Prebiotics: tools to manipulate the gut microbiome and metabolome

Perspective: Revisiting the Concepts of Prebiotic and Prebiotic Effect in Light of Scientific and Regulatory Progress - A Consensus Paper from the Global Prebiotic Association (GPA)

The term prebiotic has been used for almost three decades and has undergone numerous updates over the years. The scientific literature reveals that despite continuous efforts to establish a globally unified definition to guide jurisdictional regulations and product innovations, ambiguity continues to surround the terms prebiotic and prebiotic effect, leading to products that lack in full regulatory adherence being marketed worldwide. Thus, to reflect the current state of scientific research and knowledge and for the continuous advancement of the category, an update to the current prebiotic definition is warranted. This update includes removing the term selectivity, considering additional locations of action besides the gut, highlighting prebiotic performance benefits such as cognitive and athletic, and providing a clear standalone definition for prebiotic effect. The Global Prebiotic Association (GPA) is a leading information and industry hub committed to raising awareness about prebiotics, their emerging and well-established health benefits, and prebiotic product integrity and efficacy. In this position paper, GPA builds on previous prebiotic definitions to propose the following expanded definition for prebiotic: "a compound or ingredient that is utilized by the microbiota producing a health or performance benefit." In addition to prebiotic, GPA also defines prebiotic effect as: "a health or performance benefit that arises from alteration of the composition and/or activity of the microbiota, as a direct or indirect result of the utilization of a specific and well-defined compound or ingredient by microorganisms." With these two definitions, GPA aims to paint a clearer picture for the term prebiotic, and by incorporating an industry point of view, these updated definitions may be used alongside current scientific and regulatory perspectives to move the category forward. STATEMENT OF SIGNIFICANCE: The purpose of this paper is to revisit the concepts of prebiotic and prebiotic effect by providing a scientific-based industry perspective. The proposed definitions of prebiotic and prebiotic effect reflect the recent discoveries in metagenomics and prebiotic research after the International Scientific Association for Probiotics and Prebiotics' (ISAPP's) 2017 prebiotic definition and propose terminology changes that are timely and necessary. These changes aim to maintain the clarity and usefulness of the prebiotic definition to the scientific community, industry, healthcare providers, and consumers, while ensuring scientific validity, comprehensiveness, and justification of each part of the prebiotic definition, including abandoning the term selectivity and introducing concepts of performance benefits and prebiotic effect.

Inulin mitigated antibiotic-induced intestinal microbiota dysbiosis - a comparison of different supplementation stages

Antibiotics are unavoidable to be prescribed to subjects due to different reasons, and they decrease the relative abundance of beneficial microbes. Inulin, a fructan type of polysaccharide carbohydrate, on the contrary, could promote the growth of beneficial microbes. In this study, we investigated the effect of inulin on antibiotic-induced intestinal microbiota dysbiosis and compared their overall impact at different supplementation stages, i.e., post-antibiotic, at the time of antibiotic administration or prior to antibiotic treatment, in the C57BL/6 mice model. Although supplementation of inulin after antibiotic treatment could aid in the reconstruction of the intestinal microbial community its overall impact was limited and no remarkable differences were identified as compared to the spontaneous restoration. On the contrary, the effect of simultaneous and pre-supplementation was more remarkable. Simultaneous inulin supplementation significantly mitigated the antibiotic-induced dysbiosis based on alterations as evaluated using weighted and unweighted UniFrac distance between baseline and after treatment. Moreover, comparing the effect of simultaneous supplementation, pre-supplemented inulin further mitigated the antibiotic-induced dysbiosis, especially on the relative abundance of dominant microbes. Collectively, the current study found that the use of inulin could alleviate antibiotic-induced microbiota dysbiosis, and the best supplementation stage (overall effect as evaluated by beta diversity distance changes) was before the antibiotic treatment, then simultaneous supplementation and supplementation after the antibiotic treatment.

Next generation probiotics: Engineering live biotherapeutics

The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.

Effectiveness of Psychobiotics in the Treatment of Psychiatric and Cognitive Disorders: A Systematic Review of Randomized Clinical Trials

In this study, a systematic review of randomized clinical trials conducted from January 2000 to December 2023 was performed to examine the efficacy of psychobiotics-probiotics beneficial to mental health via the gut-brain axis-in adults with psychiatric and cognitive disorders. Out of the 51 studies involving 3353 patients where half received psychobiotics, there was a notably high measurement of effectiveness specifically in the treatment of depression symptoms. Most participants were older and female, with treatments commonly utilizing strains of Lactobacillus and Bifidobacteria over periods ranging from 4 to 24 weeks. Although there was a general agreement on the effectiveness of psychobiotics, the variability in treatment approaches and clinical presentations limits the comparability and generalization of the findings. This underscores the need for more personalized treatment optimization and a deeper investigation into the mechanisms through which psychobiotics act. The research corroborates the therapeutic potential of psychobiotics and represents progress in the management of psychiatric and cognitive disorders.

