Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems

The impact of coffee on gut microbial structure based on in vitro fecal incubation system

Coffee is globally popular beverage, renowned for its taste and stimulating properties. This study aims to explore the impact of two different types of coffee, depending on extraction methods, on the gut microbiota. Fecal samples from healthy donors (n = 20) were cultured with or without coffee using in vitro fecal incubation. Both coffee-treated groups exhibited lower microbial diversity and greater structural differences in their communities compared to the control. Notably, the Bifidobacterium genus was overrepresented in the instant coffee (IC)-treated groups, whereas the Blautia genus was underrepresented in both coffee-treated groups. Additionally, genes for TCA cycle and vitamin B6 metabolism were more prevalent in coffee-treated groups than in the control. However, the precursor pathways leading to the TCA cycle differed between the DC- and IC-treated groups, reflecting the distinct chemical compositions of each coffee type. These findings demonstrate that extraction method of coffee significantly affects its impacts on gut microbial structure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01717-7.

Extrusion treatment of rice bran insoluble fiber generates specific niches favorable for Bacteroides during in vitro fermentation

To investigate the morphological changes of insoluble fiber and their effects on microbiota modulation, particularly Bacteroides, rice bran insoluble fibers were extruded at different feed moisture levels (E20, E40, and E60). The physicochemical properties and SEM revealed that E20 exhibited the highest water holding capacity and displayed the most fragmented edges. E40 had the highest swelling holding capacity and displayed the most lamellar gaps. E60 showed minimal change in physicochemical properties but had a rough surface. After 48h fermentation, E40 showed the highest levels of Bacteroides and SCFAs. E20 and E60 resulted in a modest increase in Bacteroides abundance. SEM showed that bacteria were attached to fragmented edges, loosened lamellar gaps, and rough surfaces of the extruded insoluble fibers. The results suggested that Bacteroides gained a competitive advantage within the extrusion treatment created structural changes. Extrusion treatment can be used to generate specific niches favorable for Bacteroides.

Germination-Induced Enhancement of Brown Rice Noodle Nutritional Profile and Gut Microbiota Modulation

This study explored how germination influences the starch digestion and intestinal fermentation characteristics of brown rice noodle. The study began with in vitro starch digestion tests to assess how germination affects starch digestibility in brown rice noodles, revealing an increase in rapidly digestible starch content and a decrease in resistant starch content. Subsequently, an in vitro human fecal fermentation model was used to simulate the human intestinal environment, showing that germination altered pH levels and the production of short-chain fatty acids, particularly by increasing propionate while decreasing acetate and butyrate. Additionally, the study noted a decrease in gut microbiota diversity following fermentation, accompanied by an increase in Megamonas growth and a decrease in Bacteroides and Bifidobacterium. In conclusion, these findings suggest that germination could enhance the nutritional value and intestinal probiotic properties of brown rice noodles. This research contributes valuable insights into the role of germination in improving the nutritional properties of rice-based products and provides a foundation for further exploration into the development of health-promoting rice noodles.

Combined dilute alkali and milling process enhances the functionality and gut microbiota fermentability of insoluble corn fiber

In this study, we developed a process combining dilute alkali (NaOH or NaHCO3) and physical (disk milling and/or ball milling) treatments to improve the functionality and fermentability of corn fiber. The results showed that combining chemical with physical processes greatly improved the functionality and fermentability of corn fiber. Corn fiber treated with NaOH followed by disk milling (NaOH-DM-CF) had the highest water retention (19.5 g/g), water swelling (38.8 mL/g), and oil holding (15.5 g/g) capacities. Moreover, NaOH-DM-CF produced the largest amount (42.9 mM) of short-chain fatty acid (SCFA) during the 24-hr in vitro fermentation using porcine fecal inoculum. In addition, in vitro fermentation of NaOH-DM-CF led to a targeted microbial shifting to Prevotella (genus level), aligning with a higher fraction of propionic acid. The outstanding functionality and fermentability of NaOH-DM-CF were attributed to its thin and loose structure, decreased ester linkages and acetyl groups, and enriched structural carbohydrate exposure.

