Epilactose as a Promising Butyrate-Promoter Prebiotic via Microbiota Modulation

Epilactose is a disaccharide composed of galactose and mannose, and it is currently considered an "under development" prebiotic. In this study, we described the prebiotic potential of epilactose by in vitro fermentation using human fecal inocula from individuals following a Mediterranean diet (DM) or a Vegan diet (DV). The prebiotic effect of epilactose was also compared with lactulose and raffinose, and interesting correlations were established between metabolites and microbiota modulation. The production of several metabolites (lactate, short-chain fatty acids, and gases) confirmed the prebiotic properties of epilactose. For both donors, the microbiota analysis showed that epilactose significantly stimulated the butyrate-producing bacteria, suggesting that its prebiotic effect could be independent of the donor diet. Butyrate is one of the current golden metabolites due to its benefits for the gut and systemic health. In the presence of epilactose, the production of butyrate was 70- and 63-fold higher for the DM donor, when compared to lactulose and raffinose, respectively. For the DV donor, an increase of 29- and 89-fold in the butyrate production was obtained when compared to lactulose and raffinose, respectively. In conclusion, this study suggests that epilactose holds potential functional properties for human health, especially towards the modulation of butyrate-producing strains.

In Vitro Characterization of Polysaccharides from Fresh Tea Leaves in Simulated Gastrointestinal Digestion and Gut Microbiome Fermentation

Tea plants have a long cultivation history in the world, but there are few studies on polysaccharides from fresh tea leaves. In this study, tea polysaccharides (TPSs) were isolated from fresh tea leaves. Then, we investigated the characteristics of TPSs during in vitro simulated digestion and fermentation; moreover, the effects of TPSs on gut microbiota were explored. The results revealed that saliva did not significantly affect TPSs' molecular weight, monosaccharide composition, and reducing sugar content, indicating that TPSs cannot be digested in the oral cavity. However, TPSs were partially decomposed in the gastrointestinal tract after gastric and intestinal digestion, resulting in the release of a small amount of free glucose monosaccharides. Our in vitro fermentation experiments demonstrated that TPSs are degraded by gut microbiota, leading to short-chain fatty acid (SCFA) production and pH reduction. Moreover, TPSs increased the abundance of Bacteroides, Lactobacillus, and Bifidobacterium but reduced that of Escherichia, Shigella, and Enterococcus, demonstrating that TPSs can regulate the gut microbiome. In conclusion, TPSs are partially decomposed by gut microbiota, resulting in the production of SCFAs and the regulation of gut microbiota composition and function. Therefore, TPSs may be used to develop a prebiotic supplement to regulate the gut microbiome and improve host health.

A low-cost, easy-to-use prototype bioreactor model for the investigation of human gut microbiota: validation using a prebiotic treatment

In vitro gut models allow for the study of the impact of molecules on human gut microbiota composition and function without the implication of the host. However, current models, such as the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), are expensive, time-consuming, and require specialized personnel. Homemade in vitro models that lessen these issues have limited evidence of their humanlike functionality. In this study, we present the development of a low-cost and easy-to-use bioreactor with the proven functionality of human microbiota. In our model, we evaluated the capability of replicating human gut microbiota growth and the response of the human bacterial community to a prebiotic, resistant starch, particularly resistant starch type 2 (RS2). Our bioreactor produced an environment that was stable for pH, temperature, and anaerobic conditions. The bioreactor consistently cultivated bacterial communities over a 48 h time period, replicating the composition of the gut microbiota and the associated metabolite production response to RS2, in line with prior human studies. In response to the RS2 prebiotic, we observed an increase in Bifidobacterium adolescentis and Bifidobacterium faecale and an increase in the production of the short-chain fatty acids such as acetate, propionate, and isobutyrate. Taken together, these data demonstrate that our low-cost and user-friendly prototype bioreactor model provides a favorable environment for the growth of human gut microbiota and can mimic its response to a prebiotic.