Effect of probiotics and prebiotics on the composition of the equine fecal and seminal microbiomes and sperm quality: A pilot study

Probiotic and prebiotic effects on equine semen and gastrointestinal microbiome composition and sperm quality are unknown. This study aimed to evaluate the effects of pre-, pro- or synbiotic supplementation on fecal and semen microbiome composition and sperm quality parameters of stallions. This Latin square crossover trial involved four miniature pony stallions receiving control diet only, or addition of a pro-, pre- or synbiotic formulation. Full-length 16S rRNA gene amplicon sequencing was used to measure diversity of semen and fecal microbiomes. Total sperm count, total motility, progressive motility, DNA integrity, lipid peroxidation and mitochondrial oxidative stress, biomarkers of sperm quality, were measured after each intervention. A general linear model was employed to analyse and compare microbiome diversity measures and sperm quality data across four time points. Shannon's diversity index (alpha-diversity), and evenness of semen and gastrointestinal microbiomes were significantly different (p<0.001). A trend was observed for prebiotic effects on the diversity indices of the GI microbiome (p= 0.07). No effects of treatments were observed on either semen microbiome or sperm quality. Pre-, pro- and synbiotic supplements showed no negative effect on sperm quality parameters observed. This proof of concept provides preliminary data to inform future studies exploring the relationship between microbiomes and fertility.

Restoration of Intestinal Microbiota After Inulin Supplementation Halted: The Secondary Effect of Supplemented Inulin

SCOPE

Consumption of inulin could affect the intestinal microbiota composition. Hereby, it is aimed to investigate the intestinal microbial community restoration process when the inulin supplementation is terminated (i.e., the secondary effect).

METHODS AND RESULTS

The current study investigates the response and restoration of intestinal microbiota to/after high (Inulin-H) and low (Inulin-L) dosage of inulin supplementation or sequential antibiotics and inulin (Anti-Inulin-L) supplementation, based on analysis of 16S rRNA gene sequences in C57BL/6 mice. The number of significantly changed genera in response to inulin is highest in Anti-Inulin-L (n = 66) group, followed by Inulin-H (n = 51) and Inulin-L (n = 38) group. After inulin supplementation stops, microbiota of all studied groups tend to recover to their original states, with highest percentage of inulin-responding microbes stay significantly different at Anti-Inulin-L (93.94%) group, followed by Inulin-H (74.51%) and Inulin-L (44.12%) groups. Of note, the relative abundance of some non-inulin-responding taxa significantly increases during restoration.

CONCLUSION

Sequential antibiotics and inulin supplementation induce greatest changes in the intestinal microbial composition, followed by high and low dosage of inulin. Additionally, the changes induce by supplemented inulin in the intestinal microbial community, provide a chance for some microbes to outcompete the other microbes during the spontaneous restoration.

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions

Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing. Stool samples were collected from 20 apparently healthy dogs, manually homogenized, cryopreserved in 20% glycerol and aliquoted, frozen in liquid nitrogen and stored at -20°C or -80°C for 3, 6, 9, and 12 months. At baseline and after period of storage, aliquots were thawed and treated with propidium monoazide before fecal DNA extraction. Following long-read 16S-rRNA amplicon sequencing, bacterial community composition and diversity were compared among treatment groups. We demonstrated that fresh-frozen canine stools collected from 20 apparently healthy dogs could be stored for up to 12 months at -80°C with minimal change in microbial community composition and diversity and that storage at -80°C is superior to storage at -20°C. We also found that differences between dogs had the largest effect on community composition and diversity. Relative abundances of certain bacterial taxa, including those known to be short-chain fatty acid producers, varied significantly with specific storage temperatures and duration. Further work is required to ascertain whether fecal donor material that differs in bacterial community composition and diversity across storage conditions and duration could lead to differences in clinical efficacy for specific clinical indications of fecal microbiota transplantation.

Synbiotics as potent functional food: recent updates on therapeutic potential and mechanistic insight

Synbiotics are the specific mixtures of prebiotics with probiotics intended to give health benefits to the host by stabilizing and supporting the gut microbiota.The prebiotic substance used in the synbiotics selectively favors the growth and metabolite production of probiotics. Gut microbiome dysbiosis may lead to generation and progression of various chronic diseases. Synbiotics act synergistically to modulate the gut ecosystem for improvement of metabolic health of the host. Probiotics have been found promising against various diseases being safer, effective, as an alternative or combinatorial therapy. Specific combinations of probiotics with suitable prebiotic substrate as synbiotics, may be the more effective therapeutic agents that can provide all benefits of probiotics as well as prebiotics. Though, effective combinations, dosage, mechanism of action, safety, cost effectiveness and other clinical investigations are required to be established along with other relevant aspects. Synbiotics have the potential to be functional food of importance in future. Present review summarizes the mechanistic overview of synbiotics related to gut microbiota, therapeutic potential and promising health benefits for human illnesses according to the available literature. In present scenario, synbiotics are more promising future alternatives as therapeutics to maintain healthy microbiota inside the host gut which directly affects the onset or development ofrelated disorders or diseases.

