. This influence (termed “the gut–lung axis”) constitutes the basis for harnessing the microbiome to prevent or treat chronic respiratory diseases. Within this context, two approaches gained the most attention: the diet interventions (which shape the microbiome) and the probiotics (which exert beneficial effects directly on the host). Microbial products, which constitute a means of communication along the gut–lung axis, are only now emerging as a new class of potential therapeutics. Here, we provide a comprehensive overview of microbial products active in the airways, describe the immunological mechanisms they trigger, and discuss their clinical advantages and pitfalls.

The role of bacterial translocation in sepsis: a new target for therapy

Sepsis is a leading cause of death in critically ill patients, primarily due to multiple organ failures. It is associated with a systemic inflammatory response that plays a role in the pathogenesis of the disease. Intestinal barrier dysfunction and bacterial translocation (BT) play pivotal roles in the pathogenesis of sepsis and associated organ failure. In this review, we describe recent advances in understanding the mechanisms by which the gut microbiome and BT contribute to the pathogenesis of sepsis. We also discuss several potential treatment modalities that target the microbiome as therapeutic tools for patients with sepsis.

The Protective Effects of Inulin-Type Fructans Against High-Fat/Sucrose Diet-Induced Gestational Diabetes Mice in Association With Gut Microbiota Regulation

Background

Inulin-type fructans (ITF) have been used as prebiotics to alleviate glucose and lipid metabolism disorders. However, few studies evaluated the microbial mechanism of ITF in improving maternal metabolic status during pregnancy.

Methods

C57BL/6J mice were fed a high-fat/sucrose diet (HFD) for 4 weeks before and throughout pregnancy to induce a model of gestational diabetes mellitus (GDM). Body weight, glycolipid metabolic parameters, and fecal short-chain fatty acids (SCFAs) were assessed in the experimental process. The effects of ITF on the fecal microbiota were analyzed by 16S rRNA gene amplicon sequencing.

Results

Pregnant HFD-fed mice displayed significant insulin resistance and dyslipidemia. ITF (3.33 g/kg/day) treatment improved glucose and lipid metabolism disorder parameters in HFD-induced GDM mice and alleviated fat accumulation and glucose intolerance. The alpha diversity of the gut microbial community was increased in ITF mice, while the beta diversity returned to the level of normal chow diet (NCD) mice. Interestingly, Verrucomicrobia, Bifidobacterium, and Akkermansia were obviously enriched, while Dubosiella was obviously lessened after inulin treatment. Further analysis indicated that Dubosiella was positively correlated with markers of glycolipid metabolism disorders, whereas the ITF-supplemented diet partially reversed the changes.

Conclusion

Our results suggest that the ITF treatment may alleviate glucose and lipid metabolism disorders with the mediation of gut microbiota.

Baicalin attenuate diet-induced metabolic syndrome by improving abnormal metabolism and gut microbiota

In this work, we examined whether baicalin (BC), a bioactive flavonoid in Scutellaria baicalensis Georgi, can reduce high-fat diet (HFD)-induced metabolic syndrome (MetS) in mice. The UPLC-QTOF/MS was used for metabolome profiles analysis, and an analysis of bacterial 16S rDNA in feces was used to examine the effects of BC on gut microbiota composition. Our results showed that BC (400 mg/kg) could reduce the body weight gain, decrease hepatic fat accumulation and abnormal blood lipids, and increase insulin sensitivity after 8 weeks of treatment. BC could reverse the alteration of 7 metabolites induced by HFD and the metabolic pathways responsive to BC intervention including citrate cycle, alanine, aspartate and glutamate metabolism, glycerophospholipid metabolism, and aminoacyl-tRNA biosynthesis. 16S rDNA analysis demonstrated that BC altered the composition and function of gut microbiota in MetS mice. Notably, we found that the change in succinic acid was negatively associated with the changes in Bacteroides and Sutterella, and positively associated with the change in Mucispirillum. Moreover, we confirmed that succinic acid displayed a metabolic protective effect on MetS mice. The antibiotic treatment verified that BC exerts metabolic protection through gut microbiota. Our findings suggested BC may be a potential therapeutic drug to ameliorate diet induced MetS and gut microbiome may be a novel mechanistic target of BC for treatment of MetS.

Current Research on the Effects of Non-Digestible Carbohydrates on Metabolic Disease

Metabolic diseases (MDs), including cardiovascular diseases (CVDs) and diabetes, occur when the body’s normal metabolic processes are disrupted. Behavioral risk factors such as obesity, physical inactivity, and dietary habits are strongly associated with a higher risk of MD. However, scientific evidence strongly suggests that balanced, healthy diets containing non-digestible carbohydrates (NDCs), such as dietary fiber and resistant starch, can reduce the risk of developing MD. In particular, major properties of NDCs, such as water retention, fecal bulking, viscosity, and fermentation in the gut, have been found to be important for reducing the risk of MD by decreasing blood glucose and lipid levels, increasing satiety and insulin sensitivity, and modifying the gut microbiome. Short chain fatty acids produced during the fermentation of NDCs in the gut are mainly responsible for improvement in MD. However, the effects of NDCs are dependent on the type, source, dose, and duration of NDC intake, and some of the mechanisms underlying the efficacy of NDCs on MD remain unclear. In this review, we briefly summarize current studies on the effects of NDCs on MD and discuss potential mechanisms that might contribute to further understanding these effects.