Assessing the Gut Microbiota's Ability to Metabolize Oligomeric and Polymeric Flavan-3-ols from Aronia and Cranberry

Clinical trials investigating the health effects of flavan-3-ols yield heterogeneous results due to interindividual variability in the gut microbiota metabolism. In fact, different groups in the population have similar metabolic profiles following (-)-epicatechin and (+)-catechin gut microbial metabolism and can be regrouped into so-called metabotypes. In this study, the capacity of 34 donors to metabolize polymeric B-type flavan-3-ols from aronia and oligomeric A-type flavan-3-ols from cranberry is investigated by in vitro fecal batch fermentations. Less than 1% of the flavan-3-ols from both sources are converted into microbial metabolites, such as phenyl-γ-valerolactones (PVLs). To further confirm this result, gut microbial metabolites from flavan-3-ols are quantified in urine samples collected from participants, before and after a 4-day supplementation of cranberry extract providing 82.3 mg of flavan-3-ols per day. No significant difference is observed in the urinary excretion of flavan-3-ols microbial metabolites. Hence, it demonstrates by both in vitro and in vivo approaches that flavan-3-ols from aronia and cranberry are poorly degraded by the gut microbiota. The beneficial health impacts of these molecules likely stem from their capacity to affect gut microbiota and their interactions with the gut epithelium, rather than from their breakdown into smaller metabolites.

Intestinal Microbiome Metabolism of Cranberry (Vaccinium macrocarpon) Proanthocyanidin Dimers, but Not Trimers, Is Altered by Dysbiosis in Ulcerative Colitis Ex Vivo

Cranberries contain proanthocyanidins with different interflavan bond types and degrees of polymerization. These chemical differences may impact the metabolism of proanthocyanidins by the intestinal microbiome. In our previous study, we found that healthy microbiomes produced higher concentrations of the phenolic acid metabolites 5-(3',4'-dihydroxyphenyl)-g-valerolactone and 3-hydroxyphenylacetic acid from the cranberry extract in comparison to ulcerative colitis (UC) microbiomes ex vivo. To understand this difference, LC-ESI-MS/MS was utilized to characterize the metabolism of the precursor proanthocyanidins. Healthy microbiomes metabolized procyanidin A2, procyanidin B2, and procyanidin dimeric intermediates but not A-type trimers, to a greater extent than UC microbiomes. The metabolism of procyanidin A2 and procyanidin B2 by fecal microorganisms was then compared to identify their derived phenolic acid metabolites. 5-(3',4'-Dihydroxyphenyl)-g-valerolactone and 3-hydroxyphenylacetic acid were identified as unique metabolites of procyanidin B2. Based on these results, the metabolism of procyanidin B2 contributed to the differential metabolism observed between healthy and UC microbiomes.

Effects of In Vitro Fermentation of Polysialic Acid and Sialic Acid on Gut Microbial Community Composition and Metabolites in Healthy Humans

The influence of polysialic acid (PSA) and sialic acid (SA) on the gut microbial community composition and metabolites in healthy humans was investigated using a bionic gastrointestinal reactor. The results indicated that PSA and SA significantly changed the gut microbiota and metabolites to different degrees. PSA can increase the relative abundances of Faecalibacterium and Allisonella, whereas SA can increase those of Bifidobacterium and Megamonas. Both can significantly increase the content of short-chain fatty acids. The results of metabolome analysis showed that PSA can upregulate ergosterol peroxide and gallic acid and downregulate the harmful metabolite N-acetylputrescine. SA can upregulate 4-pyridoxic acid and lipoic acid. PSA and SA affect gut microbiota and metabolites in different ways and have positive effects on human health. These results will provide a reference for the further development of PSA- and SA-related functional foods and health products.

Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut

The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.

