Prebiotic effect of fructooligosaccharide in the simulator of the human intestinal microbial ecosystem (SHIME® model)

Diethyl ethylphosphonate retardants disturbed the gut microbiome and metabolite SCFAs in vitro based on simulator of the human intestinal microbial ecosystem

Diethyl ethylphosphonate (DEEP) as a novel organophosphorus flame retardant received increasing attention and its structure was discovered. But there are currently insufficient studies on how DEEP exposure affects the gut microbiome. In this study, the effects of DEEP on the structure and function of the human gut microbiota were examined using the SHIME system. Results from high-throughput sequencing of the 16S rRNA gene show that the high dose DEEP exposure reduced the Shannon and Simpson index in the transverse and descending colon. The Bacillota had the highest proportion while the proportion of Proteobacteria gradually decreased at the phylum level. The abundance of Escherichia, Prevotella, and Bilophila at the genus level increased with increasing doses of DEEP exposure. On the contrary, the abundance of Megasphaera, Klebsiella, and Phascolarctobacterium decreased. The short-chain fatty acids had a significant shift. With increasing doses of DEEP exposure, the concentration of acetic acid and propionic acid increased, while the concentration of butyric acid reached the highest at the medium dose of exposure. In addition, Bilophila, Psychrobacter, Escherichia, and Nostoe showed strong beneficial associations with acetic and propionic acids under DEEP exposure. Phocaeicola, Agathobacter, Klebsiella, Megasphaera, Phascolarctobacterium, and Bacteroides were negatively association with acetic and propionic acids. In a word, the study verified that exposure to different doses of DEEP can cause changes in the composition of the gut microbiome and metabolite SCFAs, which provides ideas for the investigation of other potential hazards of DEEP on human beings.

Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2)

AIMS

This study aimed to compare the effects of linear and branched fructooligosaccharides (FOS) extracted from chicory and grass (Lolium perenne), respectively on human microbiota composition, diversity, and metabolism.

METHODS AND RESULTS

To test the effects of linear and branched FOS on human microbiota we used the artificial in vitro human colon model (TIM-2). Microbiota composition and diversity were assessed by V3-V4 16S rRNA metagenomic sequencing, followed by differential taxa abundance and alpha/beta diversity analyses. SCFA/BCFA production was evaluated by gas chromatography-mass spectrometry. As a result, branched FOS had the most beneficial effects on microbial diversity and metabolite production. Also, branched FOS significantly increased the abundance of commensal bacteria associated with maintaining healthy gut functions and controlling inflammation, such as Butyricicoccus, Erysipelotrichaceae, Phascolarctobacterium, and Sutterella. Linear FOS also significantly increased the abundance of some other commensal gut bacteria (Anaerobutyricum, Lachnospiraceae, Faecalibacterium), but there were no differences in diversity metrics compared to the control.

CONCLUSIONS

The study revealed that branched FOS had the most beneficial effects compared to the linear FOS in vitro, concerning microbiota modulation, and metabolite production, making this a good candidate for further studies in food biotechnology.

Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions

In vitro studies of synthetic gut microbial communities (SGMCs) can provide valuable insights into the ecological structure and function of gut microbiota. However, the importance of the quantitative composition of an SGMC inoculum and its effect on the eventual stable in vitro microbial community has not been studied. To address this, we constructed two 114-member SGMCs differing only in their quantitative composition-one reflecting the average human fecal microbiome and another mixed in equal proportions based on cell counts. We inoculated each in an automated anaerobic multi-stage in vitro gut fermentor simulating two different colonic conditions, mimicking proximal and distal colons. We replicated this setup with two different nutrient media, periodically sampled the cultures for 27 days, and profiled their microbiome compositions using 16S rRNA gene amplicon sequencing. While nutrient medium explained 36% of the variance in microbiome composition, initial inoculum composition failed to show a statistically significant effect. Under all four conditions, paired fecal and equal SGMC inoculums converged to reach stable community compositions resembling each other. Our results have broad implications for simplifying in vitro SGMC investigations. IMPORTANCE In vitro cultivation of synthetic gut microbial communities (SGMCs) can provide valuable insights into the ecological structure and function of gut microbiota. However, it is currently not known whether the quantitative composition of the initial inoculum can influence the eventual stable in vitro community structure. Hence, using two SGMC inoculums consisting of 114 unique species mixed in either equal proportions (Eq inoculum) or resembling proportions in an average human fecal microbiome (Fec inoculum), we show that initial inoculum compositions did not influence the final stable community structure in a multi-stage in vitro gut fermentor. Under two different nutrient media and two different colon conditions (proximal and distal), both Fec and Eq communities converged to resemble each other's community structure. Our results suggest that the time-consuming preparation of SGMC inoculums may not be needed and has broad implications for in vitro SGMC studies.