Gut Microbiome Signatures Are Predictive of Cognitive Impairment in Hypertension Patients—A Cohort Study

Growing evidence has demonstrated that hypertension was associated with dysbiosis of intestinal flora. Since intestinal microbes could critically regulate neurofunction via the intestinal–brain axis, the study aimed to reveal the role and prediction value of intestinal flora alteration in hypertension-associated cognitive impairment. A cohort of 97 participants included 63 hypertension patients and 34 healthy controls. The structure of intestinal flora was analyzed by V3–V4 16S rRNA amplicon sequencing. The cognitive function was assessed using the Montreal Cognitive Assessment (MoCA) scale, and 31 patients were considered to have cognitive impairment (MoCA &lt; 26). Patients with cognitive impairment had considerable alterations in intestinal flora structure, composition, and function compared with normal-cognitive patients. In particular, the abundance of LPS-containing taxa (Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, and Escherichia–Shigella) and SCFA-producing taxon (Prevotella) significantly changed in cognition-impaired patients. Tax4Fun predication results showed downregulation of glycan biosynthesis and metabolism in hypertension patients with cognitive impairment. Additionally, the pathway was demonstrated to be significantly correlated with LPS-containing taxa (Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, and Escherichia–Shigella) and SCFA-producing taxon Prevotella. Furthermore, the taxa-based multiple joint prediction model (9×) was demonstrated to have excellent diagnostic potential for cognitive impairment of hypertension patients (AUC = 0.944). The current study revealed the involvement of intestinal microbiota dysbiosis in cognition-impaired hypertension patients and provided an objective predictive index for this cognition disorder.

Na+/Ca2+ induced the migration of soy hull polysaccharides in the mucus layer in vitro

This study aimed to investigate the mechanism of Na⁺/Ca²⁺-induced soy hull polysaccharide (SHP) migration in the mucus layer. The viscosity, potential, microstructure, SHP migration, and metabolite migration were analyzed. The results showed that Na⁺ had little effect on the viscosity of polysaccharides, while Ca²⁺ increased the viscosity of polysaccharides. Na⁺ and Ca²⁺ promoted the migration of SHP particles by reducing the zeta potential, while they decreased the migration of SHP chyle particles by increasing the aggregation. SHP was fermented by gut microbiota to produce a large number of short-chain fatty acids (SCFAs). Compared with Ca²⁺, Na⁺ increased the migration of total SCFAs in the mucus layer. The high-Na⁺/Ca²⁺ mucus internal environment had a specific effect on the transport of nutrients in the intestine.

Relationships Among Gut Microbiota, Ischemic Stroke and Its Risk Factors: Based on Research Evidence

Stroke is a highly lethal disease and disabling illness while ischemic stroke accounts for the majority of stroke. It has been found that inflammation plays a key role in the initiation and progression of stroke, and atherosclerotic plaque rupture is considered to be the leading cause of ischemic stroke. Furthermore, chronic inflammatory diseases, such as obesity, type 2 diabetes mellitus (T2DM) and hypertension, are also considered as the high-risk factors for stroke. Recently, the topic on how gut microbiota affects human health has aroused great concern. The initiation and progression of ischemic stroke has been found to have close relation with gut microbiota dysbiosis. Hence, this manuscript briefly summarizes the roles of gut microbiota in ischemic stroke and its related risk factors, and the practicability of preventing and alleviating ischemic stroke by reconstructing gut microbiota.

Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome

A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.

The Gut Microbiome Is Associated with Circulating Dietary Biomarkers of Fruit and Vegetable Intake in a Multiethnic Cohort

BACKGROUND

Results from observational studies suggest high diet quality favorably influences the human gut microbiome. Fruit and vegetable consumption is often a key contributor to high diet quality.

OBJECTIVE

To evaluate measures of gut bacterial diversity and abundance in relation to serum biomarkers of fruit and vegetable intake.

DESIGN

Secondary analysis of cross-sectional data.

PARTICIPANTS AND SETTING

Men and women from Los Angeles, CA, and Hawai'i who participated in the Multiethnic Cohort-Adiposity Phenotype Study from 2013 to 2016 (N = 1,709).

MAIN OUTCOME MEASURES

Gut microbiome diversity and composition in relation to dietary biomarkers.

STATISTICAL ANALYSIS

Carotenoid (beta carotene, alpha carotene, cryptoxanthins, lutein, lycopene, and zeaxanthin), tocopherol (α, β + γ, and δ), and retinol concentrations were assessed in serum. The α and β diversity and composition of the gut microbiome were classified based on 16S rRNA gene sequencing of bacterial DNA from self-collected fecal samples. Global differences in microbial community profiles in relation dietary biomarkers were evaluated using multivariable permutational analysis of variance. Associations of α diversity (Shannon index), β diversity (weighted and unweighted UniFrac) with center log-ratio-transformed phyla and genera abundances were evaluated using linear regression, adjusted for covariates.

RESULTS

Increasing total carotenoid, beta carotene, alpha carotene, cryptoxanthin, and lycopene concentrations were associated with higher gut bacterial diversity (Shannon Index) (P < 0.001). Total tocopherol, α-tocopherol, and δ-tocopherol concentrations contributed significantly to more than 1% of the microbiome variation in gut bacterial community: total tocopherol: 1.74%; α-tocopherol: 1.70%; and δ-tocopherol: 1.16% (P < 0.001). Higher total carotenoid was associated with greater abundance of some genera relevant for microbial macronutrient metabolism (P < 0.001).