Functional profiling of gut microbial and immune responses toward different types of dietary fiber: a step toward personalized dietary interventions

Dietary fiber plays a crucial role in maintaining gut and overall health. The objective of this study was to investigate whether different types of dietary fiber elicited specific changes in gut microbiota composition and the production of short-chain fatty acids. To test this, a longitudinal crossover study design was employed, in which healthy adult women consumed three distinct dietary fiber supplements: Inulin (fructo-oligosaccharide), Vitafiber (isomalto-oligosaccharide), and Fibremax (mixture of different fiber) during a one-week intervention period, followed by a 2-week washout period. A total of 15 g of soluble fiber was consumed daily for each supplement. Samples were collected before and after each intervention to analyze the composition of the gut microbiota by 16S rRNA sequencing and fecal levels of short-chain fatty acids measured using nuclear magnetic resonance. Phenotypic changes in peripheral blood mononuclear cells were studied in subsets of participants with higher SCFA levels post-intervention using spectral flow cytometry. The results revealed substantial stability and resilience of the overall gut bacterial community toward fiber-induced changes. However, each supplement had specific effects on gut bacterial alpha and beta diversity, SCFA production, and immune changes. Inulin consistently exerted the most pronounced effect across individuals and certain taxa were identified as potential indicators of SCFA production in response to inulin supplementation. This distinguishing feature was not observed for the other fiber supplements. Further large-scale studies are required to confirm these findings. Overall, our study implies that personalized dietary fiber intervention could be tailored to promote the growth of beneficial bacteria to maximize SCFA production and associated health benefits.

Targeting gut microbiota: new therapeutic opportunities in multiple sclerosis

Multiple sclerosis (MS) causes long-lasting, multifocal damage to the central nervous system. The complex background of MS is associated with autoimmune inflammation and neurodegeneration processes, and is potentially affected by many contributing factors, including altered composition and function of the gut microbiota. In this review, current experimental and clinical evidence is presented for the characteristics of gut dysbiosis found in MS, as well as for its relevant links with the course of the disease and the dysregulated immune response and metabolic pathways involved in MS pathology. Furthermore, therapeutic implications of these investigations are discussed, with a range of pharmacological, dietary and other interventions targeted at the gut microbiome and thus intended to have beneficial effects on the course of MS.

Influence of dietary mannan-oligosaccharides supplementation on hematological characteristics, blood biochemical parameters, immune response and histological state of laying hens

This study aimed to determine the influence of dietary mannan-oligosaccharides (MOS) on the immune system, hematological traits, blood biochemical parameters, and histological state of laying hens. At 34 wk of age, The Mandarah chicken strain's 120 laying hens and 12 cocks were divided into 4 groups, each with 30 hens and 3 cocks. The first group performed as a control group, which nourished on a basal diet. The second, third, and fourth experimental groups received 0.1, 0.2, and 0.5 g/kg of MOS and a base diet, respectively. Birds obtained MOS at numerous doses significantly (P ˂ 0.05) raised serum levels of immunoglobulin Y (IgY), immunoglobulin M (IgM), and avian influenza (AI) antibodies compared to control birds. Furthermore, adding MOS at a level of 0.1 g/kg diet significantly improved the immune response of the control group. Additionally, compared to the control group, treated birds with MOS at various dosages did not significantly enhance hematological parameters such as red blood cells (RBCs), white blood cells (WBCs), hemoglobin, and hematocrit. Compared to control birds, birds fed MOS at all levels exhibited considerably lower serum cholesterol, alanine aminotransferase (ALT), and aspartate aminotransferase (AST) values. Also, compared to other treated birds, MOS-treated birds displayed improved histological examination of the small intestine, isthmus, and testis compared to the control group, particularly in birds fed MOS at 0.1 and 0.2 g/kg diet. It could be concluded that using MOS at 0.1 or 2 g/kg diet can successfully improve the physiological performance and overall health of laying hens.

Dairy products and constituents: a review of their effects on obesity and related metabolic diseases

Obesity has become a global public health problem that seriously affects the quality of life. As an important part of human diet, dairy products contain a large number of nutrients that are essential for maintaining human health, such as proteins, peptides, lipids, vitamins, and minerals. A growing number of epidemiological investigations provide strong evidence on dairy interventions for weight loss in overweight/obese populations. Therefore, this paper outlines the relationship between the consumption of different dairy products and obesity and related metabolic diseases. In addition, we dive into the mechanisms related to the regulation of glucose and lipid metabolism by functional components in dairy products and the interaction with gut microbes. Lastly, the role of dairy products on obesity of children and adolescents is revisited. We conclude that whole dairy products exert more beneficial effect than single milk constituent on alleviating obesity and that dairy matrix has important implications for metabolic health.

Effect of Sugar Beet Pulp on the Composition and Predicted Function of Equine Fecal Microbiota

The purpose of this study is to determine the effect of the partial replacement of dietary hay with sugar beet pulp (SBP) on the composition and predicted function of the fecal microbiota of healthy adult horses. Fecal samples were collected daily for 12 days from six adult horses after removal from pasture, including a five-day acclimation period, and a seven-day period following the introduction of SBP into their diet, and compared to six untreated horses over a comparable period. Fecal DNA was subjected to 16S rRNA amplicon sequencing and a longitudinal analysis was performed comparing the composition and predicted function. While no significant treatment-associated changes in the richness, alpha diversity, or beta diversity were detected, random forest regression identified several high-importance taxonomic features associated with change over time in horses receiving SBP. A similar analysis of the predicted functional pathways identified several high-importance pathways, including those involved in the production of L-methionine and butyrate. These data suggest that feeding SBP to healthy adult horses acutely increases the relative abundance of several Gram-positive taxa, including Cellulosilyticum sp., Moryella sp., and Weissella sp., and mitigates the predicted functional changes associated with removal from pasture. Large-scale studies are needed to assess the protective effect of SBP on the incidence of the gastrointestinal conditions of horses.