Impact Assessment of vB_KpnP_K1-ULIP33 Bacteriophage on the Human Gut Microbiota Using a Dynamic In Vitro Model

New control methods are needed to counter antimicrobial resistances and the use of bacteriophages as an alternative treatment seems promising. To that end, the effect of the phage vB_KpnP_K1-ULIP33, whose host is the hypervirulent Klebsiella pneumoniae SA12 (ST23 and capsular type K1), was assessed on intestinal microbiota, using an in vitro model: the SHIME® system (Simulator of the Human Intestinal Microbial Ecosystem). After stabilization of the system, the phage was inoculated for 7 days and its persistence in the different colons was studied until its disappearance from the system. The concentration of short chain fatty acids in the colons showed good colonization of the bioreactors by the microbiota and no significant effect related to the phage treatment. Diversity (α and β), the relative abundance of bacteria, and qPCR analysis targeting different genera of interest showed no significant variation following phage administration. Even if further in vitro studies are needed to assess the efficacy of this phage against its bacterial host within the human intestinal ecosystem, the phage ULIP33 exerted no significant change on the global colonic microbiota.

Modulation of the gut microbiota: opportunities and regulatory aspects

The human gut is an intensively colonized organ containing microorganisms that can be health-promoting or pathogenic. This feature led to the development of functional foods aiming to fortify the former category at the expense of the latter. Since long, cultured products, including probiotics fortification, have been used for humans as live microbial feed additions. This review presents some of the microbes used as probiotics and discusses how supplementation with probiotics may help initiate and/or restore eubiotic composition of gut microbiota. Additionally, it considers safety and regulatory aspects of probiotics.

Direct Action of Non-Digestible Oligosaccharides against a Leaky Gut

The epithelial monolayer is the primary determinant of mucosal barrier function, and tight junction (TJ) complexes seal the paracellular space between the adjacent epithelial cells and represent the main "gate-keepers" of the paracellular route. Impaired TJ functionality results in increased permeation of the "pro-inflammatory" luminal contents to the circulation that induces local and systemic inflammatory and immune responses, ultimately triggering and/or perpetuating (chronic) systemic inflammatory disorders. Increased gut leakiness is associated with intestinal and systemic disease states such as inflammatory bowel disease and neurodegenerative diseases such as Parkinson's disease. Modulation of TJ dynamics is an appealing strategy aiming at inflammatory conditions associated with compromised intestinal epithelial function. Recently there has been a growing interest in nutraceuticals, particularly in non-digestible oligosaccharides (NDOs). NDOs confer innumerable health benefits via microbiome-shaping and gut microbiota-related immune responses, including enhancement of epithelial barrier integrity. Emerging evidence supports that NDOs also exert health-beneficial effects on microbiota independently via direct interactions with intestinal epithelial and immune cells. Among these valuable features, NDOs promote barrier function by directly regulating TJs via AMPK-, PKC-, MAPK-, and TLR-associated pathways. This review provides a comprehensive overview of the epithelial barrier-protective effects of different NDOs with a special focus on their microbiota-independent modulation of TJs.

Thermal Stability of Fructooligosaccharides Extracted from Defatted Rice Bran: A Kinetic Study Using Liquid Chromatography-Tandem Mass Spectrometry

Thermal degradation kinetics of fructooligosaccharides (FOS) in defatted rice bran were studied at temperatures of 90, 100, and 110 °C. FOS extracted from rice bran and dissolved in buffers at pH values of 5.0, 6.0, and 7.0 were prepared for the thermal treatments. The residual FOS (including 1-kestose (GF2), nystose (GF3), and 1F-fructofuranosylnystose (GF4)) contents were determined using the ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) method. The results showed that the thermal degradation kinetics of GF2, GF3, and GF4 followed a first-order kinetic model. Thermal degradation rate constants (k values) of GF2, GF3, and GF4 at different temperature and pH values were estimated using the first-order kinetic equation and SAS 9.1. As a result, these k values decreased gradually as the pH of the sample increased from 5.0 to 7.0. The Arrhenius model was applied to describe the heat dependence of the k-values. The activation energy (Ea) was calculated for each case of GF2, GF3, and GF4 degradation at pH values of 5.0, 6.0, and 7.0. The result showed that rice bran FOS is very thermostable at neutral pH while more labile at acidic pH.

Deploying an In Vitro Gut Model to Assay the Impact of the Mannan-Oligosaccharide Prebiotic Bio-Mos on the Atlantic Salmon (Salmo salar) Gut Microbiome

Alpha mannose-oligosaccharide (MOS) prebiotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be mediated through their impact on host microbial communities and their associated metabolism. Bio-Mos is a commercially available prebiotic currently used in the agri-feed industry, but studies show contrasting results of its effect on fish performance and feed efficiency. Thus, detailed studies are needed to investigate the effect of MOS supplements on the fish microbiome to enhance our understanding of the link between MOS and gut health. To assess Bio-Mos for potential use as a prebiotic growth promoter in salmonid aquaculture, we have modified an established Atlantic salmon in vitro gut model, SalmoSim, to evaluate its impact on the host microbial communities. The microbial communities obtained from ceca compartments from four adult farmed salmon were inoculated in biological triplicate reactors in SalmoSim. Prebiotic treatment was supplemented for 20 days, followed by a 6-day washout period. Inclusion of Bio-Mos in the media resulted in a significant increase in formate (P = 0.001), propionate (P = 0.037) and 3-methyl butanoic acid (P = 0.024) levels, correlated with increased abundances of several, principally, anaerobic microbial genera (Fusobacterium, Agarivorans, Pseudoalteromonas). DNA metabarcoding with the 16S rDNA marker confirmed a significant shift in microbial community composition in response to Bio-Mos supplementation with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to complementin vivo trials of microbiome modulators. IMPORTANCE In this paper we report the results of the impact of a prebiotic (alpha-MOS supplementation) on microbial communities, using an in vitro simulator of the gut microbial environment of the Atlantic salmon. Our data suggest that Bio-Mos may be of value in salmonid production as it enhances volatile fatty acid production by the microbiota from salmon pyloric ceca and correlates with a significant shift in microbial community composition with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to augment in vivo trials of microbiome modulators.