Study on Immunoregulatory Effects of Fucoidan from Sargassum graminifolium In Vivo and Immunoactivation Activity of Its Fecal Fermentation Products Using Co-Culture Model

Fucoidan, brown seaweed-derived dietary fibers (DFs), can be considered a promising candidate for modulating immune responses. Due to its structural complexity and diversity, it is unclear whether Sargassum graminifolium fucoidans (SGFs) also show marvelous immunoregulatory effects. In the present study, two fractions, SGF-1 and SGF-2, were purified from SGFs by DEAE-Sepharose Fast Flow and Sephacryl S-400 HR column chromatography. We investigated the in vivo immune regulatory activity of SGF-2 and explored the immune activation of SGF-2 fecal fermentation products with in vitro fecal fermentation combined with a Caco-2/RAW264.7 co-culture system. In vivo results exhibited that SGF-2 could elevate the thymus/spleen indices, CD8+ splenic T lymphocyte subpopulations, and CD4+ Foxp3+ splenic Tregs. The 16S high-throughput sequencing results showed that SGF-2 administration significantly increased the relative abundance of Lactobacillus, Alloprevotella, Ruminococcus, and Akkermansia. In addition, it was found that SGF-2 fermented by feces could significantly improve the phagocytosis, NO, and cytokine (TNF-α, IL-6, and IL-10) production of macrophages in the co-culture system. These results indicated that SGFs have the potential to modulate immunity and promote health by affecting the gut microbiota.

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 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.

Comprehensive Metabolite Identification of Genipin in Rats Using Ultra-High-Performance Liquid Chromatography Coupled with High Resolution Mass Spectrometry

Genipin, an aglycone of geniposide, is a rich iridoid component in the fruit of Gardenia jasminoides Ellis and has numerous biological activities. However, its metabolic profiles in vivo and vitro remain unclear. In this study, an effective analytical strategy based on ultra-high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) in positive and negative ion modes was developed to analyze and identify genipin metabolites in rat urine, blood, feces, and fecal fermentation in combination with many methods including post-collection data mining methods, high-resolution extracted ion chromatography (HREIC), and multiple mass defect filtering (MMDF). Simultaneously, the metabolites of genipin in vivo were verified by fecal fermentation of SD rats at different times. Finally, based on information such as reference substances, chromatographic retention behavior, and accurate mass determination, a total of 50 metabolites (including prototypes) were identified in vivo. Among them, 7, 31 and 28 metabolites in vivo were identified in blood, urine, and feces, respectively. Our results showed that genipin could generate different metabolites that underwent multiple metabolic reactions in vivo including methylation, hydroxylation, dehydroxylation, hydrogenation, sulfonation, glucuronidation, demethylation, and their superimposed reactions. Forty-six metabolites were verified in vitro. Meanwhile, 2 and 19 metabolites identified in blood and urine were also verified in fecal fermentation at different times. These results demonstrated that metabolites were produced in feces and reabsorbed into the body. In conclusion, the newly discovered metabolites of genipin can provide a new perspective for understanding its pharmacological effects and build the foundation for thee toxicity and safety evaluations of genipin.

Structural characterization of different starch-fatty acid complexes and their effects on human intestinal microflora

Resistant starch type 5 (RS5), a starch-lipid complex, exhibited potential health benefits in blood glucose and insulin control due to the low digestibility. The effects of the crystalline structure of starch and chain length of fatty acid on the structure, in vitro digestibility, and fermentation ability in RS5 were investigated by compounding (maize, rice, wheat, potato, cassava, lotus, and ginkgo) of different debranched starches with 12-18C fatty acid (lauric, myristic, palmitic, and stearic acids), respectively. The complex showed a V-type structure, formed by lotus and ginkgo debranched starches, and fatty acid exhibited a higher short-range order and crystallinity, and lower in vitro digestibility than others due to the neat interior structure of more linear glucan chains. Furthermore, a fatty acid with 12C (lauric acid)-debranched starches complexes had the highest complex index among all complexes, which might be attributed to the activation energy required for complex formation increased with the lengthening of the lipid carbon chain. Therefore, the lotus starch-lauric acid complex (LS12) exhibited remarkable ability in intestinal flora fermentation to produce short-chain fatty acid (SCFAs), reducing intestinal pH, and creating a favorable environment for beneficial bacteria.