Tannic acid delaying metabolism of resistant starch by gut microbiota during in vitro human fecal fermentation

This work investigated the effect of tannic acid on the fermentation rate of resistant starch. It was found that 1.0 and 1.5 μmol/L tannic acid decreased the rate of producing gas and short-chain fatty acids (SCFAs) from fermentation of resistant starch, and 1.5 μmol/mL tannic acid had a more profound effect, which confirmed that tannic acid delayed the metabolism of resistant starch. Moreover, tannic acid significantly inhibited the α-amylase activity during fermentation. On the other hand, tannic acid delayed the enrichment of some starch-degrading bacteria. Besides, fermentation of the resistant starch/tannic acid mixtures resulted in more SCFAs, particularly butyrate, and higher abundance of beneficial bacteria, including Bifidobacterium, Faecalibacterium, Blautia and Dorea, than fermentation of resistant starch after 48 h. Thus, it was inferred that tannic acid could delay the metabolism of resistant starch, which was due to its inhibitory effect on the α-amylase activity and regulatory effect on gut microbiota.

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

BACKGROUND

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

METHODS AND RESULTS

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

CONCLUSIONS

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

Analysis of the fermentation kinetics and gut microbiota modulatory effect of dried chicory root reveals the impact of the plant-cell matrix rationalizing its conversion in the distal colon

Aim: The cell matrix of plant foods has received little attention in prebiotic fiber research. We aimed to understand the impact of the plant cell matrix in dried chicory root on its breakdown in the human gut to explain its reported beneficial effects on gut and metabolic health. Methods: We applied in vitro digestion and fermentation models together with an ex vivo gut barrier integrity model. Plant cell matrix intactness in the upper gastrointestinal tract was investigated by scanning electron microscopy. Colonic breakdown of inulin, and chicory root cubes and powder was assessed by gut microbiota analysis using 16S rRNA gene amplicon sequencing and determining the kinetics of changes in pH, gas, and short-chain fatty acid (SCFA) production. Finally, effects on gut barrier integrity were explored by exposing colonic biopsies to fermentation supernatants in an Ussing chamber model. Results: The plant cell matrix of dried chicory root cubes remained intact throughout upper gastrointestinal transit. Dried chicory root fermentation resulted in higher final relative abundances of pectin-degrading Monoglobus and butyrate-producing Roseburia spp. compared to inulin and a seven-fold increase in Bifidobacterium spp. in donors where these species were present. Dried chicory root cubes yielded similar total SCFAs but higher final butyrate levels than chicory root powder or isolated inulin with less gas produced. No uniform but donor-specific effects of fermentation supernatants on the maintenance of gut barrier integrity were detected. Conclusion: The intact plant cell matrix of dried chicory root affected its colonic breakdown kinetics and microbiota, underpinning its beneficial effect in vivo.

Subcritical water treatment to modify insoluble dietary fibers from brewer's spent grain for improved functionality and gut fermentability

Lactic acid (LA)-assisted subcritical water treatment (SWT) was applied to modify the insoluble dietary fiber (IDF) from brewer's spent grain (BSG) for enhancing its functionality and gut fermentability. Modified IDFs were thoroughly characterized for their chemical and structural properties. The results revealed that increasing the treatment temperature and LA concentration reduced hemicellulose content in IDFs from 38.4 % to 0.7 %, alongside a decreased yield (84.8 %-51.4 %), reduced particle size (519.8-288.6 μm), and more porous structure of IDFs. These modifications were linked to improved functionalities, evidenced by the highest water and oil holding capacity increasing by 36 % and 67 %, respectively. Remarkably, the highest glucose adsorption capacity increased by 6.5 folds. Notably, modified IDFs exhibited slower in-vitro fermentation, elevated short-chain fatty acids (SCFAs) production, and a higher proportion of butyrate in SCFAs. These findings highlight the potential of LA-assisted SWT in transforming BSG-derived IDF into a valuable functional food ingredient.