CONCLUSIONS

Objective biomarkers of fruit and vegetable intake, particularly carotenoids, were favorably associated with gut bacterial composition and diversity in this multiethnic population. These observations provide supportive evidence that fruit and vegetable intake is related to gut bacterial composition; more work is needed to elucidate how this influences host health.

Intestinal Barrier and Permeability in Health, Obesity and NAFLD

The largest surface of the human body exposed to the external environment is the gut. At this level, the intestinal barrier includes luminal microbes, the mucin layer, gastrointestinal motility and secretion, enterocytes, immune cells, gut vascular barrier, and liver barrier. A healthy intestinal barrier is characterized by the selective permeability of nutrients, metabolites, water, and bacterial products, and processes are governed by cellular, neural, immune, and hormonal factors. Disrupted gut permeability (leaky gut syndrome) can represent a predisposing or aggravating condition in obesity and the metabolically associated liver steatosis (nonalcoholic fatty liver disease, NAFLD). In what follows, we describe the morphological-functional features of the intestinal barrier, the role of major modifiers of the intestinal barrier, and discuss the recent evidence pointing to the key role of intestinal permeability in obesity/NAFLD.

Linking physical activity with clinical, functional, and structural outcomes: an evidence map using the Osteoarthritis Initiative

Physical activity is consistently recommended across clinical practice guidelines for managing knee osteoarthritis, yet prescription rates are low. Evidence mapping uses a systematic approach to visually illustrate and summarize published evidence, highlight gaps in the literature, and formulate research questions. The purpose of this study was to review and summarize evidence published from the Osteoarthritis Initiative (OAI) linking physical activity with clinical, functional, and structural knee osteoarthritis outcomes. Electronic databases were searched until June 2021. Studies from the OAI reporting subjective (Physical Activity Scale for the Elderly, PASE) or objective (accelerometry) physical activity data were included. Scatter plots were created to represent each outcome group (clinical, functional, structural) and physical activity measure (PASE, accelerometry) to map the evidence by the directional effect (positive, interaction, negative, or no effect) associated with physical activity. Forty-two articles were included in this review. Physical activity was quantified using PASE (n = 21), accelerometry (n = 20), or both (n = 1). Studies reported consistently positive physical activity effects on clinical (n = 22) and functional (n = 20) outcomes, with few exceptions. Structural (n = 15) outcomes were largely reported as interaction effects by physical activity intensity or sex, or as no significant effect. A network of interconnected outcomes emerged, with clinical and functional outcomes often reported together, and structural outcomes reported individually. This study provides an overview of current evidence linking physical activity to multiple interrelated knee osteoarthritis outcomes using an OAI-driven model. These evidence maps can be used as a framework to guide future investigations of the effects of physical activity on knee osteoarthritis.

In Vitro Study of Cricket Chitosan's Potential as a Prebiotic and a Promoter of Probiotic Microorganisms to Control Pathogenic Bacteria in the Human Gut

In this study, cricket chitosan was used as a prebiotic. Lactobacillus fermentum, Lactobacillus acidophilus, and Bifidobacterium adolescentis were identified as probiotic bacteria. Cricket chitin was deacetylated to chitosan and added to either De Man Rogosa and Sharpe or Salmonella/Shigella bacterial growth media at the rates of 1%, 5%, 10%, or 20% to obtain chitosan-supplemented media. The growth of the probiotic bacteria was monitored on chitosan-supplemented media after 6, 12, 24, and 48 h upon incubation at 37 °C. Growth of Salmonella typhi in the presence of probiotic bacteria in chitosan-supplemented media was evaluated under similar conditions to those of the growth of probiotic bacteria by measuring growth inhibition zones (in mm) around the bacterial colonies. All chitosan concentrations significantly increased the populations of probiotic bacteria and decreased the populations of pathogenic bacteria. During growth, there was a significant pH change in the media with all probiotic bacteria. Inhibition zones from probiotic bacteria growth supernatant against Salmonella typhi were most apparent at 16 mm and statistically significant in connection with a 10% chitosan concentration. This study suggests cricket-derived chitosan can function as a prebiotic, with an ability to eliminate pathogenic bacteria in the presence of probiotic bacteria.

Insights from Bacteroides Species in Children with Type 1 Diabetes

In our previous study the enrichment of the intestinal proteome of type 1 diabetes (T1D) children with Bacteroides proteins was observed, which led us to our current study that aimed to isolate and characterize Bacteroides species from fecal samples of T1D and control children. Repetitive sequence-based PCR (rep-PCR) was used for typing the isolated Bacteroides species. The antibiotic susceptibility and mucinolytic activity of the isolates was determined. The quantification of specific bacterial groups in the fecal samples was determined by qPCR. The ability to adhere and invade the human colonic cell line HT29-MTX-E12 of strains of P. dorei, B. uniformis and P. distasonis was determined and their whole genome sequencing was performed. The results showed similar numbers of Bacteroides species in T1D and control samples, but unique Bacteroides species and a higher recovery of P. distasonis from T1D samples was observed. Rep-PCR grouped the different Bacteroides species, but no discrimination by origin was achieved. T1D children showed a significant increase in Proteobacteria and a depletion in Lactobacillus sp. All tested P. dorei, B. uniformis and P. distasonis were able to adhere to HT29-MTX-E12 cells but significant differences (p < 0.05) in the ability to invade was observed. The highest ability to invade was exhibited by P. distasonis PtF D14MH1 and P. dorei PtFD16P1, while B. uniformis strains were unable to invade. The damage to tight junctions was also observed. The presence of Lactobacillus sp. inhibited the invasion ability of P. distasonis PtF D14MH1 but not P. dorei PtFD16P1. Sequences of agonist peptides of the human natural preproinsulin and the insulin B chain insB:9-23 peptide mimics were identified. The results reported in our study stresses the continued efforts required to clarify the link between T1D and gut microbiota.