Fructooligosaccharides on inflammation, immunomodulation, oxidative stress, and gut immune response: a systematic review

CONTEXT

Evidence shows that fructooligosaccharides (FOSs) can modulate inflammatory, oxidative, and immune activity in the gut, possibly leading to a systemic response, improving human health.

OBJECTIVE

To assess the present knowledge of the effects of FOSs on inflammation, immunomodulation, oxidative stress, and gut immune response.

DATA SOURCES

Studies published between December 2000 and January 2020 were systematically searched in four databases: MEDLINE, LILACS, Web of Science, and Scopus. After the screening of 1316 articles, 8 human studies and 20 animal models were included.

DATA EXTRACTION

Data were extracted separately by 2 reviewers. For each study, the design, population, exposures, main results, and conclusion were extracted. The research questions and the risk-of-bias information were also extracted. Additionally, the risk-of-bias were analyzed to guarantee the reliability of this review.

DATA ANALYSIS

A qualitative analysis revealed that FOSs can increase bifidobacteria counts and short-chain fatty acids in the gut, stimulate IgA secretion in the colon, and decrease proinflammatory cytokines, thus influencing metabolic diseases.

CONCLUSION

Studies suggest that FOS supplementation is positively associated with an anti-inflammatory and antioxidant effect, thus enhancing the gut immune system, which may be beneficial for the host's health.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration nos 42020209865 and 42020220369.

Novel ex vivo screening assay to preselect farm specific pre- and probiotics in pigs

A novel rapid ex vivo assay was developed as part of a concept to determine potential tailor-made combinations of pre- and probiotics for individual farms. Sow faecal slurries from 20 German pig farms were anaerobically incubated with pre- and probiotics or their combinations together with pathogenic strains that are of interest in pig production. Aliquots of these slurries were then incubated with media containing antibiotic mixtures allowing only growth of the specific pathogen. Growth was monitored and lag time was used to determine the residual fitness of the pathogenic strains. The background growth could be inhibited for an Escherichia coli- and a Clostridium difficile- but not for a Clostridium perfringens strain. The prebiotic fructo-oligosaccharides (FOS) and its combination with probiotics reduced the residual fitness of the E. coli strain in some farms. However, notable exceptions occurred in other farms where FOS increased the fitness of the E. coli strain. Generally, combinations of pre- and probiotics did not show additive effects on fitness for E. coli but displayed farm dependent differences. The effects of pre- and probiotics on the residual fitness of the C. difficile strain were less pronounced, but distinct differences between single application of prebiotics and their combination with probiotics were observed. It was concluded that the initial composition of the microbiota in the samples was more determinative for incubations with the C. difficile strain than for incubations with the E. coli strain, as the presumed fermentation of prebiotic products showed less influence on the fitness of the C. difficile strain. Farm dependent differences were pronounced for both pathogenic strains and therefore, this novel screening method offers a promising approach for pre-selecting pre- and probiotics for individual farms. However, evaluation of farm metadata (husbandry, feed, management) will be crucial in future studies to determine a tailor-made solution for combinations of pre- and probiotics for individual farms. Also, refinement of the ex vivo assay in terms of on-farm processing of samples and validation of unambiguous growth for pathogenic strains from individual farms should be addressed.

In Vivo Healthy Benefits of Galacto-Oligosaccharides from Lupinus albus (LA-GOS) in Butyrate Production through Intestinal Microbiota

Animal digestive systems host microorganism ecosystems, including integrated bacteria, viruses, fungi, and others, that produce a variety of compounds from different substrates with healthy properties. Among these substrates, α-galacto-oligosaccharides (GOS) are considered prebiotics that promote the grow of gut microbiota with a metabolic output of Short Chain Fatty Acids (SCFAs). In this regard, we evaluated Lupinus albus GOS (LA-GOS) as a natural prebiotic using different animal models. Therefore, the aim of this work was to evaluate the effect of LA-GOS on the gut microbiota, SCFA production, and intestinal health in healthy and induced dysbiosis conditions (an ulcerative colitis (UC) model). Twenty C57BL/6 mice were randomly allocated in four groups (n = 5/group): untreated and treated non-induced animals, and two groups induced with 2% dextran sulfate sodium to UC with and without LA-GOS administration (2.5 g/kg bw). We found that the UC treated group showed a higher goblet cell number, lower disease activity index, and reduced histopathological damage in comparison to the UC untreated group. In addition, the abundance of positive bacteria to butyryl-CoA transferase in gut microbiota was significantly increased by LA-GOS treatment, in healthy conditions. We measured the SCFA production with significant differences in the butyrate concentration between treated and untreated healthy groups. Finally, the pH level in cecum feces was reduced after LA-GOS treatment. Overall, we point out the in vivo health benefits of LA-GOS administration on the preservation of the intestinal ecosystem and the promotion of SCFA production.