S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota

Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.

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.

Simulated Digestion and Fecal Fermentation Behaviors of Levan and Its Impacts on the Gut Microbiota

Levan is a microbial fructan widely explored in various fields owing to its excellent physical and biochemical properties. However, little is known about its digestion and fermentation characteristics in vitro. This study evaluated the potential prebiotic properties of levan obtained by enzymatic synthesis. Scanning electron microscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the primary structures of levan remained stable after saliva-gastrointestinal digestion. The microtopography, molecular weight, and functional group of levan were seriously damaged during fecal fermentation. Moreover, the total short-chain fatty acid levels increased significantly, especially for propionic acid, butyric acid, and valeric acid. The 16S rDNA sequencing showed that levan mainly increased the abundance of Firmicutes; in genus levels, certain beneficial bacteria such as Megasphaera and Megamonas genera were remarkably promoted, and the proliferation of harmful genera was inhibited (such as Cedecea and Klebsiella). Overall, this study provided new insights into the potential probiotic mechanism of levan.

In Vitro Digestion and Fecal Fermentation of Peach Gum Polysaccharides with Different Molecular Weights and Their Impacts on Gut Microbiota

In the present study, we investigated the in vitro digestion and fermentation characteristics of three peach gum polysaccharides (PGPs) of different molecular weights; i.e., AEPG2 (1.64 × 107 g/mol), DPG2 (5.21 × 105 g/mol), and LP100R (8.50 × 104 g/mol). We observed that PGPs were indigestible during the oral, gastrointestinal, and intestinal stages. However, they were utilized by the gut microbiota with utilization rates in the order of DPG2 > AEPG2 > LP100R. Furthermore, arabinose in PGPs was preferentially utilized by the gut microbiota followed by galactose and xylose. Fermentation of peach gum polysaccharides could significantly increase the production of short-chain fatty acids (SCFAs), especially n-butyric acid. In addition, PGPs with different molecular weights values were predominantly fermented by different bacterial species. AEPG2 and DPG2 were fermented by the Bacteroidetes bacteria Bacteroides, while the dominant n-butyrate-producing bacteria was Faecalibacterium. While the LP100R was fermented by Bacteroides, Parabacteroides, Phascolarctobacterium, Dialister, Lachnospiraceae, and Blautia, the dominant n-butyrate-producing bacteria was Megamonas. These results indicated that PGPs are potential prebiotics for the food industry.

Impact of Food Origin Lactiplantibacillus plantarum Strains on the Human Intestinal Microbiota in an in vitro System

We have previously isolated and characterized food-dwelling strains of Lactiplantibacillus (Lpb.) plantarum that are consumed naturally as part of the microbiota of table olives and raw milk cheeses. Despite being consumed at relatively high levels, the impact of such strains on the human gut microbiota is currently unclear. In the current study we evaluated the potential impact of food-dominant Lpb. plantarum strains on the human gut microbiota using a continuous fecal fermentation system. Daily inoculation of Lpb. plantarum strains led to significant, detectable levels in the fecal fermentation system. We examined the impact of the presence of Lpb. plantarum on the microbiota derived from two separate donors. For one donor, Lpb. plantarum increased alpha diversity and beta diversity. This was reflected in significant alterations in abundance of the unclassified genera, dominated by Enterobacteriaceae_unclass and Ruminococcaceae_unclass. The microbiota of the other donor was relatively unaffected following introduction of the Lpb. plantarum strains. Overall, the work describes the response of the human microbiota to the introduction of high levels of food-dominant Lpb. plantarum strains and indicates that the response may reflect interindividual differences between donor samples.