Elemental iron protects gut microbiota against oxygen-induced dysbiosis

Gut dysbiosis induced by oxygen and reactive oxygen species may be related to the development of inflammation, resulting in metabolic syndrome and associated-conditions in the gut. Here we show that elemental iron can serve as an antioxidant and reverse the oxygen-induced dysbiosis. Fecal samples from three healthy donors were fermented with elemental iron and/or oxygen. 16S rRNA analysis revealed that elemental iron reversed the oxygen-induced disruption of Shannon index diversity of the gut microbiota.The bacteria lacking enzymatic antioxidant systems also increased after iron treatment. Inter-individual differences, which corresponded to iron oxidation patterns, were observed for the tested donors. Gut bacteria responding to oxygen and iron treatments were identified as guilds, among which, Escherichia-Shigella was promoted by oxygen and depressed by elemental iron, while changes in bacteria such as Bifidobacterium, Blautia, Eubacterium, Ruminococcaceae, Flavonifractor, Oscillibacter, and Lachnospiraceae were reversed by elemental iron after oxygen treatment. Short-chain fatty acid production was inhibited by oxygen and this effect was partially reversed by elemental iron. These results suggested that elemental iron can regulate the oxygen/ROS state and protect the gut microbiota from oxidative stress.

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

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

Influence of structural features and feruloylation on fermentability and ability to modulate gut microbiota of arabinoxylan in in vitro fermentation

Introduction

Arabinoxylan (AX) is a versatile polysaccharide that shows various effects in modulating gut microbiota and health. The influence of arabinoxylan carbohydrate structural feature and feruloylation on fermentability and the effect of modulation of gut microbiota of AX was not clear.

Methods

Arabinoxylans from rice bran and corn bran (RAX and CAX), and their deferulyolated counterpart dRAX and dCAX were fermented using an in vitro fermentation model. Structural information was determined based on monosaccharide composition. Gas production of fermentation products, SCFAs production, pH change, and microbiota change were measured.

Results

RAX and dRAX posessed lower A/X ratio compared with CAX and dCAX. The gas and total SCFAs production were lower in RAX and dRAX, and the butyrate production were higher in RAX and dRAX compared with CAX and dCAX. Butyrate production was lower at dRAX compared to RAX. On the other hand, butyrate production was higher in dCAX than in CAX. The microbiota shift were different for the four fibers.

Discussion

The AXs from rice have a higher A/X ratio than the AXs from maize, suggesting more branching and a more complex side chain. The structural difference was crucial for the difference in fermentation pattern. Different Bacteroides species are responsible for the utilization of rice AXs and corn AXs. Although feruloylation had a minor effect on the overall fermentation pattern, it significantly affected butyrate production and alpha diversity. dRAX promoted less butyrate than RAX, which is associated with a significantly lower amount of Faecalibacterium prausnitzi. dCAX promoted more butyrate than CAX, which may be associated with a lower amount of Bacteroides ovatus and a higher amount of Blautia in dCAX compared to CAX. The effects of feruloylation on the fermentation pattern and the resulted microbiota shift of AX varied depending on the carbohydrate structure.

The sugar composition of the fibre in selected plant foods modulates weaning infants' gut microbiome composition and fermentation metabolites in vitro

Eight plant-based foods: oat flour and pureed apple, blackcurrant, carrot, gold- and green-fleshed kiwifruit, pumpkin, sweetcorn, were pre-digested and fermented with pooled inocula of weaning infants’ faecal bacteria in an in vitro hindgut model. Inulin and water were included as controls. The pre-digested foods were analysed for digestion-resistant fibre-derived sugar composition and standardised to the same total fibre concentration prior to fermentation. The food-microbiome interactions were then characterised by measuring microbial acid and gas metabolites, microbial glycosidase activity and determining microbiome structure. At the physiologically relevant time of 10 h of fermentation, the xyloglucan-rich apple and blackcurrant favoured a propiogenic metabolic and microbiome profile with no measurable gas production. Glucose-rich, xyloglucan-poor pumpkin caused the greatest increases in lactate and acetate (indicative of high fermentability) commensurate with increased bifidobacteria. Glucose-rich, xyloglucan-poor oats and sweetcorn, and arabinogalactan-rich carrot also increased lactate and acetate, and were more stimulatory of clostridial families, which are indicative of increased microbial diversity and gut and immune health. Inulin favoured a probiotic-driven consortium, while water supported a proteolytic microbiome. This study shows that the fibre-derived sugar composition of complementary foods may shape infant gut microbiome structure and metabolic activity, at least in vitro.