Shaping the gut microbiota by bioactive phytochemicals: An emerging approach for the prevention and treatment of human diseases

The human digestive tract is the cottage to trillions of live microorganisms, which regulate health and illness. A healthy Gut Microbiota (GM) is necessary for preventing microbial growth, body growth, obesity, cancer, diabetes, and enhancing immunity. The equilibrium in GM's composition and the presence/absence of critical species enable specific responses to be essential for the host's better health condition. Research evidences revealed that the dietary plants and their bioactive phytochemicals (BPs) play an extensive and critical role in shaping the GM to get beneficial health effects. BPs are also known to improve gastrointestinal health and reduce the risk of several diseases by modulating GM-mediated cellular and molecular processes. Regular intake of BPs-rich vegetables, fruits, and herbal preparations promotes probiotic bacteria, including Bifidobacteria and Lactobacillus species, while inhibiting unwanted gut residents' development Escherichia coli, and Salmonella typhimurium etc. Upon consumption, BPs contact the GM that gets transformed before being absorbed from the gastrointestinal tract. Biotransformation of BPs by GM is linked with the enhancement of bioactivity/toxicity diminishment of the BPs compared to parental phytochemicals. Therefore, the current review focuses on the role of BPs in shaping GM for the prevention and treatment of human diseases.

Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL^®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL^® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

The Application of Lactobacillus reuteri CCM 8617 and Flaxseed Positively Improved the Health of Mice Challenged with Enterotoxigenic E. coli O149:F4

The aim of our study was to monitor the effects of dietary synbiotics on experimentally infected mice. Sixty mice were divided into the following three groups: negative control group C1, positive control group C2 (mice infected with enterotoxigenic Escherichia coli O149:F4_NAL), and experimental group LF (Lactobacillus reuteri CCM 8617_RIF + 10% flaxseed + E. coli O149:F4_NAL). Supplements were administered for 42 days. Microbiological, hematological, and biochemical analyses, electrophoretic analysis of lactate dehydrogenase (LDH) isoenzymes, and analysis of fatty acids using gas chromatography and isotachophoresis were performed. We recorded higher numbers of jejunal and ileal lactic acid bacteria, lower Enterobacteriaceae counts in the feces of the animals, and an increased production of organic acids in the synbiotic-fed group. The supplements applied favored n-3 polyunsaturated fatty acid (PUFA) metabolism and inhibited n-6 PUFA metabolism; thus, they influenced the n-6 to n-3 and eicosapentaenoic to arachidonic acid ratios. Additionally, the incorporation of n-3 PUFAs to the cell membrane decreased the activity of LDH, transaminases, and alkaline phosphatase. Results obtained in our study indicate the positive effect of continuous supplementation of combination of probiotic cheese enriched with L. reuteri CCM 8617_RIF and crushed flaxseed on composition of intestinal microflora and alleviation of the course of infection induced by pathogenic bacterium E. coli O149:F4_NAL.

Emerging prospects of macro- and microalgae as prebiotic

Macro- and microalgae-based foods are becoming popular due to their high nutritious value. The algal biomass is enriched with polysaccharides, protein, polyunsaturated fatty acids, carotenoids, vitamins and minerals. However, the most promising fraction is polysaccharides (PS) or their derivatives (as dietary fibers) which are not entirely fermented by colonic bacteria hence act as potential prebiotic. Primarily, algae become famous as prominent protein sources. Recently, these are widely adopted as functional food (e.g., desserts, dairy products, oil-derivatives, pastas etc.) or animal feed (for poultry, cattle, fish etc.). Besides prebiotic and balanced amino acids source, algae derived compounds implied as therapeutics due to comprising bioactive properties to elicit immunomodulatory, antioxidative, anticancerous, anticoagulant, hepato-protective, and antihypertensive responses. Despite the above potentials, broader research determinations are inevitable to explore these algal compounds until microalgae become a business reality for broader and specific applications in all health domains. However, scale up of algal bioprocess remains a major challenge until commercial affordability is accomplished which can be possible by discovering their hidden potentials and increasing their value and application prospects. This review provides an overview of the significance of algae consumption for several health benefits in humans and animals mainly as prebiotics, however their functional food and animal feed potential are briefly covered. Moreover, their potential to develop an algal-based food industry to meet the people's requirements not only as a sustainable food solution with several health benefits but also as therapeutics is inevitable.