In Vitro Gut Fermentation of Whey Protein Hydrolysate: An Evaluation of Its Potential Modulation on Infant Gut Microbiome

Whey protein and its hydrolysate are ubiquitously consumed as nutritional supplements. This study aimed to evaluate the potential effect of whey protein hydrolysate (WPH) on the infant gut microbiome, which is more variable than that of adults. Colonic fermentation was simulated through a static digestion model and fecal culture fermentation, using feces from normal infants aged from 1−3 years old. During in vitro gut fermentation, measurements of short-chain fatty acids (SCFA) concentrations and 16S rRNA amplicon sequencing were performed. Additionally, the growth curves of cultivated probiotics were analyzed to evaluate the prebiotic potential of WPH. Besides the decline of pH in fermentation, the addition of WPH induced a significant increase in the SCFA production and also the relative abundance of Proteobacteria, Bacteroides, and Streptococcus (p < 0.05). The lower ratio of Firmicutes/Bacteroidetes in WPH-supplemented samples indicated the positive modulation of WPH on the gut microbiota, which could benefit the energy balance and metabolism of infants. The stimulation effect of WPH on the probiotics (particularly Lactobacillus acidophilus NCFM) during cultivation implied the prebiotic potential as well. Our findings shed light on WPH as a valuable dietary supplement with not only enriched resources of essential amino acids but also the potential to restore the infant gut microbiome.

In Vitro Gastrointestinal Digestion and Colonic Catabolism of Mango (Mangifera indica L.) Pulp Polyphenols

Mango (Mangifera indica L.), a fruit with sensorial attractiveness and extraordinary nutritional and phytochemical composition, is one of the most consumed tropical varieties in the world. A growing body of evidence suggests that their bioactive composition differentiates them from other fruits, with mango pulp being an especially rich and diverse source of polyphenols. In this study, mango pulp polyphenols were submitted to in vitro gastrointestinal digestion and colonic fermentation, and aliquots were analyzed by HPLC-HRMS. The main phenolic compounds identified in the mango pulp were hydroxybenzoic acid-hexoside, two mono-galloyl-glucoside isomers and vanillic acid. The release of total polyphenols increased after the in vitro digestion, with an overall bioaccessibility of 206.3%. Specifically, the most bioaccessible mango polyphenols were gallic acid, 3-O-methylgallic acid, two hydroxybenzoic acid hexosides, methyl gallate, 3,4-dihydroxybenzoic acid and benzoic acid, which potentially cross the small intestine reaching the colon for fermentation by the resident microbiota. After 48 h of fecal fermentation, the main resultant mango catabolites were pyrogallol, gallic and 3,4-dihydroxybenzoic acids. This highlighted the extensive transformation of mango pulp polyphenols through the gastrointestinal tract and by the resident gut microbiota, with the resultant formation of mainly simple phenolics, which can be considered as biomarkers of the colonic metabolism of mango.

Extracellular Vesicles Produced by Bifidobacterium longum Export Mucin-Binding Proteins

