A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

Promoting the Emerging Role of Pulse By-Products as Valuable Sources of Functional Compounds and Novel Food Ingredients

The growth of the human population worldwide has increased food demand, generating the massive production of foods and consequently causing enormous production of waste every year. The indiscriminate exploitation of the already limited natural resources has also generated serious environmental and economic crises. The use, or reuse, of waste or by-products represents a viable solution to constrain the problem by promoting alternative routes of exploitation with multiple food and biotechnological applications. This review focuses on the most recent advances in the valorization of food by-products, with specific reference to legume-derived by-products. The main technological solutions for reintroducing and/or valorizing food waste are reported together with a critical discussion of the main pros and cons of each alternative, supported by practical case studies whenever available. First, the possibility to exploit the by-products as valuable sources of functional compounds is presented by reviewing both conventional and innovative extraction techniques tailored to provide functional extracts with multiple food, pharmaceutical, and biotechnological applications. Second, the possibility to valorize the by-products as novel food ingredients by inclusion in different formulations, either as a whole or as hydrolyzed/fermented derivatives, is also presented and discussed. To the best of our knowledge, several of the technological solutions discussed have found only limited applications for waste or by-products derived from the legume production chain; therefore, great efforts are still required to gain the full advantages of the intrinsic potential of pulse by-products.

Health Benefits and Safety of Postbiotics Derived from Different Probiotic Species

Nowadays, the usage of probiotics in the food industry has become common. It has been proven that probiotics have many health benefits, such as adjusting the intestinal microbiome, boosting the immune system, and enhancing anti-inflammatory and anti-cancer activities. However, in recent years, some concerns have arisen about the consumption of probiotics, especially in vulnerable populations such as elderly, infants, and people with underlying diseases. As a result, finding a new alternative to probiotics that has the same function as probiotics and is safer has been prioritized. In recent years, postbiotics have been introduced as a great replacement for probiotics. However, the safety of these compounds is not exactly confirmed due to the limited in vivo research. In this review, the definition, classification, activities, limitations, and some advantages of postbiotics over probiotics are discussed. Finally, the limited published data about the safety of postbiotics is summarized.

Cellular and Microbial In Vitro Modelling of Gastrointestinal Cancer

Human diseases are multifaceted, starting with alterations at the cellular level, damaging organs and their functions, and disturbing interactions and immune responses. In vitro systems offer clarity and standardisation, which are crucial for effectively modelling disease. These models aim not to replicate every disease aspect but to dissect specific ones with precision. Controlled environments allow researchers to isolate key variables, eliminate confounding factors and elucidate disease mechanisms more clearly. Technological progress has rapidly advanced model systems. Initially, 2D cell culture models explored fundamental cell interactions. The transition to 3D cell cultures and organoids enabled more life-like tissue architecture and enhanced intercellular interactions. Advanced bioreactor-based devices now recreate the physicochemical environments of specific organs, simulating features like perfusion and the gastrointestinal tract's mucus layer, enhancing physiological relevance. These systems have been simplified and adapted for high-throughput research, marking significant progress. This review focuses on in vitro systems for modelling gastrointestinal tract cancer and the side effects of cancer treatment. While cell cultures and in vivo models are invaluable, our main emphasis is on bioreactor-based in vitro modelling systems that include the gut microbiome.

Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement

Food safety is a global concern, with millions suffering from foodborne diseases annually. The World Health Organization (WHO) reports significant morbidity and mortality associated with contaminated food consumption, and this emphasizes the critical need for comprehensive food safety measures. Recent attention has turned to postbiotics, metabolic byproducts of probiotics, as potential agents for enhancing food safety. Postbiotics, including organic acids, enzymes, and bacteriocins, exhibit antimicrobial and antioxidant properties that do not require live organisms, and this offers advantages over probiotics. This literature review critically examines the role of postbiotics in gut microbiome modulation and applications in the food industry. Through an extensive review of existing literature, this study evaluates the impact of postbiotics on gut microbiome composition and their potential as functional food ingredients. Research indicates that postbiotics are effective in inhibiting food pathogens such as Staphylococcus aureus, Salmonella enterica, and Escherichia coli, as well as their ability to prevent oxidative stress-related diseases, and they also show promise as alternatives to conventional food preservatives that can extend food shelf life by inhibiting harmful bacterial growth. Their application in functional foods contributes to improved gut health and reduced risk of foodborne illnesses. Findings suggest that postbiotics hold promise for improving health and preservation by inhibiting pathogenic bacteria growth and modulating immune responses.

Evaluating functionalities of food components by a model simulating human intestinal microbiota constructed at Kobe University

In this era of pandemics, reducing the risk of lifestyle-related diseases (LRD) by functional foods is of paramount importance. The conventional process of functional food development almost invariably involves in vitro, animal, and human intervention trials, but differences in intestinal environments between humans and experimental animals make it difficult to develop functional foods that are truly effective in humans. Thus, it is necessary to construct a model that simulates the human intestinal environment to evaluate the functionality of any food component before subjecting it to a human intervention trial. In this review, we provide an overview of a model simulating human intestinal microbiota constructed at Kobe University and its use as a tool to identify food components that contribute to the prevention and treatment of LRD.

Ascomycetes yeasts: The hidden part of human microbiome

The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.

Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota

BACKGROUND

Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies.

METHODS AND RESULTS

Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80 °C or 4 °C) significantly influenced either microbial composition at 16 h of anaerobic culture or the principal components of the metabolome at 8 or 16 h. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2'-fucosyllactose or dextrose).

CONCLUSIONS

These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16 hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota.

Mechanism of procyanidins for health functionality by improving the intestinal environment

Procyanidins are one of the polyphenols consisting of multiple flavan-3-ols (eg epicatechin). They have a complex chemical structure, with the degree of polymerization and linked position of flavan-3-ols varying among various foods, such as apples and chocolate. Physiological functional studies of procyanidins have investigated their mechanisms in cells and animals based on their antioxidant effects. Recently, the intestinal environment, including the intestinal microflora, has played an important role in the energy metabolism and health status of the host. Regulation of the intestinal environment by dietary polyphenols is becoming a new concept in health functions, and we have begun to investigate the mechanism of apple procyanidins, focusing on the gut microbiota and metabolites in our functional research. In this minireview, we will discuss the effects of procyanidin ingestion on the gut microbiota and metabolites.