Lactobacillus strains derived from human gut ameliorate metabolic disorders via modulation of gut microbiota composition and short-chain fatty acids metabolism

Regulation on gut microbiota and short-chain fatty acids (SCFAs) are believed to be a pathway to suppress the development of metabolic syndrome. In this study, three Lactobacillus strains derived from the human gut were investigated for their effects on alleviation of metabolic disorders. These strains were individually administered to metabolic disorder rats induced by high-fat-high-sucrose (HFHS) diet. Each strain exhibited its own characteristics in attenuating the impaired glucose-insulin homeostasis, hepatic oxidative damage and steatosis. Correlation analysis between SCFAs and host metabolic parameters suggested that Lactobacillus protective effects on metabolic disorders are partly mediated by recovery of SCFAs production, especially the faecal acetic acid. Correspondingly, it indicated that probiotics restore the gut microbiota dysbiosis in different extent, thereby protect against metabolic disorders in a manner that is associated with microbiota, but not totally reverse the changed composition of microbiota to the normal state. Thus, Lactobacillus strains partly protect against diet-induced metabolic syndrome by microbiota modulation and acetate elevation.

Reference values for intake of six types of soluble and insoluble fibre in healthy UK inhabitants based on the UK Biobank data

OBJECTIVE

To obtain a set of reference values for the intake of different types of dietary fibre in a healthy UK population.

DESIGN

This descriptive cross-sectional study used the UK Biobank data to estimate the dietary patterns of healthy individuals. Data on fibre content in different foods were used to calculate the reference values which were then calibrated using real-world data on total fibre intake.

SETTING

UK Biobank is a prospective cohort study of over 500 000 individuals from across the United Kingdom with the participants aged between 40 and 69 years.

PARTICIPANTS

UK Biobank contains information on over 500 000 participants. This study was performed using the data on 19 990 individuals (6941 men, 13 049 women) who passed stringent quality control and filtering procedures and had reported above-zero intake of the analysed foods.

RESULTS

A set of reference values for the intake of six different types of soluble and insoluble fibres (cellulose, hemicelluloses, pectin and lignin), including the corresponding totals, was developed and calibrated using real-world data.

CONCLUSIONS

To our knowledge, this is the first study to establish specific reference values for the intake of different types of dietary fibre. It is well known that effects exerted by different types of fibre both directly and through modulation of microbiota are numerous. Conceivably, a deficit or excess intake of specific types of dietary fibre may detrimentally affect human health. Filling this knowledge gap opens new avenues for research in discussion in studies of nutrition and microbiota and offers valuable tools for practitioners worldwide.

Co-Encapsulated Synbiotics and Immobilized Probiotics in Human Health and Gut Microbiota Modulation

Growing interest in the development of innovative functional products as ideal carriers for synbiotics, e.g., nutrient bars, yogurt, chocolate, juice, ice cream, and cheese, to ensure the daily intake of probiotics and prebiotics, which are needed to maintain a healthy gut microbiota and overall well-being, is undeniable and inevitable. This review focuses on the modern approaches that are currently being developed to modulate the gut microbiota, with an emphasis on the health benefits mediated by co-encapsulated synbiotics and immobilized probiotics. The impact of processing, storage, and simulated gastrointestinal conditions on the viability and bioactivity of probiotics together with prebiotics such as omega-3 polyunsaturated fatty acids, phytochemicals, and dietary fibers using various delivery systems are considered. Despite the proven biological properties of synbiotics, research in this area needs to be focused on the proper selection of probiotic strains, their prebiotic counterparts, and delivery systems to avoid suppression of their synergistic or complementary effect on human health. Future directions should lead to the development of functional food products containing stable synbiotics tailored for different age groups or specifically designed to fulfill the needs of adjuvant therapy.

Resource Competition and Host Feedbacks Underlie Regime Shifts in Gut Microbiota

AbstractThe spread of an enteric pathogen in the human gut depends on many interacting factors, including pathogen exposure, diet, host gut environment, and host microbiota, but how these factors jointly influence infection outcomes remains poorly characterized. Here we develop a model of host-mediated resource competition between mutualistic and pathogenic taxa in the gut that aims to explain why similar hosts, exposed to the same pathogen, can have such different infection outcomes. Our model successfully reproduces several empirically observed phenomena related to transitions between healthy and infected states, including (1) the nonlinear relationship between pathogen inoculum size and infection persistence, (2) the elevated risk of chronic infection during or after treatment with broad-spectrum antibiotics, (3) the resolution of gut dysbiosis with fecal microbiota transplants, and (4) the potential protection from infection conferred by probiotics. We then use the model to explore how host-mediated interventions-namely, shifts in the supply rates of electron donors (e.g., dietary fiber) and respiratory electron acceptors (e.g., oxygen)-can potentially be used to direct gut community assembly. Our study demonstrates how resource competition and ecological feedbacks between the host and the gut microbiota can be critical determinants of human health outcomes. We identify several testable model predictions ready for experimental validation.