Extracellular proteins are important factors in host-microbe interactions; however, the specific factors that enable bifidobacterial adhesion and survival in the gastrointestinal (GI) tract are not fully characterized. Here, we discovered that Bifidobacterium longum NCC2705 cultured in bacterium-free supernatants of human fecal fermentation broth released a myriad of particles into the extracellular environment. The aim of this study was to characterize the physiological properties of these extracellular particles. The particles, approximately 50 to 80 nm in diameter, had high protein and double-stranded DNA contents, suggesting that they were extracellular vesicles (EVs). A proteomic analysis showed that the EVs primarily consisted of cytoplasmic proteins with crucial functions in essential cellular processes. We identified several mucin-binding proteins by performing a biomolecular interaction analysis of phosphoketolase, GroEL, elongation factor Tu (EF-Tu), phosphoglycerate kinase, transaldolase (Tal), and heat shock protein 20 (Hsp20). The recombinant GroEL and Tal proteins showed high binding affinities to mucin. Furthermore, the immobilization of these proteins on microbeads affected the permanence of the microbeads in the murine GI tract. These results suggest that bifidobacterial exposure conditions that mimic the intestine stimulate B. longum EV production. The resulting EVs exported several cytoplasmic proteins that may have promoted B. longum adhesion. This study improved our understanding of the Bifidobacterium colonization strategy in the intestinal microbiome.IMPORTANCE Bifidobacterium is a natural inhabitant of the human gastrointestinal (GI) tract. Morphological observations revealed that extracellular appendages of bifidobacteria in complex microbial communities are important for understanding its adaptations to the GI tract environment. We identified dynamic extracellular vesicle (EV) production by Bifidobacterium longum in bacterium-free fecal fermentation broth that was strongly suggestive of differing bifidobacterial extracellular appendages in the GI tract. In addition, export of the adhesive moonlighting proteins mediated by EVs may promote bifidobacterial colonization. This study provides new insight into the roles of EVs in bifidobacterial colonization processes as these bacteria adapt to the GI environment.

In Vitro Fermentation of Sheep and Cow Milk Using Infant Fecal Bacteria

While human milk is the optimal food for infants, formulas that contain ruminant milk can have an important role where breastfeeding is not possible. In this regard, cow milk is most commonly used. However, recent years have brought interest in other ruminant milk. While many similarities exist between ruminant milk, there are likely enough compositional differences to promote different effects in the infant. This may include effects on different bacteria in the large bowel, leading to different metabolites in the gut. In this study sheep and cow milk were digested using an in vitro infant digestive model, followed by fecal fermentation using cultures inoculated with fecal material from two infants of one month and five months of age. The effects of the cow and sheep milk on the fecal microbiota, short-chain fatty acids (SCFA), and other metabolites were investigated. Significant differences in microbial, SCFA, and metabolite composition were observed between fermentation of sheep and cow milk using fecal inoculum from a one-month-old infant, but comparatively minimal differences using fecal inoculum from a five-month-old infant. These results show that sheep milk and cow milk can have differential effects on the gut microbiota, while demonstrating the individuality of the gut microbiome.

A Small In Vitro Fermentation Model for Screening the Gut Microbiota Effects of Different Fiber Preparations

The development of prebiotic fibers requires fast high-throughput screening of their effects on the gut microbiota. We demonstrated the applicability of a mictotiter plate in the in vitro fermentation models for the screening of potentially-prebiotic dietary fibers. The effects of seven rye bran-, oat- and linseed-derived fiber preparations on the human fecal microbiota composition and short-chain fatty acid production were studied. The model was also used to study whether fibers can alleviate the harmful effects of amoxicillin-clavulanate on the microbiota. The antibiotic induced a shift in the bacterial community in the absence of fibers by decreasing the relative amounts of Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Lachnospiraceae and Ruminococcaceae, and increasing proteobacterial Sutterilaceae levels from 1% to 11% of the total microbiota. The fermentation of rye bran, enzymatically treated rye bran, its insoluble fraction, soluble oat fiber and a mixture of rye fiber:soluble oat fiber:linseed resulted in a significant increase in butyrate production and a bifidogenic effect in the absence of the antibiotic. These fibers were also able to counteract the negative effects of the antibiotic and prevent the decrease in the relative amount of bifidobacteria. Insoluble and soluble rye bran fractions and soluble oat fiber were the best for controlling the level of proteobacteria at the level below 2%.