Postbiotics: Functional Food Materials and Therapeutic Agents for Cancer, Diabetes, and Inflammatory Diseases

Postbiotics are (i) "soluble factors secreted by live bacteria, or released after bacterial lysis, such as enzymes, peptides, teichoic acids, peptidoglycan-derived muropeptides, polysaccharides, cell-surface proteins and organic acids"; (ii) "non-viable metabolites produced by microorganisms that exert biological effects on the hosts"; and (iii) "compounds produced by microorganisms, released from food components or microbial constituents, including non-viable cells that, when administered in adequate amounts, promote health and wellbeing". A probiotic- and prebiotic-rich diet ensures an adequate supply of these vital nutrients. During the anaerobic fermentation of organic nutrients, such as prebiotics, postbiotics act as a benevolent bioactive molecule matrix. Postbiotics can be used as functional components in the food industry by offering a number of advantages, such as being added to foods that are harmful to probiotic survival. Postbiotic supplements have grown in popularity in the food, cosmetic, and healthcare industries because of their numerous health advantages. Their classification depends on various factors, including the type of microorganism, structural composition, and physiological functions. This review offers a succinct introduction to postbiotics while discussing their salient features and classification, production, purification, characterization, biological functions, and applications in the food industry. Furthermore, their therapeutic mechanisms as antibacterial, antiviral, antioxidant, anticancer, anti-diabetic, and anti-inflammatory agents are elucidated.

Postbiotic production: harnessing the power of microbial metabolites for health applications

Postbiotics, which are bioactive substances derived from the metabolic processes of beneficial microbes, have received considerable attention in the field of microbiome science in recent years, presenting a promising path for exploration and innovation. This comprehensive analysis looks into the multidimensional terrain of postbiotic production, including an extensive examination of diverse postbiotic classes, revealing their sophisticated mechanisms of action and highlighting future applications that might significantly affect human health. The authors thoroughly investigate the various mechanisms that support postbiotic production, ranging from conventional fermentation procedures to cutting-edge enzyme conversion and synthetic biology approaches. The review, as an acknowledgment of the field's developing nature, not only highlights current achievements but also navigates through the problems inherent in postbiotic production. In order to successfully include postbiotics in therapeutic interventions and the production of functional food ingredients, emphasis is given to critical elements, including improving yields, bolstering stability, and assuring safety. The knowledge presented herein sheds light on the expanding field of postbiotics and their potential to revolutionize the development of novel therapeutics and functional food ingredients.

Establishment of porcine fecal-derived ex vivo microbial communities to evaluate the impact of livestock feed on gut microbiome

Sustainable livestock production requires reducing competition for food and feed resources and increasing the utilization of food by-products in livestock feed. This study describes the establishment of an anaerobic batch culture model to simulate pig microbiota and evaluate the effects of a food by-product, wakame seaweed stalks, on ex vivo microbial communities. We selected one of the nine media to support the growth of a bacterial community most similar in composition and diversity to that observed in pig donor feces. Supplementation with wakame altered the microbial profile and short-chain fatty acid composition in the ex vivo model, and a similar trajectory was observed in the in vivo pig experimental validation. Notably, the presence of wakame increased the abundance of Lactobacillus species, which may have been due to cross-feeding with Bacteroides. These results suggest the potential of wakame as a livestock feed capable of modulating the pig microbiome. Collectively, this study highlights the ability to estimate the microbiome changes that occur when pigs are fed a specific feed using an ex vivo culture model.

Effects of Synbiotic Lacticaseibacillus paracasei, Bifidobacterium breve, and Prebiotics on the Growth Stimulation of Beneficial Gut Microbiota

The gut microbiota is a complex community of microorganisms that plays a vital role in maintaining overall health, and is comprised of Lactobacillus and Bifidobacterium. The probiotic efficacy and safety of Lacticaseibacillus paracasei and Bifidobacterium breve for consumption were confirmed by in vitro experiments. The survival rate of the probiotics showed a significant decline in in vitro gut tract simulation; however, the survival rate was more than 50%. Also, the probiotics could adhere to Caco-2 cell lines by more than 90%, inhibit the pathogenic growths, deconjugate glycocholic acid and taurodeoxycholic acid through activity of bile salt hydrolase (BSH) proteins, and lower cholesterol levels by over 46%. Regarding safety assessment, L. paracasei and B. breve showed susceptibility to some antibiotics but resistance to vancomycin and were examined as γ-hemolytic strains. Anti-inflammatory properties of B. breve with Caco-2 epithelial cell lines showed the significantly highest value (p < 0.05) for interleukin-10. Furthermore, probiotics and prebiotics (inulin, fructooligosaccharides, and galactooligosaccharides) comprise synbiotics, which have potential effects on the increased abundance of beneficial microbiota, but do not affect the growth of harmful bacteria in feces samples. Moreover, the highest concentration of short chain fatty acid was of acetic acid, followed by propionic and butyric acid.

Effects of blackcurrant extract on indole and ammonia productions in an in vitro human fecal culture model

Blackcurrant is available as a traditional medicine in Europe. However, the detailed effects of blackcurrant on the human gut microbiota remain unknown. In this study, we investigated the prebiotic effects of a blackcurrant extract using a human fecal culture model in six healthy subjects. Feces were individually inoculated into a medium with or without the blackcurrant extract and then fermented for 48 hr under anaerobic conditions. The results obtained from analysis of samples from the fermented medium demonstrated that after 48 hr of fermentation, the pH of the medium with the blackcurrant extract was significantly decreased (control, 6.62 ± 0.20; blackcurrant extract, 6.41 ± 0.33; p=0.0312). A 16S rRNA gene sequencing analysis of the microbiota of the fermented medium showed a significant increase in the relative abundance of Bifidobacteriaceae. In measuring the concentrations of putrefactive components in the fermented medium, we found that the blackcurrant extract significantly reduced ammonia levels and displayed a tendency toward reduced indole levels. Our results suggest that blackcurrant extract could be a potential ingredient for relief of putrefactive components in the gut.

Sulfated and non-sulfated chondroitin affect the composition and metabolism of human colonic microbiota simulated in an in vitro fermentation system

Chondroitin sulfate (CS) is a family of glycosaminoglycans and have a wide range of applications in dietary supplements and pharmaceutical drugs. In this study, we evaluated the effects of several types of CS, differing in their sulfated positions, on the human colonic microbiota and their metabolites. CS (CSA, CSC, and CSE) and non-sulfated chondroitin (CH) were added into an in vitro human colonic microbiota model with fecal samples from 10 healthy individuals. CS addition showed a tendency to increase the relative abundance of Bacteroides, Eubacterium, and Faecalibacterium, and CSC and CSE addition significantly increased the total number of eubacteria in the culture of the Kobe University Human Intestinal Microbiota Model. CSE addition also resulted in a significant increase in short-chain fatty acid (SCFA) levels. Furthermore, addition with CSC and CSE increased the levels of a wide range of metabolites including lysine, ornithine, and Ile-Pro-Pro, which could have beneficial effects on the host. However, significant increases in the total number of eubacteria, relative abundance of Bacteroides, and SCFA levels were also observed after addition with CH, and the trends in the effects of CH addition on metabolite concentrations were identical to those of CSC and CSE addition. These results provide novel insight into the contribution of the colonic microbiota to the beneficial effects of dietary CS.