Antioxidant activity and short-chain fatty acid production of lactic acid bacteria isolated from Korean individuals and fermented foods

Compounds of the cell walls of heat-killed lactic acid bacteria show immunomodulatory properties which boost immunological systems, and are used ad postbiotics (paraprobiotics). In this study, we used 17 different heat-killed isolates as postbiotics and evaluated their anti-inflammatory potential on the expression of proinflammatory mediators and cellular signaling pathways of murine macrophage, RAW 264.7 cells. Bifidobacterium bifidum MG731 showed the high 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity (90.6%), followed by Bifidobacterium lactis MG741 (59.6%). The Bi. lactis MG741 showed the high ABTS free radical scavenging activity (99.5%), followed by Lactobacillus plantarum MG989 (98.9%), Lactobacillus salivarius MG242 (97.1%), and Bi. bifidum MG731 (96.1%). In addition, Bi. bifidum MG731 showed the lowest nitric oxide production (4.28 µM), followed by B. lactis MG741 (10.80 µM), L. salivarius MG242 (14.60 µM), and L. plantarum MG989 (19.60 µM). The selected strains showed a decreased nitric oxide production via downregulation of inducible nitric oxide synthase and cyclooxygenase 2, which were upregulated via LPS-stimulated RAW 264.7 macrophages. Short-chain fatty acids (SCFA) including acetic, propionic, and butyric acid were produced by four strains. The Bi. bifidum MG731 showed total SCFAs production (4998.6 µg/g), Bi. lactis MG741 (2613.9 µg/g), L. salivarius MG242 (1456.1 µg/g), and L. plantarum MG989 (630.2 µg/g). These results indicated that the various selected strains may possess an anti-inflammatory potential and provide a molecular basis for the development of functional probiotics.

High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids

Dietary shifts can have a direct impact on the gut microbiome by preferentially selecting for microbes capable of utilizing the various dietary nutrients. The intake of dietary fiber has decreased precipitously in the last century, while consumption of processed foods has increased. Fiber, or microbiota-accessible carbohydrates (MACs), persist in the digestive tract and can be metabolized by specific bacteria encoding fiber-degrading enzymes. The digestion of MACs results in the accumulation of short-chain fatty acids (SCFAs) and other metabolic by-products that are critical to human health. Here, we implemented a 2-week dietary fiber intervention aiming for 40 to 50 g of fiber per day within the context of a course-based undergraduate research experience (CURE) (n = 20). By coupling shotgun metagenomic sequencing and targeted gas chromatography-mass spectrometry (GC-MS), we found that the dietary intervention significantly altered the composition of individual gut microbiomes, accounting for 8.3% of the longitudinal variability within subjects. Notably, microbial taxa that increased in relative abundance as a result of the diet change included known MAC degraders (i.e., Bifidobacterium and Lactobacillus). We further assessed the genetic diversity within Bifidobacterium, assayed by amplification of the groEL gene. Concomitant with microbial composition changes, we show an increase in the abundance of genes involved in inositol degradation. Despite these changes in gut microbiome composition, we did not detect a consistent shift in SCFA abundance. Collectively, our results demonstrate that on a short-term timescale of 2 weeks, increased fiber intake can induce compositional changes of the gut microbiome, including an increase in MAC-degrading bacteria.

IMPORTANCE A profound decrease in the consumption of dietary fiber in many parts of the world in the last century may be associated with the increasing prevalence of type II diabetes, colon cancer, and other health problems. A typical U.S. diet includes about ∼15 g of fiber per day, far less fiber than the daily recommended allowance. Changes in dietary fiber intake affect human health not only through the uptake of nutrients directly but also indirectly through changes in the microbial community and their associated metabolism. Here, we conducted a 2-week diet intervention in healthy young adults to investigate the impact of fiber consumption on the gut microbiome. Participants increased their average fiber consumption by 25 g/day on average for 2 weeks. The high-fiber diet intervention altered the gut microbiome of the study participants, including increases in known fiber-degrading microbes, such as Bifidobacterium and Lactobacillus.

Studying host genetic background effects on multimorbidity of intestinal cancer development, type 2 diabetes and obesity in response to oral bacterial infection and high-fat diet using the collaborative cross (CC) lines

Background

Multimorbidity of intestinal cancer (IC), type 2 diabetes (T2D) and obesity is a complex set of diseases, affected by environmental and genetic risk factors. High-fat diet (HFD) and oral bacterial infection play important roles in the etiology of these diseases through inflammation and various biological mechanisms.

Methods

To study the complexity of this multimorbidity, we used the collaborative cross (CC) mouse genetics reference population. We aimed to study the multimorbidity of IC, T2D, and obesity using CC lines, measuring their responses to HFD and oral bacterial infection. The study used 63 mice of both sexes generated from two CC lines (IL557 and IL711). For 12 weeks, experimental mice were maintained on specific dietary regimes combined with co-infection with oral bacteria Porphyromonas gingivalis and Fusobacterium nucleatum, while control groups were not infected. Body weight (BW) and results of a intraperitoneal glucose tolerance test (IPGTT) were recorded at the end of 12 weeks, after which length and size of the intestines were assessed for polyp counts.