Metabolism of Stilbenoids by Human Faecal Microbiota

Stilbenoids are dietary phenolics with notable biological effects on humans. Epidemiological, clinical, and nutritional studies from recent years have confirmed the significant biological effects of stilbenoids, such as oxidative stress protection and the prevention of degenerative diseases, including cancer, cardiovascular diseases, and neurodegenerative diseases. Stilbenoids are intensively metabolically transformed by colon microbiota, and their corresponding metabolites might show different or stronger biological activity than their parent molecules. The aim of the present study was to determine the metabolism of six stilbenoids (resveratrol, oxyresveratrol, piceatannol, thunalbene, batatasin III, and pinostilbene), mediated by colon microbiota. Stilbenoids were fermented in an in vitro faecal fermentation system using fresh faeces from five different donors as an inoculum. The samples of metabolized stilbenoids were collected at 0, 2, 4, 8, 24, and 48 h. Significant differences in the microbial transformation among stilbene derivatives were observed by liquid chromatography mass spectrometry (LC/MS). Four stilbenoids (resveratrol, oxyresveratrol, piceatannol and thunalbene) were metabolically transformed by double bond reduction, dihydroxylation, and demethylation, while batatasin III and pinostilbene were stable under conditions simulating the colon environment. Strong inter-individual differences in speed, intensity, and pathways of metabolism were observed among the faecal samples obtained from the donors.

In Vitro Fecal Fermentation of High Pressure-Treated Fruit Peels Used as Dietary Fiber Sources

Fruit by-products are being investigated as non-conventional alternative sources of dietary fiber (DF). High hydrostatic pressure (HHP) treatments have been used to modify DF content as well as its technological and physiological functionality. Orange, mango and prickly pear peels untreated (OU, MU and PPU) and HHP-treated at 600 MPa (OP/55 °C and 20 min, MP/22 °C and 10 min, PPP/55 °C and 10 min) were evaluated. Untreated and treated fruit peels were subjected to fecal in vitro fermentations. The neutral sugar composition and linkage glycosidic positions were related to the production of short chain fatty acids (SCFA) resulting from the fermentation of the materials. After HHP-treatments, changes from multibranched sugars to linear sugars were observed. After 24 h of fermentation, OP yielded the highest amount of SCFA followed by PPU and MP (389.4, 282.0 and 204.6 μmol/10 mg DF, respectively). HHP treatment increased the SCFA concentration of orange and mango peel by 7 and 10.3% respectively, compared with the untreated samples after 24 h of fermentation. The results presented herein suggest that fruit peels could be used as good fermentable fiber sources, because they yielded high amounts of SCFA during in vitro fermentations.

The Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colon

Ex vivo colon fermentation systems are highly versatile as models for analyzing gastrointestinal tract microbiota composition and functionality. Ex vivo colon models range in size and functionality from bench-top micro fermenters to large units housed in individualized cabinets. The length of set-up time (including stabilization periods) for each fermentation system can range from hours to weeks to months. The aim of this study was to investigate a single-use cassette mini-fermentation system as a reproducible batch model of the colon. The online data log from the cassettes (triplicate wells across four different cassettes, n = 12) was sensitive enough to identify real-time changes in pH, temperature, dissolved oxygen or liquid addition (sodium hydroxide) during the runs which could be addressed if an alarm set-point was triggered. The alpha diversity indices also showed little variation between cassettes with the samples clustering around the mean. The weighted beta diversity PCoA analysis illustrated that 95% of the variance between the samples was accounted for by the time-point and not the fermentation run/cassette used. The variation in taxonomic diversity between cassettes was limited to less than 20 out of 115 genera. This study provides evidence that micro-bioreactors provide some very attractive advantages as batch models for the human colon. We show for the first time the use of the micro-Matrix a 24-well sophisticated parallel controlled cassette-based bioreactors as a batch colon model. We demonstrated a high level of reproducibility across fermentation cassettes when used in conjunction with a standardized fecal microbiota. The machine can operate 24 individual fermentations simultaneously and are relatively cost effective. Based on next generation sequencing analysis, the micro-bioreactors offer a high degree of reproducibility together with high-throughput capacity. This makes it a potential system for large screening projects that can then be scaled up to large fermenters or human/animal in vivo experiments.