Probiotic infant cereal improves children's gut microbiota: Insights using the Simulator of Human Intestinal Microbial Ecosystem (SHIME®)

Infant́s gut microbiota can be modulated by many factors, including mode of delivery, feeding regime, maternal diet/weight and probiotic and prebiotic consumption. The gut microbiota in dysbiosis has been associated with innumerous diseases. In this sense, early childhood intestinal microbiome modulation can be a strategy for disease prevention. This study had the purpose to evaluate the effect of an infant cereal with probiotic (Bifidobacterium animalis ssp. lactis BB-12®) on infant́s intestinal microbiota using SHIME®, which simulates human gastrointestinal conditions. The ascending colon was inoculated with fecal microbiota from three children (2-3 years old). NH₄⁺, short chain fatty acids (SCFASs) and microbiota composition were determined by selective ion electrode, GC/MS and 16S sequencing, respectively. After treatment, butyric acid production increased (p < 0.05) 52% and a decrease in NH₄⁺ production was observed (p < 0.01). The treatment stimulated an increase (p < 0.01) of Lactobacillaceae families, more precisely L. gasseri and L. kefiri. L. gasseri has been associated with the prevention of allergic rhinitis in children and L. kefiri in the prevention of obesity. Thus, infant cereal with BB-12® is able to stimulate the growth of L. gasseri and L. kefiri in a beneficial way, reducing NH₄⁺ and increasing the production of SCFAs, especially butyric acid, in SHIME®.

The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives

Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.

A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches

Resistant starches (RS) are dietary compounds processed by the gut microbiota into metabolites, such as butyrate, that are beneficial to the host. The production of butyrate by the microbiome appears to be affected by the plant source and type of RS as well as the individual's microbiota. In this study, we used in vitro culture and metaproteomic methods to explore individual microbiome's functional responses to RS2 (enzymatically-resistant starch), RS3 (retrograded starch) and RS4 (chemically-modified starch). Results showed that RS2 and RS3 significantly altered the protein expressions in the individual gut microbiomes, while RS4 did not result in significant protein changes. Significantly elevated protein groups were enriched in carbohydrate metabolism and transport functions of families Eubacteriaceae, Lachnospiraceae and Ruminococcaceae. In addition, Bifidobacteriaceae was significantly increased in response to RS3. We also observed taxon-specific enrichments of starch metabolism and pentose phosphate pathways corresponding to this family. Functions related to starch utilization, ABC transporters and pyruvate metabolism pathways were consistently increased in the individual microbiomes in response to RS2 and RS3. Given that these taxon-specific responses depended on the type of carbohydrate sources, we constructed a functional ecological network to gain a system-level insight of functional organization. Our results suggest that while some microbes tend to be functionally independent, there are subsets of microbes that are functionally co-regulated by environmental changes, potentially by alterations of trophic interactions.

Probiotic low-fat fermented goat milk with passion fruit by-product: In vitro effect on obese individuals' microbiota and on metabolites production

This study aimed to evaluate the impact of a two-week treatment period with probiotic low-fat fermented goat milk by Lactobacillus casei Lc-1, supplemented with passion fruit by-product (1%), on the modulation of gut microbiota from obese individuals using the Simulator of Human Intestinal Microbial Ecosystem (SHIME) system. The effects were carried out through the study of gut microbiota composition, using 16S rRNA next generation sequencing, quantification of short-chain fatty acids (SCFA) and ammonium ions. The microbiota composition changed across three vessels representing the colon regions, because of fermented milk treatment. Fermented goat milk administration caused a reduction of bacteria belonging to genera Prevotella, Megamonas and Succinivibrio, which can produce SCFA, and an increase of Lactobacillus and Bifidobacterium genera in all simulated colon regions. There was no effect on SCFA and on ammonium ions concentration during treatment period. Fermented milk shifted the obese donors' microbiota without changing metabolites production. It happens, possibly, due to a balance in abundances among bacterial genera that can produce or not SCFA, and among bacterial genera with high or low proteolytic activity. Our outcomes help to clarify the effects of the ingestion of a probiotic low-fat fermented goat milk product on colon microbiota composition.

Bringing the digestibility of prebiotics into focus: update of carbohydrate digestion models

Oro-gastrointestinal digestion of dietary carbohydrates involves up to six different carbohydrases in a multistage process. Enzymes from the small intestinal brush border membrane play a major role in the digestibility of these substrates. However, to date, the inclusion of these small intestinal enzymes has been dismissed in most in vitro studies carried out, despite their importance in the degradation of carbohydrates. Several in vitro and in vivo studies have demonstrated the capability of brush border enzymes to degrade certain "non-digestible" carbohydrates to a different extent depending on their structural composition (monomeric composition, glycosidic linkage, etc.). In this sense, considering the available evidence, mucosal disaccharidases embedded in the small intestinal brush border membrane vesicles must be considered in addition to α-amylases; therefore, new approaches for the evaluation of the digestibility of carbohydrates have been recently reported. These new methods based on the utilization of the small intestinal enzymes present in the brush border membrane aim to fulfill the final and key step of the digestion of carbohydrates in the small intestine. Here, rat small intestinal extract enzymes as well as brush border membrane vesicles from pig have emerged as very reliable and useful tools to evaluate carbohydrate digestion. Thus, this review aims to go briefly through the most relevant digestion methods for carbohydrates that are currently available and to highlight the new improved methods, which include mammalian intestinal enzymes, and their current use in the evaluation of the digestibility of prebiotics.