Supplementation with Chlorella vulgaris, Chlorella protothecoides, and Schizochytrium sp. increases propionate-producing bacteria in in vitro human gut fermentation

BACKGROUND

Gut microbiota are major contributors to host metabolism and are considered as potential targets of novel therapeutics. Microalgae have a strong potential for use as prebiotics because they are a rich source of proteins, fatty acids, fiber, and minerals for nutritional supplementation in humans. Nevertheless, there has been insufficient research into the effect of microalgae on gut microbiota. To investigate the effects of three edible microalgae (Chlorella vulgaris, Chlorella protothecoides, and Schizochytrium sp.) on gut microbiota, simulated digestion and colonic fermentation were examined.

RESULTS

Following in vitro digestion, the microalgae displayed different levels of bioaccessibility and the nutrient analysis revealed that unabsorbed nutrients during the digestion process could be used for colonic fermentation. Following colonic fermentation, the control, inulin, and microalgae groups displayed different metabolite tendencies when investigated with nuclear magnetic resonance (NMR) spectroscopic analysis. In particular, microalgae supplementation increased the proportion of propionate in the colonic culture (control: 19.14%, Inulin: 18.38%, C. vulgaris: 25.80%, C. protothecoides: 25.46%, and Schizochytrium sp.: 25.56%). Microbial profiling analysis using 16S rRNA gene sequencing also disclosed that the relative abundance of Bacteroides (control: 1.91%, inulin: 2.61%, C. vulgaris: 14.77%, C. protothecoides: 11.17%, and Schizochytrium sp.: 5.51%) and Dialister (control: 0.08%, inulin: 2.06%, C. vulgaris: 6.79%, C. protothecoides: 4.45%, and Schizochytrium sp.: 4.48%), involved in propionate metabolism increased more than in the inulin group.

CONCLUSION

Our findings suggest the potential use of microalgae as a functional food to increase propionate generation because propionate has been reported to be effective in weight loss and the inhibition of pathogen infection. © 2020 Society of Chemical Industry.

Response of the Human Milk Microbiota to A Maternal Prebiotic Intervention is Individual and Influenced by Maternal Age

Maternal bacteria are shared with infants via breastfeeding. Prebiotics modulate the gut microbiota, promoting health benefits. We investigated whether the maternal diet supplementation with a prebiotic (fructooligosaccharides, FOS) could influence the milk microbiota. Twenty-eight lactating women received 4.5 g of fructooligosaccharides + 2 g of maltodextrin (FOS group) and twenty-five received 2 g of maltodextrin (placebo group) for 20 days. Breast-milk samples were taken before and after the intervention. The DNA from samples was used for 16S rRNA sequencing. No statistical differences between the groups were found for the bacterial genera after the intervention. However, the distances of the trajectories covered by paired samples from the beginning to the end of the supplementation were higher for the FOS group (p = 0.0007) indicating greater changes in milk microbiota compared to the control group. Linear regression models suggested that the maternal age influenced the response for FOS supplementation (p = 0.02). Interestingly, the pattern of changes to genus abundance upon supplementation was not shared between mothers. We demonstrated that manipulating the human milk microbiota through prebiotics is possible, and the maternal age can affect this response.&nbsp.