Prebiotic and Anti-Adipogenic Effects of Radish Green Polysaccharide

Radish (Raphanus sativus L.) greens are consumed as a source of nutrition, and their polysaccharides such as rhamnogalacturonan-I possess certain beneficial properties. This study investigated the prebiotic effects of a radish green polysaccharide (RGP) on gut health and obesity. The prebiotic activity of RGP was evaluated based on the pH changes and short-chain fatty acids (SCFAs) concentration. The results showed that 0.5% RGP had a higher prebiotic activity score than inulin and increased SCFAs production in all five prebiotic strains. Moreover, RGP inhibited fat accumulation in 3T3-L1 adipocytes, indicating its potential to reduce obesity. Overall, these findings suggested that the polysaccharide of radish greens has prebiotic effects and may serve as a beneficial prebiotic for gut health and obesity.

A short-term bioreactor assay to assess the effect of essential oils on a microbiota derived from piglet's intestinal content

BACKGROUND

Modulating the microbiota is an emerging way to improve pig health. In-vitro bioreactor systems can be used to reproduce intestinal microbiota to study modulating avenues. In this study, a continuous feeding system to support a microbiota derived from piglet colonic contents, over 72 h, was developed. The microbiota from piglets was collected and used as inoculum. The culture media was derived from an artificial digestion of piglet feed. The microbiota diversity in time, the reproducibility between replicates and the diversity of the bioreactor microbiota compared to the inoculum was assessed. Essential oils were used as a proof of concept to assess the in vitro microbiota modulation. The microbiota diversity was assessed by 16S rRNA amplicon sequencing. Quantitative PCR was also used for total bacteria, lactobacilli and Enterobacteria.

RESULTS

At the start of the assay, the bioreactor microbiota diversity was similar to the inoculum. Time and replication affected the bioreactor microbiota diversity. Between 48 and 72 h, no statistical variation of the microbiota diversity was observable. After a 48 h running period, thymol and carvacrol were added at 200 ppm or 1000 ppm for 24 h. No microbiota modification was observed by sequencing. Quantitative PCR results showed a significant growth of lactobacilli when thymol was used at 1000 ppm, where only a trend was observed with the 16S analysis.

CONCLUSIONS

This study presents a bioreactor assay that can be used as a tool for rapid screening of additives and suggests that the effects of essential oils on the microbiota are subtle, acting against a few bacterial genera.

Effects of partially hydrolyzed guar gums of different molecular weights on a human intestinal in vitro fermentation model

Partially hydrolyzed guar gums (PHGGs) are prebiotic soluble dietary fibers. High molecular-weight PHGGs have rapid fermentation and high short-chain fatty acid (SCFA) productivity rates, compared to low molecular-weight PHGGs. Therefore, low molecular-weight PHGGs may have less pronounced prebiotic effects than high molecular-weight PHGGs. However, the effects of PHGGs of different molecular weights on the human intestinal microbiota, as well as their fermentation ability and prebiotic effects, have not been investigated. The aim of this study was to evaluate the effects of two PHGGs of different molecular weights, Sunfiber-R (SF-R; 20 kDa) and Sunfiber-V (SF-V; 5 kDa), on human colonic microbiota and SCFA production. A human intestinal in vitro fermentation model was operated by fecal samples with and without the PHGGs. The addition of 0.2% SF-R or SF-V increased the relative abundance of Bacteroides spp., especially that of Bacteroides uniformis. This increase corresponded to a significant (p = 0.030) and non-significant (p = 0.073) increase in propionate production in response to SF-R and SF-V addition, respectively. Both fibers increased the relative abundance of Faecalibacterium and stimulated an increase in the abundance of unclassified Lachnospiraceae and Bifidobacterium. In conclusion, the low molecular-weight PHGG exerted prebiotic effects on human colonic microbiota to increase SCFA production and bacteria that are beneficial to human health in a manner similar to that of the high molecular-weight forms of PHGG.

An in vitro platform for study of the human gut microbiome under an oxygen gradient

The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. We have developed an in vitro 40-plex platform that provides an oxygen gradient to support simultaneous maintenance of microaerobic and anaerobic microbes from the gut microbiome that can aid in rapid characterization of microbial interactions and direct comparison of individual microbiome samples. In this report, we demonstrate that the platform more closely maintained the microbial diversity and composition of human donor fecal microbiome samples than strict anaerobic conditions. The oxygen gradient established in the platform allowed the stratification and subsequent sampling of diverse microbial subpopulations that colonize microaerobic and anaerobic micro-environments. With the ability to run forty samples in parallel, the platform has the potential to be used as a rapid screening tool to understand how the gut microbiome responds to environmental perturbations such as toxic compound exposure, dietary changes, or pharmaceutical treatments.

Fermentation Supernatant of Elderly Feces with Inulin and Partially Hydrolyzed Guar Gum Maintains the Barrier of Inflammation-Induced Caco-2/HT29-MTX-E12 Co-Cultured Cells

Intestinal barrier function declines with aging. We evaluated the effect of dietary fibers and indigestible oligosaccharides on intestinal barrier function by altering the microbiota of the elderly. The feces were anaerobically cultured with indigestible dextrin, inulin, partially hydrolyzed guar gum (PHGG), lactulose, raffinose, or alginate, and the fermented supernatant was added to inflammation-induced Caco-2/HT29-MTX-E12 co-cultured cells. Our data showed that inulin- and PHGG-derived supernatants exerted a protective effect on the intestinal barrier. The protective effect was significantly positively correlated with total short-chain fatty acids (SCFAs) and butyric acid production in the supernatant and negatively correlated with the claudin-2 (CLDN2) gene expression in the cultured cells. Furthermore, we showed that the CLDN2 levels are regulated by butyric acid. Thus, inulin and PHGG can change the intestinal environment of the elderly and maintain the intestinal barrier by accelerating the production of SCFAs and modifying the expression levels of barrier function-related genes.

Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota

Hyaluronan (HA) is a high-molecular-weight glycosaminoglycan and widely distributed in all connective tissues and organs with diverse biological functions. HA has been increasingly used as dietary supplements targeted to joint and skin health for humans. We here first report isolation of bacteria from human feces that are capable of degrading HA to lower molecular weight HA oligosaccharides (oligo-HAs). The bacteria were successfully isolated via a selective enrichment method, in which the serially diluted feces of healthy Japanese donors were individually incubated in an enrichment medium containing HA, followed by the isolation of candidate strains from streaked HA-containing agar plates and selection of HA-degrading strains by measuring HA using an ELISA. Subsequent genomic and biochemical assays identified the strains as Bacteroides finegoldii, B. caccae, B. thetaiotaomicron, and Fusobacterium mortiferum. Furthermore, our HPLC analysis revealed that the strains degraded HA to oligo-HAs of various lengths. Subsequent quantitative PCR assay targeting the HA degrading bacteria showed that their distribution in the Japanese donors varied. The evidence suggests that dietary HA is degraded by the human gut microbiota with individual variation to oligo-HAs components, which are more absorbable than HA, thereby exerting its beneficial effects.

Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model

Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.

Postbiotics: Current Trends in Food and Pharmaceutical Industry

Postbiotics are non-viable bacterial products or metabolic byproducts produced by probiotic microorganisms that have biologic activity in the host. Postbiotics are functional bioactive compounds, generated in a matrix during anaerobic fermentation of organic nutrients like prebiotics, for the generation of energy in the form of adenosine triphosphate. The byproducts of this metabolic sequence are called postbiotics, these are low molecular weight soluble compounds either secreted by live microflora or released after microbial cell lysis. A few examples of widely studied postbiotics are short-chain fatty acids, microbial cell fragments, extracellular polysaccharides, cell lysates, teichoic acid, vitamins, etc. Presently, prebiotics and probiotics are the products on the market; however, postbiotics are also gaining a great deal of attention. The numerous health advantages of postbiotic components may soon lead to an increase in consumer demand for postbiotic supplements. The most recent research aspects of postbiotics in the food and pharmaceutical industries are included in this review. The review encompasses a brief introduction, classification, production technologies, characterization, biological activities, and potential applications of postbiotics.

Short-Chain Fatty Acid Receptors and Blood Pressure Regulation: Council on Hypertension Mid-Career Award for Research Excellence 2021

The gut microbiome influences host physiology and pathophysiology through several pathways, one of which is microbial production of chemical metabolites which interact with host signaling pathways. Short-chain fatty acids (SCFAs) are a class of gut microbial metabolites known to activate multiple signaling pathways in the host. Growing evidence indicates that the gut microbiome is linked to blood pressure, that SCFAs modulate blood pressure regulation, and that delivery of exogenous SCFAs lowers blood pressure. Given that hypertension is a key risk factor for cardiovascular disease, the examination of novel contributors to blood pressure regulation has the potential to lead to novel approaches or treatments. Thus, this review will discuss SCFAs with a focus on their host G protein-coupled receptors including GPR41 (G protein-coupled receptor 41), GPR43, and GPR109A, as well as OLFR78 (olfactory receptor 78) and OLFR558. This includes a discussion of the ligand profiles, G protein coupling, and tissue distribution of each receptor. We will also review phenotypes relevant to blood pressure regulation which have been reported to date for Gpr41, Gpr43, Gpr109a, and Olfr78 knockout mice. In addition, we will consider how SCFA signaling influences physiology at baseline, and, how SCFA signaling may contribute to blood pressure regulation in settings of hypertension. In sum, this review will integrate current knowledge regarding how SCFAs and their receptors regulate blood pressure.

An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota

Lytic bacteriophages are considered safe for human consumption as biocontrol agents against foodborne pathogens, in particular in ready-to-eat foodstuffs. Phages could, however, evolve to infect different hosts when passing through the gastrointestinal tract (GIT). This underlines the importance of understanding the impact of phages towards colonic microbiota, particularly towards bacterial families usually found in the colon such as the Enterobacteriaceae. Here we propose in vitro batch fermentation as model for initial safety screening of lytic phages targeting Shiga toxin-producing Escherichia coli (STEC). As inoculum we used faecal material of three healthy donors. To assess phage safety, we monitored fermentation parameters, including short chain fatty acid production and gas production/intake by colonic microbiota. We performed shotgun metagenomic analysis to evaluate the outcome of phage interference with colonic microbiota composition and functional potential. During the 24 h incubation, concentrations of phage and its host were also evaluated. We found the phage used in this study, named E. coli phage vB_EcoS_Ace (Ace), to be safe towards human colonic microbiota, independently of the donors’ faecal content used. This suggests that individuality of donor faecal microbiota did not interfere with phage effect on the fermentations. However, the model revealed that the attenuated STEC strain used as phage host perturbed the faecal microbiota as based on metagenomic analysis, with potential differences in metabolic output. We conclude that the in vitro batch fermentation model used in this study is a reliable safety screening for lytic phages intended to be used as biocontrol agents.

An Updated Review on Prebiotics: Insights on Potentials of Food Seeds Waste as Source of Potential Prebiotics

Prebiotics are a group of biological nutrients that are capable of being degraded by microflora in the gastrointestinal tract (GIT), primarily Lactobacilli and Bifidobacteria. When prebiotics are ingested, either as a food additive or as a supplement, the colonic microflora degrade them, producing short-chain fatty acids (SCFA), which are simultaneously released in the colon and absorbed into the blood circulatory system. The two major groups of prebiotics that have been extensively studied in relation to human health are fructo-oligosaccharides (FOS) and galactooligosaccharides (GOS). The candidature of a compound to be regarded as a prebiotic is a function of how much of dietary fiber it contains. The seeds of fruits such as date palms have been reported to contain dietary fiber. An increasing awareness of the consumption of fruits and seeds as part of the daily diet, as well as poor storage systems for seeds, have generated an enormous amount of seed waste, which is traditionally discarded in landfills or incinerated. This cultural practice is hazardous to the environment because seed waste is rich in organic compounds that can produce hazardous gases. Therefore, this review discusses the potential use of seed wastes in prebiotic production, consequently reducing the environmental hazards posed by these wastes.