Intestinal gases: influence on gut disorders and the role of dietary manipulations

The inner workings of the intestines, in which the body and microbiome intersect to influence gut function and systemic health, remain elusive. Carbon dioxide, hydrogen, methane and hydrogen sulfide, as well as a variety of trace gases, are generated by the chemical interactions and microbiota within the gut. Profiling of these intestinal gases and their responses to dietary changes can reveal the products and functions of the gut microbiota and their influence on human health. Indeed, different tools for measuring these intestinal gases have been developed, including newly developed gas-sensing capsule technology. Gases can, according to their type, concentration and volume, induce or relieve abdominal symptoms, and might also have physiological, pathogenic and therapeutic effects. Thus, profiling and modulating intestinal gases could be powerful tools for disease prevention and/or therapy. As the interactions between the microbiota, chemical constituents and fermentative substrates of the gut are principally influenced by dietary intake, altering the diet, which, in turn, changes gas profiles, is the main therapeutic approach for gastrointestinal disorders. An improved understanding of the complex interactions within the intestines that generate gases will enhance our ability to prevent, diagnose, treat and monitor many gastrointestinal disorders.

In vitro Gastrointestinal Models for Prebiotic Carbohydrates: A Critical Review

Background:

In the last decade, various consortia and companies have created standardized digestion protocols and gastrointestinal simulators, such as the protocol proposed by the INFOGEST Consortium, the simulator SHIME, the simulator simgi®, the TIM, etc. Most of them claim to simulate the entire human gastrointestinal tract. However, few results have been reported on the use of these systems with potential prebiotic carbohydrates.

Methods:

This critical review addresses the existing data on the analysis of prebiotic carbohydrates by different in vitro gastrointestinal simulators, the lack of parameters that could affect the results, and recommendations for their enhancement.

Results:

According to the reviewed data, there is a lack of a realistic approximation of the small intestinal conditions, mainly because of the absence of hydrolytic conditions, such as the presence of small intestinal brush border carbohydrases that can affect the digestibility of different carbohydrates, including prebiotics.

Conclusion:

There is a necessity to standardize and enhance the small intestine simulators to study the in vitro digestibility of carbohydrates.

A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro

Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.

Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro

We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.

Use of a combination of in vitro models to investigate the impact of chlorpyrifos and inulin on the intestinal microbiota and the permeability of the intestinal mucosa

Dietary exposure to the organophosphorothionate pesticide chlorpyrifos (CPF) has been linked to dysbiosis of the gut microbiota. We therefore sought to investigate whether (i) CPF's impact extends to the intestinal barrier and (ii) the prebiotic inulin could prevent such an effect. In vitro models mimicking the intestinal environment (the SHIME®) and the intestinal mucosa (Caco-2/TC7 cells) were exposed to CPF. After the SHIME® had been exposed to CPF and/or inulin, we assessed the system's bacterial and metabolic profiles. Extracts from the SHIME®'s colon reactors were then transferred to Caco-2/TC7 cultures, and epithelial barrier integrity and function were assessed. We found that inulin co-treatment partially reversed CPF-induced dysbiosis and increased short-chain fatty acid production in the SHIME®. Furthermore, co-treatment impacted tight junction gene expression and inhibited pro-inflammatory signaling in the Caco-2/TC7 intestinal cell line. Whereas, an isolated in vitro assessment of CPF and inulin effects provides useful information on the mechanism of dysbiosis, combining two in vitro models increases the in vivo relevance.

Influence of polyphenol rich seabuckthorn berries juice on release of polyphenols and colonic microbiota on exposure to simulated human digestion model

The present study investigated the effect of polyphenol rich Sea buckthorn berries juice (SBJ) on colonic microbial composition and diversity using in vitro simulated gut model. The release of polyphenols, their antioxidant activity and impact on microbial diversity was evaluated under long term fermentation for 21 days. The treatment of colonic reactors with basal feed supplemented with SBJ resulted in an increase in population and diversity of beneficial bacteria as revealed by viable cell count and PCR-DGGE. A higher release of phenolics was observed, which resulted in higher antioxidant activity in the colonic reactors throughout the treatment period (p < 0.05). Higher content of resveratrol, rutin and chlorogenic acid were observed in ascendens colon whereas quercetin, ferulic and caeffic acid level were higher in descendens colon due to biotransformation of polyphenols in the later part of colon. The Principal Component Analysis also indicated the stimulatory effect of SBJ on the beneficial microbial population of Lactobacilli, Bacteroides/Prevotella and Bifidobacteria in all the three reactors. It also confirmed higher release of polyphenolic compounds and associated antioxidant activities in descendens colon.

Effects of Probiotics, Prebiotics, and Synbiotics on Human Health

The human gastrointestinal tract is colonised by a complex ecosystem of microorganisms. Intestinal bacteria are not only commensal, but they also undergo a synbiotic co-evolution along with their host. Beneficial intestinal bacteria have numerous and important functions, e.g., they produce various nutrients for their host, prevent infections caused by intestinal pathogens, and modulate a normal immunological response. Therefore, modification of the intestinal microbiota in order to achieve, restore, and maintain favourable balance in the ecosystem, and the activity of microorganisms present in the gastrointestinal tract is necessary for the improved health condition of the host. The introduction of probiotics, prebiotics, or synbiotics into human diet is favourable for the intestinal microbiota. They may be consumed in the form of raw vegetables and fruit, fermented pickles, or dairy products. Another source may be pharmaceutical formulas and functional food. This paper provides a review of available information and summarises the current knowledge on the effects of probiotics, prebiotics, and synbiotics on human health. The mechanism of beneficial action of those substances is discussed, and verified study results proving their efficacy in human nutrition are presented.