Results

Polyp counts ranged between 2 and 10 per CC line. The combination of HFD and infection significantly reduced (P < .01) the colon polyp size of IL557 females to 2.5 cm2, compared to the other groups. Comparing BW gain, IL557 males on HFD gained 18 g, while the females gained 10 g under the same conditions and showed the highest area under curve (AUC) values of 40 000-45 000 (min mg/dL) in the IPGTT.

Conclusion

The results show that mice from different genetic backgrounds respond differently to a high fat diet and oral infection in terms of polyp development and glucose tolerance, and this effect is gender related.

kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets

The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt.

Characterization, prebiotic and immune-enhancing activities of rhamnogalacturonan-I-rich polysaccharide fraction from molokhia leaves

Plant-derived polysaccharides possess potential health benefits that improve intestinal health and the immune system. Molokhia leaves have a large amount of mucilage polysaccharide; in the present study, crude polysaccharide extract was prepared from molokhia leaves. The molecular weight of molokhia leaf polysaccharide fraction (MPF) was estimated to be 51.2 × 10³ Da. Polysaccharide was methylated and the structure of MPF was mainly composed of rhamnogalacturonan-I structure with side chains, such as galactans and linear glucan (starch), as shown by GC-MS analysis. To study the biofunctional effects of MPF, its prebiotic and intestinal immune-enhancing activities were assayed in vitro. MPF exhibited good prebiotic activity, as shown by its high prebiotic scores, and increased contents of total short-chain fatty acids on five probiotic strains. In addition, MPF showed immune-enhancing activity on Peyer's patches, as revealed by the high bone marrow cell proliferating activity and production of immunoglobulin A and cytokines. These results demonstrate that MPF may be a potential beneficial prebiotic and intestinal immune-enhancer, which may have wide implications in the food industry.

Evidence mapping to assess the available research on fiber, whole grains, and health

Evidence mapping is a useful methodology for characterizing existing research on a broad topic and identifying gaps in the scientific literature. Evidence mapping entails conducting a systematic literature search and extracting information on study details, often in the form of a database. Researchers at Tufts University and the North American branch of the International Life Sciences Institute created the Diet-Related Fibers & Human Health Outcomes Database, which is publicly available and updated annually. The database captures intervention studies examining dietary fiber and 10 predefined physiological health outcomes, including weight/adiposity, blood pressure, gut microbiota, and bone health. The database and subsequent potential for evidence mapping may be particularly useful in light of new food labeling requirements by the US Food and Drug Administration that require fibers to have accepted scientific evidence of a physiological health benefit in order to be labeled as "dietary fiber." Following the success of the fiber database, Tufts University and the General Mills Bell Institute of Health and Nutrition collaborated to develop a whole grain database and evidence map. This work successfully highlighted the need for better consistency in how whole grains are reported with respect to amount and type of whole grains and intervention compliance.

Consumption of Dietary Fiber from Different Sources during Pregnancy Alters Sow Gut Microbiota and Improves Performance and Reduces Inflammation in Sows and Piglets

Although the direct effects of dietary fiber on gut microbiota composition have been studied extensively, systematic evaluation of different fiber sources on gut health and inflammatory responses of sows and their offspring has rarely been conducted. Excessive reactive oxygen species produced by overactive metabolic processes during late pregnancy and lactation of sows leads to increased endotoxin levels, disordered gut microbiota, decreased SCFA production, and secretion of proinflammatory factors, which in turn causes local inflammation of the gut, potential damage of the gut microbial barrier, increased gut permeability, increased blood endotoxin levels (resulting in systemic inflammation), and ultimately decreased sow and piglet performance.

In pregnant and lactating sows, metabolism and immunity undergo drastic changes, which can lead to constipation, abortion, and intrauterine growth restriction (IUGR) and reduce production performance. Dietary fiber can regulate animal gut microbiota, alleviate inflammatory responses, and improve performance. Here, 48 sows (Large × Landrace) were randomly allocated to groups including, control, and with alfalfa meal (AM), beet pulp, and soybean skin dietary supplementation for 60 days of gestation. The AM diet decreased IUGR, increased food intake during lactation, and promoted the reproductive performance and physical condition of sows. Further, the AM diet significantly reduced markers of intestinal permeability (reactive oxygen species and endotoxin) in sow serum, and of systemic inflammation (interleukin-6 [IL-6] and tumor necrosis factor alpha) in sow feces and serum, as well as piglet serum, while it increased the anti-inflammatory marker, IL-10, in sow serum and feces. The AM diet also significantly affected gut microbiota by increasing the relative abundance of proinflammatory bacteria, while decreasing anti-inflammatory bacteria. Moreover, the total short-chain fatty acid (SCFA) content was higher in feces from sows fed an AM diet, with butyric acid content significantly higher during lactation, than in controls. Sow performance was correlated with intestinal permeability, inflammation, and gut microbiota, which were also vertically transmitted to piglets. Our results are significant for guiding feed management in the pig breeding industry. Further, the “sows to piglets” model provides a reference for the effect of dietary fiber on the gastrointestinal function of human mothers and infants.

IMPORTANCE Although the direct effects of dietary fiber on gut microbiota composition have been studied extensively, systematic evaluation of different fiber sources on gut health and inflammatory responses of sows and their offspring has rarely been conducted. Excessive reactive oxygen species produced by overactive metabolic processes during late pregnancy and lactation of sows leads to increased endotoxin levels, disordered gut microbiota, decreased SCFA production, and secretion of proinflammatory factors, which in turn causes local inflammation of the gut, potential damage of the gut microbial barrier, increased gut permeability, increased blood endotoxin levels (resulting in systemic inflammation), and ultimately decreased sow and piglet performance. Our results showed that supplementation of the diet with alfalfa meal in mid and late pregnancy can reverse this process. Our findings lay a foundation for improving the gut health of sows and piglets and provide insights into the study of the gastrointestinal tract function in human mothers and infants.