The influence of dietary patterns on skin bacterial diversity, composition, and co-occurrence relationships at forearm and neck sites of healthy Korean adults

AIMS

Diet and nutrition are important aspects of skin physiology and health. However, the influence of diet on the bacterial flora of different skin sites is not well understood. Therefore, we investigated the relationship between dietary patterns (DPs) and skin bacterial flora on the forearm (a dry site) and the neck (a sebaceous site) of healthy Korean adults.

METHODS AND RESULTS

In metagenomics analysis, Shannon and Simpson indices were higher on the forearm than on the neck and were negatively correlated with the two dominant species, Cutibacterium acnes and Staphylococcus epidermidis, on two skin sites. In addition, the Simpson index of the forearm was positively associated with DP1 (characterized by a high intake of vegetables, mushrooms, meat, fish and shellfish, seaweed, and fat and oil), while that on the neck was negatively associated with DP2 (characterized by a high intake of fast food). A high intake of DP1 was associated with a lower abundance of dominant species, including C. acnes, and higher degrees of the co-occurrence network, whereas a high intake of DP2 was associated with the opposite pattern.

CONCLUSIONS

Specific diets may impact both skin bacterial diversity and composition, as well as the co-occurrence of bacteria, which may vary across different skin sites.

Prebiotics Progress Shifts in the Intestinal Microbiome That Benefits Patients with Type 2 Diabetes Mellitus

Hypoglycemic medications that could be co-administered with prebiotics and functional foods can potentially reduce the burden of metabolic diseases such as Type 2 Diabetes Mellitus (T2DM). The efficacy of drugs such as metformin and sulfonylureas can be enhanced by the activity of the intestinal microbiome elaborated metabolites. Functional foods such as prebiotics (e.g., oligofructose) and dietary fibers can treat a dysbiotic gut microbiome by enhancing the diversity of microbial niches in the gut. These beneficial shifts in intestinal microbiome profiles include an increased abundance of bacteria such as Faecalibacterium prauznitzii, Akkermancia muciniphila, Roseburia species, and Bifidobacterium species. An important net effect is an increase in the levels of luminal SCFAs (e.g., butyrate) that provide energy carbon sources for the intestinal microbiome in cross-feeding activities, with concomitant improvement in intestinal dysbiosis with attenuation of inflammatory sequalae and improved intestinal gut barrier integrity, which alleviates the morbidity of T2DM. Oligosaccharides administered adjunctively with pharmacotherapy to ameliorate T2DM represent current plausible treatment modalities.

Non-dairy prebiotics: Conceptual relevance with nutrigenomics and mechanistic understanding of the effects on human health

The increasing health awareness of consumers has made a shift towards vegan and non-dairy prebiotics counterparts. Non-dairy prebiotics when fortified with vegan products have interesting properties and widely found its applications in food industry. The chief vegan products that have prebiotics added include water-soluble plant-based extracts (fermented beverages, frozen desserts), cereals (bread, cookies), and fruits (juices & jelly, ready to eat fruits). The main prebiotic components utilized are inulin, oligofructose, polydextrose, fructooligosaccharides, and xylooligosaccharides. Prebiotics' formulations, type and food matrix affect food products, host health, and technological attributes. Prebiotics from non-dairy sources have a variety of physiological effects that help to prevent and treat chronic metabolic diseases. This review focuses on mechanistic insight on non-dairy prebiotics affecting human health, how nutrigenomics is related to prebiotics development, and role of gene-microbes' interactions. The review will provide industries and researchers with important information about prebiotics, mechanism of non-dairy prebiotics and microbe interaction as well as prebiotic based vegan products.

Dose-dependent effects of xylooligosaccharides on glycemic regulation with L. rhamnosus CCFM1060 in diabetic mice

Dietary intervention with the probiotic Lactobacillus rhamnosus CCFM1060 has been proved to be effective on glycemic regulation in diabetic mice. Therefore characterization of the potential symbiotic effect of prebiotic xylooligosaccharides (XOS) with L. rhamnosus CCFM1060 would be desirable. In this study, we evaluated any dose-dependent relationship between XOS and L. rhamnosus CCFM1060, and the potential impact on glycemic regulation. Diabetic mice were randomly assigned to receive 5 × 10⁹ CFU mL^-1L. rhamnosus CCFM1060, 5 × 10⁹ CFU mL^-1L. rhamnosus CCFM1060 with 250 mg kg^-1 XOS (L-LXOS), or 5 × 10⁹ CFU mL^-1L. rhamnosus CCFM1060 with 500 mg kg^-1 XOS (L-HXOS) for 7 weeks. In addition to characterization of the host metabolism, the intestinal microbiota were analyzed using 16S rRNA gene sequencing. The results showed that L. rhamnosus alone and L-LXOS intervention significantly alleviated diabetes symptoms and increased the populations of short-chain fatty acid (SCFA)-producing bacteria. The intake of L-HXOS had an adverse effect on glucose metabolism, causing increased insulin resistance and inflammation. Although a significant increase in the relative abundance of Bifidobacterium was observed in the L-HXOS group, the abundance of SCFA-producing bacteria, such as Romboutsia and Clostrudium sensu stricto 1, decreased. KEGG pathway analysis revealed that the adverse effects of L-HXOS intervention might be attributed to the metabolic pathways involved in amino acid, cofactor, and vitamin metabolism. This study revealed that L. rhamnosus CCFM1060 combined with different doses of XOS exerted dose-dependent effects on glucose metabolism. Therefore, the type and dose of prebiotics should be carefully evaluated when developing individualized symbiotic formula.