Impact of multi-functional fermented goat milk beverage on gut microbiota in a dynamic colon model

The aim of this research was to evaluate the effect of grape probiotic fermented beverages made of goat milk, with or without added grape pomace on gut microbiota in a Simulator of Human Intestinal Microbial Ecosystem (SHIME®). SHIME® model was used to investigate to assess changes in microbial composition and fermentation metabolites (short- and branched-chain fatty acids and ammonium), as well as under the antioxidant capacity. The results demonstrated that the beverages formulated, with or without grape pomace extract, exhibited high dietary fiber, oleic acid, phenolic compounds content and antioxidant activity. Both beverages also kept L. rhamnosus and S. thermophilus viable during their passage through the intestinal tract and had a positive effect on gut microbiota metabolism, increasing the antioxidant capacity and the production of short-chain fatty acids, and decreasing the ammonium concentration. Therefore, the multifunctional beverages formulated in this study can offer a new perspective for the production of foods with positive potential effects on human health.

Changes in Composition and Function of Human Intestinal Microbiota Exposed to Chlorpyrifos in Oil as Assessed by the SHIME® Model

The presence of pesticide residues in food is a public health problem. Exposure to these substances in daily life could have serious effects on the intestine—the first organ to come into contact with food contaminants. The present study investigated the impact of a low dose (1 mg/day in oil) of the pesticide chlorpyrifos (CPF) on the community structure, diversity and metabolic response of the human gut microbiota using the SHIME^® model (six reactors, representing the different parts of the gastrointestinal tract). The last three reactors (representing the colon) were inoculated with a mixture of feces from human adults. Three time points were studied: immediately before the first dose of CPF, and then after 15 and 30 days of CPF-oil administration. By using conventional bacterial culture and molecular biology methods, we showed that CPF in oil can affect the gut microbiota. It had the greatest effects on counts of culturable bacteria (with an increase in Enterobacteria, Bacteroides spp. and clostridia counts, and a decrease in bifidobacterial counts) and fermentative activity, which were colon-segment-dependent. Our results suggest that: (i) CPF in oil treatment affects the gut microbiota (although there was some discordance between the culture-dependent and culture-independent analyses); (ii) the changes are “SHIME^®-compartment” specific; and (iii) the changes are associated with minor alterations in the production of short-chain fatty acids and lactate.

Yacon (Smallanthus sonchifolius) as a Food Supplement: Health-Promoting Benefits of Fructooligosaccharides

Yacon (Smallanthus sonchifolius), a perennial plant of the family Asteraceae native to the Andean regions of South America, is an abundant source of fructooligosaccharides (FOS). This comprehensive review of the literature addressed the role of yacon supplementation in promoting health and reducing the risk of chronic diseases. According to several preclinical and clinical trials, FOS intake favors the growth of health-promoting bacteria while reducing pathogenic bacteria populations. Moreover, the endproducts of FOS fermentation by the intestinal microbiota, short chain fatty acids (SCFA), act as substrates or signaling molecules in the regulation of the immune response, glucose homeostasis and lipid metabolism. As a result, glycemic levels, body weight and colon cancer risk can be reduced. Based on these findings, most studies reviewed concluded that due to their functional properties, yacon roots may be effectively used as a dietary supplement to prevent and treat chronic diseases.

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

The colon is inhabited by a dense population of microorganisms, the so-called “gut microbiota,” able to ferment carbohydrates and proteins that escape absorption in the small intestine during digestion. This microbiota produces a wide range of metabolites, including short chain fatty acids (SCFA). These compounds are absorbed in the large bowel and are defined as 1-6 carbon volatile fatty acids which can present straight or branched-chain conformation. Their production is influenced by the pattern of food intake and diet-mediated changes in the gut microbiota. SCFA have distinct physiological effects: they contribute to shaping the gut environment, influence the physiology of the colon, they can be used as energy sources by host cells and the intestinal microbiota and they also participate in different host-signaling mechanisms. We summarize the current knowledge about the production of SCFA, including bacterial cross-feedings interactions, and the biological properties of these metabolites with impact on the human health.

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

The colon is inhabited by a dense population of microorganisms, the so-called "gut microbiota," able to ferment carbohydrates and proteins that escape absorption in the small intestine during digestion. This microbiota produces a wide range of metabolites, including short chain fatty acids (SCFA). These compounds are absorbed in the large bowel and are defined as 1-6 carbon volatile fatty acids which can present straight or branched-chain conformation. Their production is influenced by the pattern of food intake and diet-mediated changes in the gut microbiota. SCFA have distinct physiological effects: they contribute to shaping the gut environment, influence the physiology of the colon, they can be used as energy sources by host cells and the intestinal microbiota and they also participate in different host-signaling mechanisms. We summarize the current knowledge about the production of SCFA, including bacterial cross-feedings interactions, and the biological properties of these metabolites with impact on the human health.