Bidirectional associations between sleep quality or quantity, and dietary intakes or eating behaviors in children 6-12 years old: a systematic review with evidence mapping

CONTEXT

Although dietary advice has long been a cornerstone of a healthy lifestyle, how sleep quality and quantity may interact with dietary intake or eating behaviors remains unclear.

OBJECTIVE

To consider a bidirectional relationship between sleep and diet in children aged 6-12 years via a systematic review following PRISMA guidelines.

DATA SOURCES

Relevant trials and observational studies were identified by searching the PubMed, Medline, Embase, and CENTRAL databases up to June 1, 2019, without language or date restrictions and supplemented with hand searching. Recognized procedures and reporting standards were applied.

DATA EXTRACTION

Data on participant characteristics, study parameters, diet measures, sleep measures, and findings of study quality assessment criteria were collected.

DATA ANALYSIS

Forty-five articles involving 308 332 participants on a diverse range of topics were included. Meta-analyses were planned but were impossible to perform due to high study heterogeneity. Most studies (82%) were cross-sectional, which prevented examining directionality of the observed associations. Risk of bias was assessed for trial, cohort studies, and cross-sectional studies, using the Cochrane Risk of Bias Tool or Newcastle Ottawa Scale.

RESULTS

Of 16 studies in which the effect of sleep on dietary intake was investigated, 81% (n = 13) reported a significant association. All studies (n = 8) of sugar-sweetened or caffeinated beverages reported a negative association with sleep, and in 6 of 7 studies in which eating behaviors were investigated, associations with sleep were reported. The use of objective measures of sleep and diet were scarce, with most trials and studies relying on subjective measures of sleep (68%) or diet (93%).

CONCLUSION

Because most studies investigating the relationship between sleep and diet in this age group are cross-sectional, temporality could not be determined. Additional randomized controlled trials and long-term cohort studies in middle childhood, particularly those using objective rather than questionnaire measures of sleep, are required to better understand interactions between diet and sleep.

SYSTEMATIC REVIEW REGISTRATION

Prospectively registered with PROSPERO International Prospective Register of Systematic Reviews (CRD42018091647).

Prebiotic Impacts of Soybean Residue (Okara) on Eubiosis/Dysbiosis Condition of the Gut and the Possible Effects on Liver and Kidney Functions

Okara is a white-yellow fibrous residue consisting of the insoluble fraction of the soybean seeds remaining after extraction of the aqueous fraction during the production of tofu and soymilk, and is generally considered a waste product. It is packed with a significant number of proteins, isoflavones, soluble and insoluble fibers, soyasaponins, and other mineral elements, which are all attributed with health merits. With the increasing production of soy beverages, huge quantities of this by-product are produced annually, which poses significant disposal problems and financial issues for producers. Extensive studies have been done on the biological activities, nutritional values, and chemical composition of okara as well as its potential utilization. Owing to its peculiar rich fiber composition and low cost of production, okara might be potentially useful in the food industry as a functional ingredient or good raw material and could be used as a dietary supplement to prevent varied ailments such as prevention of diabetes, hyperlipidemia, obesity, as well as to stimulate the growth of intestinal microbes and production of microbe-derived metabolites (xenometabolites), since gut dysbiosis (imbalanced microbiota) has been implicated in the progression of several complex diseases. This review seeks to compile scientific research on the bioactive compounds in soybean residue (okara) and discuss the possible prebiotic impact of this fiber-rich residue as a functional diet on eubiosis/dysbiosis condition of the gut, as well as the consequential influence on liver and kidney functions, to facilitate a detailed knowledge base for further exploration, implementation, and development.

"Adjusting Internal Organs and Dredging Channel" Electroacupuncture Ameliorates Insulin Resistance in Type 2 Diabetes Mellitus by Regulating the Intestinal Flora and Inhibiting Inflammation

INTRODUCTION

Traditional Chinese acupuncture has been demonstrated to be beneficial for treatment of type 2 diabetes mellitus (T2DM). The mechanism of acupuncture on T2DM is crucial for their biological activity as well as their usefulness as tools in biology and medicine. However, its mechanism is poorly understood.

METHODS

In an effort to explore the mechanism, eight db/db mice (a type of spontaneous T2DM mouse) were treated with adjusting internal organs and dredging channel electroacupuncture (AODCEA) for 2 weeks. Another eight db/db mice were fed as T2DM group (T2DMG), and eight db/m mice were set as normal control group (NCG). Lipopolysaccharide (LPS), interleukin-6 (IL-6), and diabetes-related indicators, such as fasting blood glucose (FBG) and triglyceride (TG), were detected by enzyme-linked immune sorbent assay (ELISA). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing to evaluate the effect of AODCEA on intestinal flora. The amount of short-chain fatty acids (SCFAs) in the feces were determined by gas chromatography-mass spectrometry (GC-MS).