Characterizing conjugative plasmids from an antibiotic-resistant dataset for use as broad-host delivery vectors

Human microbiome engineering is increasingly proposed as a way to modulate health outcomes. However, one of the current limitations to engineering microbial communities in situ is delivery of a genetic payload for introducing or modifying genes. Indeed, there is a need to identify novel broad-host delivery vectors for microbiome engineering. Therefore, in this study, we characterized conjugative plasmids from a publicly available dataset of antibiotic-resistant isolate genomes in order to identify potential broad-host vectors for further applications. From the 199 closed genomes available in the CDC & FDA AR Isolate Bank, we identified 439 plasmids, of which 126 were predicted to be mobilizable and 206 conjugative. Various characteristics of the conjugative plasmids, such as size, replication origin, conjugation machinery, host defense mechanisms, and plasmid stability proteins, were analyzed to determine these plasmids' potential host-range. Following this analysis, we clustered plasmid sequences and chose 22 unique, broad-host range plasmids that would be suitable for use as delivery vectors. This novel set of plasmids will provide a valuable resource for engineering microbial communities.

The Role of the Microbiome in the Pathogenesis and Treatment of Asthma

The role of the microbiome in the pathogenesis and treatment of asthma is significant. The purpose of this article is to show the interplay between asthma and the microbiome, and main areas that require further research are also highlighted. The literature search was conducted using the PubMed database. After a screening process of studies published before May 2023, a total of 128 articles were selected in our paper. The pre-treatment bronchial microbiome in asthmatic patients plays a role in their responsiveness to treatment. Gut microbiota and its dysbiosis can contribute to immune system modulation and the development of asthma. The association between the microbiome and asthma is complex. Further research is necessary to clarify which factors might moderate that relationship. An appropriate gut microbiome and its intestinal metabolites are a protective factor for asthma development. Prebiotics and certain dietary strategies may have a prophylactic or therapeutic effect, but more research is needed to establish final conclusions. Although the evidence regarding probiotics is ambiguous, and most meta-analyses do not support the use of probiotic intake to reduce asthma, several of the most recent studies have provided promising effects. Further studies should focus on the investigation of specific strains and the examination of their mechanistic and genetic aspects.

Potential of algae-derived alginate oligosaccharides and β-glucan to counter inflammation in adult zebrafish intestine

Alginate oligosaccharides (AOS) are natural bioactive compounds with anti-inflammatory properties. We performed a feeding trial employing a zebrafish (Danio rerio) model of soybean-induced intestinal inflammation. Five groups of fish were fed different diets: a control (CT) diet, a soybean meal (SBM) diet, a soybean meal+β-glucan (BG) diet and 2 soybean meal+AOS diets (alginate products differing in the content of low molecular weight fractions - AL, with 31% < 3kDa and AH, with 3% < 3kDa). We analyzed the intestinal transcriptomic and plasma metabolomic profiles of the study groups. In addition, we assessed the expression of inflammatory marker genes and histological alterations in the intestine. Dietary algal β-(1, 3)-glucan and AOS were able to bring the expression of certain inflammatory genes altered by dietary SBM to a level similar to that in the control group. Intestinal transcriptomic analysis indicated that dietary SBM changed the expression of genes linked to inflammation, endoplasmic reticulum, reproduction and cell motility. The AL diet suppressed the expression of genes related to complement activation, inflammatory and humoral response, which can likely have an inflammation alleviation effect. On the other hand, the AH diet reduced the expression of genes, causing an enrichment of negative regulation of immune system process. The BG diet suppressed several immune genes linked to the endopeptidase activity and proteolysis. The plasma metabolomic profile further revealed that dietary SBM can alter inflammation-linked metabolites such as itaconic acid, taurochenodeoxycholic acid and enriched the arginine biosynthesis pathway. The diet AL helped in elevating one of the short chain fatty acids, namely 2-hydroxybutyric acid while the BG diet increased the abundance of a vitamin, pantothenic acid. Histological evaluation revealed the advantage of the AL diet: it increased the goblet cell number and length of villi of the intestinal mucosa. Overall, our results indicate that dietary AOS with an appropriate amount of < 3kDa can stall the inflammatory responses in zebrafish.

Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome?