Role of Postbiotics in Diet-Induced Metabolic Disorders

Although the prevalence of metabolic disorders has progressively increased over the past few decades, metabolic disorders can only be effectively treated with calorie restriction and improved physical activity. Recent research has focused on altering the gut microbiome using prebiotics, probiotics, and postbiotics because various metabolic syndromes are caused by gut microbial dysbiosis. Postbiotics, substances produced or released by microorganism metabolic activities, play an important role in maintaining and restoring host health. Because postbiotics have a small amount of literature on their consumption, there is a need for more experiments on short- and long-term intake. This review discusses current postbiotic research, categories of postbiotics, positive roles in metabolic syndromes, and potential therapeutic applications. It covers postbiotic pleiotropic benefits, such as anti-obesity, anti-diabetic, and anti-hypertensive qualities, that could aid in the management of metabolic disorders. Postbiotics are promising tools for developing health benefits and therapeutic goals owing to their clinical, technical, and economic properties. Postbiotic use is attractive for altering the microbiota; however, further studies are needed to determine efficacy and safety.

Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?

Raffinose family oligosaccharides (RFOs) are widespread across the plant kingdom, and their concentrations are related to the environment, genotype, and harvest time. RFOs are known to carry out many functions in plants and humans. In this paper, we provide a comprehensive review of RFOs, including their beneficial and anti-nutritional properties. RFOs are considered anti-nutritional factors since they cause flatulence in humans and animals. Flatulence is the single most important factor that deters consumption and utilization of legumes in human and animal diets. In plants, RFOs have been reported to impart tolerance to heat, drought, cold, salinity, and disease resistance besides regulating seed germination, vigor, and longevity. In humans, RFOs have beneficial effects in the large intestine and have shown prebiotic potential by promoting the growth of beneficial bacteria reducing pathogens and putrefactive bacteria present in the colon. In addition to their prebiotic potential, RFOs have many other biological functions in humans and animals, such as anti-allergic, anti-obesity, anti-diabetic, prevention of non-alcoholic fatty liver disease, and cryoprotection. The wide-ranging applications of RFOs make them useful in food, feed, cosmetics, health, pharmaceuticals, and plant stress tolerance; therefore, we review the composition and diversity of RFOs, describe the metabolism and genetics of RFOs, evaluate their role in plant and human health, with a primary focus in grain legumes.

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.

The final fate of food: On the establishment of in vitro colon models

The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.

Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity

The gut microbiome has emerged as a key regulator of obesity; however, its role in brown adipose tissue (BAT) metabolism and association with obesity remain to be elucidated. We found that the levels of circulating branched-chain amino acids (BCAA) and their cognate α-ketoacids (BCKA) were significantly correlated with the body weight in humans and mice and that BCAA catabolic defects in BAT were associated with obesity in diet-induced obesity (DIO) mice. Pharmacological systemic enhancement of BCAA catabolic activity reduced plasma BCAA and BCKA levels and protected against obesity; these effects were reduced in BATectomized mice. DIO mice gavaged with Bacteroides dorei and Bacteroides vulgatus exhibited improved BAT BCAA catabolism and attenuated body weight gain, which were not observed in BATectomized DIO mice. Our data have highlighted a possible link between the gut microbiota and BAT BCAA catabolism and suggest that Bacteroides probiotics could be used for treating obesity.

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Gut microbiota regulated BAT BCAA catabolism

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Bacteroides promoted BAT BCAA catabolism and inhibited obesity

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Bacteroides suppressed BAT inflammation that contributed to BAT BCAA catabolic defect

Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization

There are numerous bacteria reside within the mammalian gastrointestinal tract. Among the intestinal bacteria, Akkermansia, Bacteroides, Bifidobacterium, and Ruminococcus closely interact with the intestinal mucus layer and are, therefore, known as mucosal bacteria. Mucosal bacteria use host or dietary glycans for colonization via adhesion, allowing access to the carbon source that the host’s nutrients provide. Cell wall or membrane proteins, polysaccharides, and extracellular vesicles facilitate these mucosal bacteria-host interactions. Recent studies revealed that the physiological properties of Bacteroides and Bifidobacterium significantly change in the presence of co-existing symbiotic bacteria or markedly differ with the spatial distribution in the mucosal niche. These recently discovered strategic colonization processes are important for understanding the survival of bacteria in the gut. In this review, first, we introduce the experimental models used to study host-bacteria interactions, and then, we highlight the latest discoveries on the colonization properties of mucosal bacteria, focusing on the roles of the cell surface architecture regarding Bacteroides and Bifidobacterium.

In vitro models to evaluate ingestible devices: Present status and current trends

Orally ingestible medical devices offer significant opportunity in the diagnosis and treatment of gastrointestinal conditions. Their development necessitates the use of models that simulate the gastrointestinal environment on both a macro and micro scale. An evolution in scientific technology has enabled a wide range of in vitro, ex vivo and in vivo models to be developed that replicate the gastrointestinal tract. This review describes the landscape of the existing range of in vitro tools that are available to characterize ingestible devices. Models are presented with details on their benefits and limitations with regards to the evaluation of ingestible devices and examples of their use in the evaluation of such devices is presented where available. The multitude of models available provides a suite of tools that can be used in the evaluation of ingestible devices that should be selected on the functionality of the device and the mechanism of its function.

Multiunit In Vitro Colon Model for the Evaluation of Prebiotic Potential of a Fiber Plus D-Limonene Food Supplement

The search for new fiber supplements that can claim to be "prebiotic" is expanding fast, as the role of prebiotics and intestinal microbiota in well-being has been well established. This work explored the prebiotic potential of a novel fiber plus D-Limonene supplement (FLS) in comparison to fructooligosaccharides (FOS) over distal colonic fermentation with the in vitro model MICODE (multi-unit in vitro colon gut model). During fermentation, volatilome characterization and core microbiota quantifications were performed, then correlations among volatiles and microbes were interpreted. The results indicated that FLS generated positive effects on the host gut model, determining: (i) eubiosis; (ii) increased abundance of beneficial bacteria, as Bifidobacteriaceae; (iii) production of beneficial compounds, as n-Decanoic acid; (iv) reduction in detrimental bacteria, as Enterobaceteriaceae; (v) reduction in detrimental compounds, as skatole. The approach that we followed permitted us to describe the prebiotic potential of FLS and its ability to steadily maintain the metabolism of colon microbiota over time. This aspect is two-faced and should be investigated further because if a fast microbial turnover and production of beneficial compounds is a hallmark of a prebiotic, the ability to reduce microbiota changes and to reduce imbalances in the productions of microbial metabolites could be an added value to FLS. In fact, it has been recently demonstrated that these aspects could serve as an adjuvant in metabolic disorders and cognitive decline.