RESULTS

Our results indicate that AODCEA treatment can reduce diabetes-related indicators. We observed the increased probiotics such as Blautia and Lactobacillus and decreased opportunist pathogens (Alistipes, Helicobacter, Prevotella) by AODCEA interventions. Importantly, the total amount of SCFAs in the feces of T2DM mice was promoted by AODCEA. Finally, obviously alleviated systemic inflammation was exhibited through AODCEA treatment by detection of lipopolysaccharide (LPS) and interleukin-6 (IL-6) in serum.

CONCLUSION

AODCEA can reshape the structure of intestinal flora, which can increase intestinal SCFAs, affect the circulating LPS level, and reduce the inflammatory response.

Nutrition and the gut microbiome during critical illness: A new insight of nutritional therapy

Changes in the microbiome in response to environmental influences can affect the overall health. Critical illness is considered one of the major environmental factors that can potentially influence the normal gut homeostasis. It is associated with pathophysiological effects causing damage to the intestinal microbiome. Alteration of intestinal microbial composition during critical illness may subsequently compromise the integrity of the intestinal epithelial barrier and intestinal mucosa absorptive function. Many factors can impact the microbiome of critically ill patients including ischemia, hypoxia and hypotension along with the iatrogenic effects of therapeutic agents and the lack of enteral feeds. Factors related to disease state and medication are inevitable and they are part of the intensive care unit (ICU) exposure. However, a nutritional intervention targeting gut microbiota might have the potential to improve clinical outcomes in the critically ill population given the extensive vascular and lymphatic links between the intestines and other organs. Although nutrition is considered an integral part of the treatment plan of critically ill patients, still the role of nutritional intervention is restricted to improve nitrogen balance. What is dismissed is whether the nutrients we provide are adequate and how they are processed and utilised by the host and the microbiota. Therefore, the goal of nutrition therapy during critical illness should be extended to provide good quality feeds with balanced macronutrient content to feed up the entire body including the microbiota and host cells. The main aim of this review is to examine the current literature on the effect of critical illness on the gut microbiome and to highlight the role of nutrition as a factor affecting the intestinal microbiome-host relationship during critical illness.

Molecular Insights Into O-Linked Glycan Utilization by Gut Microbes

O-linked glycosylation is a post-translational modification found mainly in eukaryotic cells, which covalently attaches oligosaccharides to secreted proteins in certain threonine or serine residues. Most of O-glycans have N-acetylgalactosamine (GalNAc) as a common core. Several glycoproteins, such as mucins (MUCs), immunoglobulins, and caseins are examples of O-glycosylated structures. These glycans are further elongated with other monosaccharides and sulfate groups. Some of them could be found in dairy foods, while others are produced endogenously, in both cases interacting with the gut microbiota. Interestingly, certain gut microbes can access, release, and consume O-linked glycans as a carbon source. Among these, Akkermansia muciniphila, Bifidobacterium bifidum, and Bacteroides thetaiotaomicron are prominent O-linked glycan utilizers. Their consumption strategies include specialized α-fucosidases and α-sialidases, in addition to endo-α-N-acetylgalactosaminidases that release galacto-N-biose (GNB) from peptides backbones. O-linked glycan utilization by certain gut microbes represents an important niche that allows them to predominate and modulate host responses such as inflammation. Here, we focus on the distinct molecular mechanisms of consumption of O-linked GalNAc glycans by prominent gut microbes, especially from mucin and casein glycomacropeptide (GMP), highlighting the potential of these structures as emerging prebiotics.

Gut microbiota and therapeutic approaches for dysbiosis in irritable bowel syndrome: recent developments and future perspectives

Increased knowledge regarding the implications of gut microbiota in irritable bowel syndrome (IBS) suggests that a disturbed intestinal microenvironment (dysbiosis) might promote the development and maintenance of IBS symptoms and affects several pathways in the pathology of this multifactorial disease. Accordingly, manipulation of the gut microbiota in order to improve IBS symptoms has evolved as a novel treatment strategy in the last decade. Several different approaches have been investigated in order to improve the gut microbiota composition. Dietary modifications including supplementation with fibers, prebiotics, and probiotics are shown to improve symptoms and composition of gut microbiota in IBS; however, the exact probiotic mixture beneficial for each individual remains to be identified. The use of antibiotics still needs confirmation, although promising results have been reported with use of rifaximin. Fecal microbiota transplantation (FMT) has recently gained a lot of attention, and several placebo-controlled trials investigating FMT obtain promising results regarding symptom reduction and gut microbiota manipulation in IBS. However, more data regarding long-term effects are needed before FMT can be integrated as a customized treatment for IBS in the clinical routine.

Role of diet and lifestyle modification in the management of nonalcoholic fatty liver disease and type 2 diabetes

Nonalcoholic fatty liver disease (NAFLD) is considered as the hepatic evidence of insulin resistance which is the hallmark of type 2 diabetes. NAFLD is considered as the risk factor for developing type 2 diabetes and has a high frequency of occurrence in those with existing type 2 diabetes. Compared with patients with only NAFLD or type 2 diabetes, these patients show a poor metabolic profile and increase mortality. Hence, effective treatment strategies are necessary. Here, we review the role of diet and lifestyle modification in the management of NAFLD and type 2 diabetes. Based on the available studies, it has been shown that the addition of any kind of physical activity or exercise is beneficial for patients with both NAFLD and type 2 diabetes. Proper dietary management leads to weight loss are also effective in improving metabolic parameters in patients with both NAFLD and type 2 diabetes. In conclusion, it is clear that increasing physical activity or exercise is effective in improving metabolic parameters in patients who are suffering with both NAFLD and type 2 diabetes.