Dysregulated immune system with a failure to recognize self from non-self-antigens is one of the common pathogeneses seen in autoimmune diseases. The complex interplay of genetic and environmental factors is important for the occurrence and development of the disease. Among the environmental factors, disturbed gut microbiota (gut dysbiosis) has recently attracted particular attention, especially with advancement in human microbiome research. Although the alterations in microbiota have been seen in various autoimmune diseases, including those of nervous system, there is paucity of information on neuromuscular system diseases. Myasthenia gravis (MG) is one such rare autoimmune disease of neuromuscular junction, and is caused by generation of pathogenic autoantibodies to components of the postsynaptic muscle endplate. In the recent years, accumulating evidences have endorsed the key role of host microbiota, particularly those of gut, in the pathogenesis of MG. Differential microbiota composition, characterized by increased abundance of Fusobacteria, Bacteroidetes, and Proteobacteria, and decreased abundance of Actinobacteria and Firmicutes, has been seen in MG patients in comparison to healthy subjects. Disturbance of microbiota composition, particularly reduced ratio of Firmicutes/Bacteroidetes, alter the gut permeability, subsequently triggering the immunological response. Resultant reduction in levels of short chain fatty acids (SCFAs) is another factor contributing to the immunological response in MG patients. Modulation of gut microbiota via intervention of probiotics, prebiotics, synbiotics, postbiotics (metabiotics), and fecal microbiota transplantation (FMT) is considered to be the futuristic approach for the management of MG. This review summarizes the role of gut microbiota and their metabolites (postbiotics) in the progression of MG. Also, various bacteriotherapeutic approaches involving gut microbiota are discussed for the prevention of MG progression.

Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential

Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.

A Comparative Evaluation of the Structural and Biomechanical Properties of Food-Grade Biopolymers as Potential Hydrogel Building Blocks

The aim of this study was to conduct a comparative assessment of the structural and biomechanical properties of eight selected food-grade biopolymers (pea protein, wheat protein, gellan gum, konjac gum, inulin, maltodextrin, psyllium, and tara gum) as potential hydrogel building blocks. The prepared samples were investigated in terms of the volumetric gelling index, microrheological parameters, physical stability, and color parameters. Pea protein, gellan gum, konjac gum, and psyllium samples had high VGI values (100%), low solid−liquid balance (SLB < 0.5), and high macroscopic viscosity index (MVI) values (53.50, 59.98, 81.58, and 45.62 nm−2, respectively) in comparison with the samples prepared using wheat protein, maltodextrin, and tara gum (SLB > 0.5, MVI: 13.58, 0.04, and 0.25 nm−2, respectively). Inulin had the highest elasticity index value (31.05 nm−2) and MVI value (590.17 nm−2). The instability index was the lowest in the case of pea protein, gellan gum, konjac gum, and inulin (below 0.02). The color parameters and whiteness index (WI) of each biopolymer differed significantly from one another. Based on the obtained results, pea protein, gellan gum, konjac gum, and psyllium hydrogels had similar structural and biomechanical properties, while inulin hydrogel had the most diverse properties. Wheat protein, maltodextrin, and tara gum did not form a gel structure.

Codonopsis pilosula oligosaccharides modulate the gut microbiota and change serum metabolomic profiles in high-fat diet-induced obese mice

Obesity has become a major health problem worldwide, linked to gut microbiota imbalance and chronic inflammation. This study aims to evaluate whether Codonopsis pilosula oligosaccharides (CPOs) can alleviate obesity and related metabolic complications in high-fat diet (HFD) induced obese mice. Male C57BL/6J mice were fed with a HFD for 16 weeks and treated daily with CPOs (500 mg kg^-1). CPO supplementation decreased body weight and fat accumulation and improved glucose tolerance in HFD-fed mice. CPOs also reversed the effects of the HFD on inflammatory markers and improved macrophage infiltration. The results of gut microbiota analysis showed that CPOs could also regulate gut microbiota composition, significantly increasing the abundance of the beneficial bacteria Muribaculaceae spp., Alistipes and Clostridium and decreasing the abundance of the harmful bacteria Rikenella, Enterobacteriaceae spp., Collinsella and Megasphaera in HFD mice. Based on serum non-targeted metabolomics analysis, 20 key metabolites responding to CPO treatment were identified, and their biological functions were mainly related to tryptophan and bile acid metabolism. The results demonstrate that CPO supplementation can ameliorate HFD-induced obesity and obesity-related metabolic disorders. It can be used as a novel gut microbiota modulator to prevent HFD-induced gut dysbiosis.

Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics

SignificanceAntibiotic exposure stands among the most used interventions to drive microbial communities away from undesired states. How the ecology of microbial communities shapes their recovery-e.g., posttreatment shifts toward Clostridioides difficile infections in the gut-after antibiotic exposure is poorly understood. We study community response to antibiotics using a model community that can reach two alternative states. Guided by theory, our experiments show that microbial growth following antibiotic exposure can counteract antibiotic susceptibility in driving transitions between alternative community states. This makes it possible to reverse the outcome of antibiotic exposure through modifying growth dynamics, including cooperative growth, of community members. Our research highlights the relevance of simple ecological models to better understand the long-term effects of antibiotic treatment.