Influence of Cultivation pH on Composition, Diversity, and Metabolic Production in an In Vitro Human Intestinal Microbiota

Fecal microbiota transplantation, an alternative treatment method for gastrointestinal diseases, has a high recovery rate, but comes with disadvantages, such as high donor requirements and the low storability of stool. A solution to overcome these problems is the cultivation of an in vitro microbiota. However, the influence of cultivation conditions on the pH are yet unknown. In this study, the influence of the cultivation pH (6.0–7.0) on the system’s behavior and characteristics, including cell count, metabolism, and microbial composition, was investigated. With an increasing cultivation pH, an increase in cell count, total amount of SCFAs, acetate, propionate, and the abundance of Bacteroidetes and Verrucomicrobia were observed. For the concentration of butyrate and the abundance of Actinobacteria and Firmicutes, a decrease with increasing pH was determined. For the concentration of isovalerate, the abundance of Proteobacteria and diversity (richness and Shannon effective), no effect of the pH was observed. Health-promoting genera were more abundant at lower pH levels. When cultivating an in vitro microbiota, all investigated pH values created a diverse and stable system. Ultimately, therefore, the choice of pH creates significant differences in the established in vitro microbiota, but no clear recommendations for a special value can be made.

Pulse-based snacks as functional foods: Processing challenges and biological potential

Despite their high nutritional value and potential health benefits, pulse intake has not increased in the last three decades. Several strategies have been implemented to increase pulse consumption, such as their incorporation in bakery products, breakfast cereals, and snacks. The inclusion of pulses in these products could be an alternative to satisfy the consumers' demand for healthy foods. However, pulse-based snacks face important challenges, including reducing antinutritional factors, achieving consumer acceptance, and consolidating the pulse-based snacks as functional foods. This review summarizes and discusses methods for producing snacks where cereals or tubers were replaced with at least 50% pulses. Also, it briefly assesses their effect on nutritional composition, antinutritional factors, sensory acceptance, and different health benefits evaluations. Extruded snacks exhibited high protein and dietary fiber and low fat content, contrary to the high fat content of deep fat-fried snacks. Meanwhile, baked snacks presented moderate concentrations of protein, dietary fiber, and lipids. Pulses must be pretreated using process combinations such as soaking, dehulling, cooking, fermentation, germination, and extrusion to reduce the antinutritional factors. Pulse-based snacks show good sensory acceptance. However, sensory evaluation should be more rigorous using additional untrained judges. Several studies have evaluated the health benefits of pulse-based snacks. More research is needed to validate scientifically the health benefits associated with their consumption. Pulse-based snacks could be an alternative to improve the nutritional composition of commercially available snacks. The use of pulses as ingredients of healthier snacks represents an important alternative for the food industry due to their low cost, sensory characteristics, high nutritional profile, and environmental benefits.

W27 IgA suppresses growth of Escherichia in an in vitro model of the human intestinal microbiota

W27 monoclonal immunoglobulin A (IgA) suppresses pathogenic Escherichia coli cell growth; however, its effect on the human intestine remains unclear. We aimed to determine how W27 IgA affects the human colonic microbiota using the in vitro microbiota model. This model was established using fecal samples collected from 12 healthy volunteers; after anaerobic cultivation, each model was found to retain the genera found in the original human fecal samples. After pre-incubating W27 IgA with the respective fecal sample under aerobic conditions, the mixture of W27 IgA (final concentration, 0.5 μg/mL) and each fecal sample was added to the in vitro microbiota model and cultured under anaerobic conditions. Next-generation sequencing of the bacterial 16S rRNA gene revealed that W27 IgA significantly decreased the relative abundance of bacteria related to the genus Escherichia in the model. Additionally, at a final concentration of 5 μg/mL, W27 IgA delayed growth in the pure culture of Escherichia coli isolated from human fecal samples. Our study thus revealed the suppressive effect of W27 IgA on the genus Escherichia at relatively low-concentrations and the usefulness of an in vitro microbiota model to evaluate the effect of IgA as a gut microbiota regulator.

The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training

Short-chain fatty acids (SCFAs) are metabolites produced in the gut via microbial fermentation of dietary fibers referred to as microbiota-accessible carbohydrates (MACs). Acetate, propionate, and butyrate have been observed to regulate host dietary nutrient metabolism, energy balance, and local and systemic immune functions. In vitro and in vivo experiments have shown links between the presence of bacteria-derived SCFAs and host health through the blunting of inflammatory processes, as well as purported protection from the development of illness associated with respiratory infections. This bank of evidence suggests that SCFAs could be beneficial to enhance the athlete's immunity, as well as act to improve exercise recovery via anti-inflammatory activity and to provide additional energy substrates for exercise performance. However, the mechanistic basis and applied evidence for these relationships in humans have yet to be fully established. In this narrative review, we explore the existing knowledge of SCFA synthesis and the functional importance of the gut microbiome composition to induce SCFA production. Further, changes in gut microbiota associated with exercise and various dietary MACs are described. Finally, we provide suggestions for future research and practical applications, including how these metabolites could be manipulated through dietary fiber intake to optimize immunity and energy metabolism.

Establishment of an In Vitro System of the Human Intestinal Microbiota: Effect of Cultivation Conditions and Influence of Three Donor Stool Samples

Fecal microbiota transplantation (FMT) is an alternative method for the treatment of gastrointestinal diseases with a high recovery rate. Disadvantages are ethical concerns, high donor requirements and the low storability of stool samples. The cultivation of an in vitro microbiota in a continuous bioreactor was established as an alternative to FMT to overcome these problems. In this study, the influence of the system parameters and donor stool characteristics was investigated. Each continuous colonic fermentation system was inoculated with feces from three different donors until a stable state was established. The influence of the fermentation conditions on the system's behavior regarding cell count, metabolic activity, short-chain fatty acid profile and microbiota composition as well as richness and diversity was assessed. Cultivation conditions were found to affect the microbial system: the number of cells and the production of short-chain fatty acids increased. The abundance of Actinobacteria and Firmicutes decreased, Bacteroidetes increased, while Proteobacteria and Verrucomicrobia remained largely unaffected. Diversity in the in vitro system decreased, but richness was unaffected. The cultivation of stool from different donors revealed that the performance of the created in vitro system was similar and comparable, but unique characteristics of the composition of the original stool remained.