Variations in prebiotic oligosaccharide fermentation by intestinal lactic acid bacteria

Prebiotic oligosaccharides confer health benefits on the host by modulating the gut microbiota. Intestinal lactic acid bacteria (LAB) are potential targets of prebiotics; however, the metabolism of oligosaccharides by LAB has not been fully characterized. Here, we studied the metabolism of eight oligosaccharides by 19 strains of intestinal LAB. Among the eight oligosaccharides used, 1-kestose, lactosucrose and galactooligosaccharides (GOSs) led to the greatest increases in the numbers of the strains tested. However, mono- and disaccharides accounted for more than half of the GOSs used, and several strains only metabolized the mono- and di-saccharides in GOSs. End product profiles indicated that the amounts of lactate produced were generally consistent with the bacterial growth recorded. Oligosaccharide profiling revealed the interesting metabolic manner in Lactobacillus paracasei strains, which metabolized all oligosaccharides, but left sucrose when cultured with fructooligosaccharides. The present study clearly indicated that the prebiotic potential of each oligosaccharide differs.

Continuously Ingesting Fructooligosaccharide Can't Maintain Rats' Gut Bifidobacterium at a High Level

Fructooligosaccharide (FOS) has been reported to increase Lactobacillus and Bifidobacterium populations in animal and human gut. Hence, it has been utilized to regulate the balance of gut microbiota. In this study, we compared the effects of high-FOS (HFOS) diet on normal and obese rats' gut Lactobacillus and Bifidobacterium, with high-soybean-fibers (HSF) diet as control. The results showed that the level of Bifidobacterium population substantially increased at week 4 in groups of rats fed the HFOS diet (P < 0.05), but significantly reduced to a small level at week 8 (P < 0.05); the abundance of Lactobacillus was increased in normal rats (P < 0.05), but decreased in obese rats (P < 0.05). The HSF diet did not promote the growth of Lactobacillus and Bifidobacterium in rats' gut. The findings suggested that Bifidobacterium population could not be maintained at a high level when the rats continuously ingested the HFOS diet for 8 wk; additionally, Lactobacillus population could adapt to a relatively stable level with the consumption of HFOS diet.

PRACTICAL APPLICATION

Fructooligosaccharide (FOS) is one of the most popular prebiotics, and it is widely used in infant formulas, which is aiming to increase the growth of probiotics like Lactobacillus and Bifidobacterium. This study discovered new growth rhythm of Bifidobacterium based on a high-FOS diet. The growth of Bifidobacterium was first promoted but receded in the end. This finding is highly instructive and meaningful for the application of fructooligosaccharide in probiotic or prebiotic food.

Gut Function-Enhancing Properties and Metabolic Effects of Dietary Indigestible Sugars in Rodents and Rabbits

Indigestible sugars (iS) have received particular interest in food and nutrition research due to their prebiotic properties and other health benefits in humans and animals. The main aim of this review article is to summarize the current knowledge regarding digestive and health-enhancing properties of iS such as sugar alcohols, oligosacharides, and polysaccharides, in rodents and rabbits. Besides ameliorating gut health, iS ingestion also elicits laxative effects and stimulate intestinal permeability and fluid secretions, thereby shortening digesta transit time and increasing stool mass and quality. In rodents and rabbits, as hindgut fermenters, consumption of iS leads to an improved nutrient digestibility, too. Cecal fermentation of iS reduces luminal pH and extends wall tissue facilitating absorption of key dietary minerals across hindgut. The microbial fermentation of iS also enhances excessive blood nitrogen (N) flowing into the cecum to be used as N source for bacterial growth, enhancing N retention in cecotrophic animals. This review also highlights the impact of iS on improving lipid metabolism, mainly by lowering cholesterol and triglycerides levels in the blood. The paper serves as an index of the current knowledge of iS effects in rodents and rabbits and also identifies gaps of knowledge that need to be addressed by future research.

Metabolism of Fructooligosaccharides in Lactobacillus plantarum ST-III via Differential Gene Transcription and Alteration of Cell Membrane Fluidity

Although fructooligosaccharides (FOS) can selectively stimulate the growth and activity of probiotics and beneficially modulate the balance of intestinal microbiota, knowledge of the molecular mechanism for FOS metabolism by probiotics is still limited. Here a combined transcriptomic and physiological approach was used to survey the global alterations that occurred during the logarithmic growth of Lactobacillus plantarum ST-III using FOS or glucose as the sole carbon source. A total of 363 genes were differentially transcribed; in particular, two gene clusters were induced by FOS. Gene inactivation revealed that both of the clusters participated in the metabolism of FOS, which were transported across the membrane by two phosphotransferase systems (PTSs) and were subsequently hydrolyzed by a β-fructofuranosidase (SacA) in the cytoplasm. Combining the measurements of the transcriptome- and membrane-related features, we discovered that the genes involved in the biosynthesis of fatty acids (FAs) were repressed in cells grown on FOS; as a result, the FA profiles were altered by shortening of the carbon chains, after which membrane fluidity increased in response to FOS transport and utilization. Furthermore, incremental production of acetate was observed in both the transcriptomic and the metabolic experiments. Our results provided new insights into gene transcription, the production of metabolites, and membrane alterations that could explain FOS metabolism in L. plantarum.