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

Distinct fermentation of human milk oligosaccharides 3-FL and LNT2 and GOS/inulin by infant gut microbiota and impact on adhesion of Lactobacillus plantarum WCFS1 to gut epithelial cells

Human milk oligosaccharides (hMOs) are unique bioactive components in human milk. 3-Fucosyllactose (3-FL) is an abundantly present hMO that can be produced in sufficient amounts to allow application in infant formula. Lacto-N-triaose II (LNT2) can be obtained by acid hydrolysis of lacto-N-neotetraose (LNnT). Both 3-FL and LNT2 have been shown to have health benefits, but their impact on infant microbiota composition and microbial metabolic products such as short-chain fatty acids (SCFAs) is unknown. To gain more insight in fermentability, we performed in vitro fermentation studies of 3-FL and LNT2 using pooled fecal microbiota from 12-week-old infants. The commonly investigated galacto-oligosaccharides (GOS)/inulin (9 : 1) served as control. Compared to GOS/inulin, we observed a delayed utilization of 3-FL, which was utilized at 60.3% after 36 h of fermentation, and induced the gradual production of acetic acid and lactic acid. 3-FL specifically enriched bacteria of Bacteroides and Enterococcus genus. LNT2 was fermented much faster. After 14 h of fermentation, 90.1% was already utilized, and production of acetic acid, succinic acid, lactic acid and butyric acid was observed. LNT2 specifically increased the abundance of Collinsella, as well as Bifidobacterium. The GOS present in the GOS/inulin mixture was completely fermented after 14 h, while for inulin, only low DP was rapidly utilized after 14 h. To determine whether the fermentation might lead to enhanced colonization of commensal bacteria to gut epithelial cells, we investigated adhesion of the commensal Lactobacillus plantarum WCFS1 to Caco-2 cells. The fermentation digesta of LNT2 collected after 14 h, 24 h, and 36 h, and GOS/inulin after 24 h of fermentation significantly increased the adhesion of L. plantarum WCFS1 to Caco-2 cells, while 3-FL had no such effect. Our findings illustrate that fermentation of hMOs is very structure-dependent and different from the commonly applied GOS/inulin, which might lead to differential potencies to stimulate adhesion of commensal cells to gut epithelium and consequent microbial colonization. This knowledge might contribute to the design of tailored infant formulas containing specific hMO molecules to meet the need of infants during the transition from breastfeeding to formula.

Nutritional Interventions and the Gut Microbiome in Children

The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: (a) Can diet modify the composition, diversity, or function of the gut microbiome, and (b) will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Adequacy of calcium and vitamin D reduces inflammation, β-catenin signaling, and dysbiotic Parasutterela bacteria in the colon of C57BL/6 mice fed a western-style diet

Adoption of an obesogenic diet low in calcium and vitamin D (CaD) leads to increased obesity, colonic inflammation, and cancer. However, the underlying mechanisms remain to be elucidated. We tested the hypothesis that CaD supplementation (from inadequacy to adequacy) may reduce colonic inflammation, oncogenic signaling, and dysbiosis in the colon of C57BL/6 mice fed a Western diet. Male C57/BL6 mice (4-weeks old) were assigned to 3 dietary groups for 36 weeks: (1) AIN76A as a control diet (AIN); (2) a defined rodent "new Western diet" (NWD); or (3) NWD with CaD supplementation (NWD/CaD). Compared to the AIN, mice receiving the NWD or NWD/CaD exhibited more than 0.2-fold increase in the levels of plasma leptin, tumor necrosis factor α (TNF-α) and body weight. The levels of plasma interleukin 6 (IL-6), inflammatory cell infiltration, and β-catenin/Ki67 protein (oncogenic signaling) were increased more than 0.8-fold in the NWD (but not NWD/CaD) group compared to the AIN group. Consistent with the inflammatory phenotype, colonic secondary bile acid (inflammatory bacterial metabolite) levels increased more than 0.4-fold in the NWD group compared to the NWD/CaD and AIN groups. Furthermore, the abundance of colonic Proteobacteria (e.g., Parasutterela), considered signatures of dysbiosis, was increased more than four-fold; and the α diversity of colonic bacterial species, indicative of health, was decreased by 30% in the NWD group compared to the AIN and NWD/CaD groups. Collectively, CaD adequacy reduces colonic inflammation, β-catenin oncogenic signaling, secondary bile acids, and bacterial dysbiosis in mice fed with a Western diet.

Prebiotics mannan-oligosaccharides accelerate sexual maturity in rats: A randomized preclinical study

Background and Aim:

The prebiotics, mannan-oligosaccharides (MOS), demonstrate the ability to increase probiotic microorganisms and fixation and removal of pathogens associated with chronic systemic inflammation in the digestive system. Inflammatory processes play an important role in modulating the brain-intestinal axis, including maintaining male reproductive function and spermatogenesis and regulating stress. The aim of the present study was to evaluate the action of MOS on testosterone and corticosterone concentrations and the reproductive system development of rats in the growth phase as an animal model.

Materials and Methods:

In total, 128 male rats were used, randomly divided into four experimental groups (n=32): Control; MOS 1; MOS 2; and MOS 3. From each group, eight animals were sacrificed in four experimental moments (14, 28, 42, and 56 days, respectively, moments 1, 2, 3, and 4) and hormonal measurements and histological evaluations were performed.

Results:

The results revealed the effect of diet, MOS, and timing on testicle weight (p<0.05). At moments 3 and 4, the groups supplemented with MOS showed higher concentrations of testosterone and decreased corticosterone levels throughout the experimental period. Groups supplemented with MOS showed an increase in the frequency of relative sperm and sperm scores. The radii of the seminiferous tubules presented a significant statistical effect of the diet, moments, and diet + moment interaction.