The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota

Purpose

Plasma trimethylamine-N-oxide (TMAO) levels have been shown to correlate with increased risk of metabolic diseases including cardiovascular diseases. TMAO exposure predominantly occurs as a consequence of gut microbiota-dependent trimethylamine (TMA) production from dietary substrates including choline, carnitine and betaine, which is then converted to TMAO in the liver. Reducing microbial TMA production is likely to be the most effective and sustainable approach to overcoming TMAO burden in humans. Current models for studying microbial TMA production have numerous weaknesses including the cost and length of human studies, differences in TMA(O) metabolism in animal models and the risk of failing to replicate multi-enzyme/multi-strain pathways when using isolated bacterial strains. The purpose of this research was to investigate TMA production from dietary precursors in an in-vitro model of the human colon.

Methods

TMA production from choline, l-carnitine, betaine and γ-butyrobetaine was studied over 24–48 h using an in-vitro human colon model with metabolite quantification performed using LC–MS.

Results

Choline was metabolised via the direct choline TMA-lyase route but not the indirect choline–betaine-TMA route, conversion of l-carnitine to TMA was slower than that of choline and involves the formation of the intermediate γ-BB, whereas the Rieske-type monooxygenase/reductase pathway for l-carnitine metabolism to TMA was negligible. The rate of TMA production from precursors was choline > carnitine > betaine > γ-BB. 3,3-Dimethyl-1-butanol (DMB) had no effect on the conversion of choline to TMA.

Conclusion

The metabolic routes for microbial TMA production in the colon model are consistent with observations from human studies. Thus, this model is suitable for studying gut microbiota metabolism of TMA and for screening potential therapeutic targets that aim to attenuate TMA production by the gut microbiota.

Trial registration number

NCT02653001 (http://www.clinicaltrials.gov), registered 12 Jan 2016.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00394-021-02572-6.

Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design

The importance of the gut microbiota in human health and disease progression makes it a target for research in both the biomedical and nutritional fields. To date, a number of in vitro systems have been designed to recapitulate the gut microbiota of the colon ranging in complexity from the application of a single vessel to cultivate the community in its entirety, to multi-stage systems that mimic the distinct regional microbial communities that reside longitudinally through the colon. While these disparate types of in vitro designs have been employed previously, information regarding similarities and differences between the communities that develop within was less defined. Here, a comparative analysis of the population dynamics and functional production of short-chain fatty acids (SCFAs) was performed using the gut microbiota of the same donor cultured using a single vessel and a 3-stage colon system. The results found that the single vessel communities maintained alpha diversity at a level comparable to the distal regions of the 3-stage colon system. Yet, there was a marked difference in the type and abundance of taxa, particularly between families Enterobacteriaceae, Bacteroidaceae, Synergistaceae, and Fusobacteriaceae. Functionally, the single vessel community produced significantly less SCFAs compared to the 3-stage colon system. These results provide valuable information on how culturing technique effects gut microbial composition and function, which may impact studies relying on the application of an in vitro strategy. This data can be used to justify experimental strategy and provides insight on the application of a simplified versus complex study design. KEY POINTS : • A mature gut microbiota community can be developed in vitro using different methods. • Beta diversity metrics are affected by the in vitro culturing method applied. • The type and amount of short-chain fatty acids differed between culturing methods.

Novel and emerging prebiotics: Advances and opportunities

Consumers are conscientiously changing their eating preferences toward healthier options, such as functional foods enriched with pre- and probiotics. Prebiotics are attractive bioactive compounds with multidimensional beneficial action on both human and animal health, namely on the gastrointestinal tract, cardiometabolism, bones or mental health. Conventionally, prebiotics are non-digestible carbohydrates which generally present favorable organoleptic properties, temperature and acidic stability, and are considered interesting food ingredients. However, according to the current definition of prebiotics, application categories other than food are accepted, as well as non-carbohydrate substrates and bioactivity at extra-intestinal sites. Regulatory issues are considered a major concern for prebiotics since a clear understanding and application of these compounds among the consumers, regulators, scientists, suppliers or manufacturers, health-care providers and standards or recommendation-setting organizations are of utmost importance. Prebiotics can be divided in several categories according to their development and regulatory status. Inulin, galactooligosaccharides, fructooligosaccharides and lactulose are generally classified as well established prebiotics. Xylooligosaccharides, isomaltooligosaccharides, chitooligosaccharides and lactosucrose are classified as "emerging" prebiotics, while raffinose, neoagaro-oligosaccharides and epilactose are "under development." Other substances, such as human milk oligosaccharides, polyphenols, polyunsaturated fatty acids, proteins, protein hydrolysates and peptides are considered "new candidates." This chapter will encompass actual information about the non-established prebiotics, mainly their physicochemical properties, market, legislation, biological activity and possible applications. Generally, there is a lack of clear demonstrations about the effective health benefits associated with all the non-established prebiotics. Overcoming this limitation will undoubtedly increase the demand for these compounds and their market size will follow the consumer's trend.

Growth-promoting effect of alginate on Faecalibacterium prausnitzii through cross-feeding with Bacteroides

Faecalibacterium prausnitzii is a commensal gut bacterium that is thought to provide protection against inflammatory diseases. However, this bacterium is extremely oxygen sensitive, which limits its industrial application as a probiotic. The use of prebiotics to increase the abundance of this bacterium in the gut is an alternative strategy to achieve its possible health-promoting effect. We evaluated nine substances as candidate prebiotics for F. prausnitzii using a pH-controlled single-batch fermenter as a human gut microbiota model. Of them, alginate markedly increased the relative abundance of F. prausnitzii, as determined by the significant increase in the number of 16S rRNA sequences corresponding to this bacterial taxon in the fecal fermentation samples detected by real-time PCR. However, F. prausnitzii strains were incapable of utilizing alginate in monoculture, implying that an interaction with another gut microbe was required. There was a positive correlation between the relative abundance of F. prausnitzii and that of Bacteroides when cultured in medium containing alginate as the sole carbon source, indicative of cross-feeding between these bacteria. Interestingly, the ratio of acetic acid, a known substrate for F. prausnitzii, produced by Bacteroides was significantly higher in the alginate-containing medium than in media containing other prebiotic candidates. Bacterially degraded alginate oligosaccharides (AOS) remained in the medium after Bacteroides monoculture, and an isolate of F. prausnitzii was able to utilize a portion of them. Genomic sequencing revealed that the strain that consumed the AOS contained an ATP-binding cassette transporter, an alginate lyase, and AlgQ1/2 homologs encoding solute-binding proteins. Furthermore, in real-time PCR analyses, AlgQ1/2 homologs were detected in fecal samples collected from 309 of 452 (68.4%) Japanese subjects. Thus, the products of alginate assimilation by Bacteroides may promote the growth of F. prausnitzii.