Conclusion:

It was concluded that the three different MOS prebiotics brought forward sexual maturity.

Restoration of dysbiotic human gut microbiome for homeostasis

The human microbiome is a complex and dynamic ecosystem, and the imbalance of its microbial community structure from the normal state is termed dysbiosis. The dysbiotic gut microbiome has been proved to be related to several pathological conditions like Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), Colorectal Cancer (CRC), etc., and several other extra-intestinal conditions like Type 1 & 2 diabetes, obesity, etc. The complex gut microbial ecosystem starts to build before the birth of an individual. It is known to get affected by several factors such as birth mode, individual lifestyle, dietary practices, medications, and antibiotics. A dysbiotic microbiome can potentially hamper host homeostasis due to its role in immune modulation, metabolism, nutrient synthesis, etc. Restoration of the dysbiotic gut microbiome has emerged as a promising aid and a better therapeutic approach. Several approaches have been investigated to achieve this goal, including prebiotics and probiotics, Fecal Microbiota Transplantation (FMT), extracellular vesicles, immune modulation, microbial metabolites, dietary interventions, and phages. This review discusses the various factors that influence the human microbiome with respect to their cause-effect relationship and the effect of gut microbiome compositional changes on the brain through the gut-brain axis. We also discuss the practices used globally for gut microbiome restoration purposes, along with their effectiveness.

Xylooligosaccharides Increase Bifidobacteria and Lachnospiraceae in Mice on a High-Fat Diet, with a Concomitant Increase in Short-Chain Fatty Acids, Especially Butyric Acid

Effects of xylooligosaccharides (XOSs) as well as a mixture of XOS, inulin, oligofructose, and partially hydrolyzed guar gum (MIX) in mice fed a high-fat diet (HFD) were studied. Control groups were fed an HFD or a low-fat diet. Special attention was paid to the cecal composition of the gut microbiota and formation of short-chain fatty acids, but metabolic parameters were also documented. The XOS group had significantly higher cecum levels of acetic, propionic, and butyric acids than the HFD group, and the butyric acid content was higher in the XOS than in the MIX group. The cecum microbiota of the XOS group contained more Bifidobacteria, Lachnospiraceae, and S24-7 bacteria than the HFD group. A tendency of lower body weight gain was observed on comparing the XOS and HFD groups. In conclusion, the XOS was shown to be a promising prebiotic candidate. The fiber diversity in the MIX diet did not provide any advantages compared to the XOS diet.

Shaping the Future of Probiotics and Prebiotics

Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.

The Role of Microbiota in Neutrophil Regulation and Adaptation in Newborns

Newborns are highly susceptible to infections and mainly rely on innate immune functions. Reduced reactivity, delayed activation and subsequent failure to resolve inflammation however makes the neonatal immune system a very volatile line of defense. Perinatal microbiota, nutrition and different extra-uterine factors are critical elements that define long-term outcomes and shape the immune system during the neonatal period. Neutrophils are first responders and represent a vital component of the immune system in newborns. They have long been regarded as merely executive immune cells, however this notion is beginning to shift. Neutrophils are shaped by their surrounding and adaptive elements have been described. The role of “innate immune memory” and the main triangle connection microbiome—neutrophil—adaptation will be discussed in this review.

Probiotics, Prebiotics, Synbiotics, and Paraprobiotics as a Therapeutic Alternative for Intestinal Mucositis

Intestinal mucositis, a cytotoxic side effect of the antineoplastic drug 5-fluorouracil (5-FU), is characterized by ulceration, inflammation, diarrhea, and intense abdominal pain, making it an important issue for clinical medicine. Given the seriousness of the problem, therapeutic alternatives have been sought as a means to ameliorate, prevent, and treat this condition. Among the alternatives available to address this side effect of treatment with 5-FU, the most promising has been the use of probiotics, prebiotics, synbiotics, and paraprobiotics. This review addresses the administration of these "biotics" as a therapeutic alternative for intestinal mucositis caused by 5-FU. It describes the effects and benefits related to their use as well as their potential for patient care.

Circulating Pro- and Anti-Inflammatory Metabolites and Its Potential Role in Rheumatoid Arthritis Pathogenesis

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease that affects synovial joints, leading to inflammation, joint destruction, loss of function, and disability. Although recent pharmaceutical advances have improved the treatment of RA, patients often inquire about dietary interventions to improve RA symptoms, as they perceive pain and/or swelling after the consumption or avoidance of certain foods. There is evidence that some foods have pro- or anti-inflammatory effects mediated by diet-related metabolites. In addition, recent literature has shown a link between diet-related metabolites and microbiome changes, since the gut microbiome is involved in the metabolism of some dietary ingredients. But diet and the gut microbiome are not the only factors linked to circulating pro- and anti-inflammatory metabolites. Other factors including smoking, associated comorbidities, and therapeutic drugs might also modify the circulating metabolomic profile and play a role in RA pathogenesis. This article summarizes what is known about circulating pro- and anti-inflammatory metabolites in RA. It also emphasizes factors that might be involved in their circulating concentrations and diet-related metabolites with a beneficial effect in RA.