The Kobe University Human Intestinal Microbiota Model for gut intervention studies

The human gut harbors a complex microbial community that performs a range of metabolic, physiological, and immunological functions. The host and its inhabiting microorganisms are often referred to as a "superorganism." Dysbiosis of gut microflora has been associated with the pathogenesis of intestinal disorders including inflammatory bowel disease, colorectal cancer, and extra-intestinal disorders such as cardiovascular disease. Therefore, gut microbiome interventions are important for the prevention and treatment of diseases. However, ethical, economic, scientific, and time constraints limit the outcome of human intervention or animal studies targeting gut microbiota. We recently developed an in vitro batch fermentation model (the Kobe University Human Intestinal Microbiota Model, KUHIMM) that is capable of hosting a majority of gut microbial species in humans and also detects the metabolites produced by microorganisms in real time. In this mini review, we elucidated the characteristics of the KUHIMM and its applicability in analyzing the effect of diet, drugs, probiotics, and prebiotics on intestinal bacteria. In addition, we introduce as examples its application to disease models, such as ulcerative colitis, in which intestinal bacteria are intricately involved in the process of pathogenesis. We also discuss the potential of the KUHIMM in precision medicine. KEY POINTS: • In vitro gut fermentation model to simulate human colonic microbiota • Screening of potential prebiotics and probiotic candidates in healthy model • Construction of disease models of ulcerative colitis and coronary artery disease.

Colonic In Vitro Model Assessment of the Prebiotic Potential of Bread Fortified with Polyphenols Rich Olive Fiber

The use of olive pomace could represent an innovative and low-cost strategy to formulate healthier and value-added foods, and bakery products are good candidates for enrichment. In this work, we explored the prebiotic potential of bread enriched with Polyphenol Rich Fiber (PRF), a defatted olive pomace byproduct previously studied in the European Project H2020 EcoProlive. To this aim, after in vitro digestion, the PRF-enriched bread, its standard control, and fructo-oligosaccharides (FOS) underwent distal colonic fermentation using the in vitro colon model MICODE (multi-unit colon gut model). Sampling was done prior, over and after 24 h of fermentation, then metabolomic analysis by Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (SPME GCMS), 16S-rDNA genomic sequencing of colonic microbiota by MiSeq, and absolute quantification of main bacterial species by qPCR were performed. The results indicated that PRF-enriched bread generated positive effects on the host gut model: (i) surge in eubiosis; (ii) increased abundance of beneficial bacterial groups, such as Bifidobacteriaceae and Lactobacillales; (iii) production of certain bioactive metabolites, such as low organic fatty acids; (iv) reduction in detrimental compounds, such as skatole. Our study not only evidenced the prebiotic role of PRF-enriched bread, thereby paving the road for further use of olive by-products, but also highlighted the potential of the in vitro gut model MICODE in the critical evaluation of functionality of food prototypes as modulators of the gut microbiota.

Growth stimulation of Bifidobacterium from human colon using daikenchuto in an in vitro model of human intestinal microbiota

Daikenchuto (DKT) is a Japanese traditional herbal (Kampo) medicine containing ginseng, processed ginger, and Japanese or Chinese pepper. We aimed to determine how DKT affects human colonic microbiota. An in vitro microbiota model was established using fecal inocula collected from nine healthy volunteers, and each model was found to retain operational taxonomic units similar to the ones in the original human fecal samples. DKT was added to the in vitro microbiota model culture at a concentration of 0.5% by weight. Next-generation sequencing of bacterial 16S rRNA gene revealed a significant increase in the relative abundance of bacteria related to the Bifidobacterium genus in the model after incubation with DKT. In pure cultures, DKT significantly promoted the growth of Bifidobacterium adolescentis, but not that of Fusobacterium nucleatum or Escherichia coli. Additionally, in pure cultures, B. adolescentis transformed ginsenoside Rc to Rd, which was then probably utilized for its growth. Our study reveals the in vitro bifidogenic effect of DKT that likely contributes to its beneficial effects on the human colon.

Enhanced methane production from cellulose using a two-stage process involving a bioelectrochemical system and a fixed film reactor

BACKGROUND

It is desirable to improve the anaerobic digestion processes of recalcitrant materials, such as cellulose. Enhancement of methane (CH₄) production from organic molecules was previously accomplished through coupling a bioelectrochemical system (BES); however, scaling-up BES-based production is difficult. Here, we developed a two-stage process consisting of a BES using low-cost and low-reactive carbon sheets as the cathode and anode, and a fixed film reactor (FFR) containing conductive material, i.e., carbon fiber textiles (CFTs) (:BES → FFR). By controlling the cathodic current at 2.7 μA/cm² without abiotic H₂ production, the three-electrode BES system was operated to mimic a microbial electrolysis cell.

RESULTS

The thermophilic BES (inlet pH: 6.1) and FFR (inlet pH: 7.5) were operated using hydraulic retention times (HRTs) of 2.5 and 4.2 days, respectively, corresponding to a cellulose load of 3555.6 mg-carbon (C)/(L day). The BES → FFR process achieved a higher CH₄ yield (37.5%) with 52.8 vol% CH₄ in the product gas compared to the non-bioelectrochemical system (NBES) → FFR process, which showed a CH₄ yield of 22.1% with 46.8 vol% CH₄. The CH₄ production rate (67.5 mM/day) obtained with the BER → FFR process was much higher than that obtained using electrochemical methanogenesis (0.27 mM/day). Application of the electrochemical system or CFTs improved the yields of CH₄ with the NBES → FFR or BES → non-fixed film reactor process, respectively. Meta 16S rRNA sequencing revealed that putative cellulolytic bacteria (identified as Clostridium species) were present in the BES and NBES, and followed (BES→ and NBES→) FFR. Notably, H₂-consuming methanogens, Methanobacterium sp. and Methanosarcina sp., showed increased relative abundances in the suspended fraction and attached fraction of (BES→) FFR, respectively, compared to that of (NBES→) FFR, although these methanogens were observed at trace levels in the BES and NBES.

CONCLUSIONS

These results indicate that bioelectrochemical preprocessing at a low current effectively induces interspecies H₂ transfer in the FFR with conductive material. Sufficient electrochemical preprocessing was observed using a relatively short HRT. This type of two-stage process, BES → FFR, is useful for stabilization and improvement of the biogas (CH₄) production from cellulosic material, and our results imply that the two-stage system developed here may be useful with other recalcitrant materials.