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

In vitro gut microbiome models could provide timely and cost-efficient solutions to study microbiome responses to drugs. For this purpose, in vitro models that maintain the functional and compositional profiles of in vivo gut microbiomes would be extremely valuable. Here, we present a 96-deep well plate-based culturing model (MiPro) that maintains the functional and compositional profiles of individual gut microbiomes, as assessed by metaproteomics, while allowing a four-fold increase in viable bacteria counts. Comparison of taxon-specific functions between pre- and post-culture microbiomes shows a Pearson's correlation coefficient r of 0.83 ± 0.03. In addition, we show a high degree of correlation between gut microbiome responses to metformin in the MiPro model and those in mice fed a high-fat diet. We propose MiPro as an in vitro gut microbiome model for scalable investigation of drug-microbiome interactions such as during high-throughput drug screening.

Dose-Dependent Alterations to In Vitro Human Microbiota Composition and Butyrate Inhibition by a Supercritical Carbon Dioxide Hops Extract

Hop cones (Humulus lupulus L.) have been used throughout history as an additive in beer brewing and as herbal supplements with medicinal and culinary properties. The objective of this study was to ascertain the effect of a range of concentrations of a supercritical CO2 extract of hops on the composition and metabolism of human gut bacterial communities using in vitro batch culture systems. Fermentations were conducted over 24 h using a mixed human fecal inoculum. Microbial metabolism was assessed by measuring organic acid production and microbial community alterations were determined by 16S rRNA gene sequencing. Butyrate, an important short chain fatty acid in maintaining colonic well-being, decreased at elevated concentrations of hops, which may partly be accounted for by the concomitant reduction of Eubacterium and Coprococcus, known butyrate-producing genera, and also the inhibition of Bifidobacterium, a beneficial organism that has a butyrogenic effect through metabolic cross-feeding with intestinal commensals. The hops compounds also caused dose-dependent increases in the potentially pathogenic Enterobacteriaceae and potentially beneficial Akkermansia. Thus, hops compounds had a significant impact on the structure of the bacterial consortium, which warrants further study including human clinical trials.

Prebiotics from acorn and sago prevent high-fat-diet-induced insulin resistance via microbiome-gut-brain axis modulation

Role of gut microbiome in obesity and type 2 diabetes (T2D) became apparent from several independent studies indicating that gut microbiome modulators like prebiotics may improve microbiome perturbations (dysbiosis) to ameliorate metabolic derangements. We herein isolate water soluble, nondigestible polysaccharides from five plant-based foods (acorn, quinoa, sunflower, pumpkin seeds and sago) and assess their impact on human fecal microbiome and amelioration of high-fat-diet (HFD)-induced obesity/T2D in mice. During polysaccharide isolation, purification, biochemical and digestion resistance characterization, and fermentation pattern by human fecal microbiome, we select acorn- and sago-derived prebiotics (on the basis of relatively higher purity and yield and lower protein contamination) and examine their effects in comparison to inulin. Prebiotics treatments in human fecal microbiome culture system not only preserve microbial diversity but also appear to foster beneficial bacteria and short-chain fatty acids (SCFAs). Feeding of acorn- and sago-derived prebiotics ameliorates HFD-induced glucose intolerance and insulin resistance in mice, with effects comparatively superior to those seen in inulin-fed mice. Feeding of both of novel prebiotics as well as inulin increases SCFAs levels in the mouse gut. Interestingly, gut hyperpermeability and mucosal inflammatory markers were significantly reduced upon prebiotics feeding in HFD-fed mice. Hypothalamic energy signaling in terms of increased expression of pro-opiomelanocortin was also modulated by prebiotics administration. Results demonstrate that these (and/or such) novel prebiotics can ameliorate HFD-induced defects in glucose metabolism via positive modulation of gut-microbiome-brain axis and hence could be useful in preventing/treating diet-induced obesity/T2D.

Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model

Ingestion of silver nanoparticles (AgNPs) is inevitable linked to their widespread use in food, medicines and other consumer products. However, their effects on human microbiota at non-lethal concentrations remain poorly understood. In this study, the interactions among 1 μg mL^-1 AgNPs, the intestinal microbiota, and the probiotic Bacillus subtilis (BS) were tested using in-vitro batch fermentation models inoculated with human fecal matter. Results from metagenomic investigations revealed that the core bacterial community was not affected by the exposure of AgNPs and BS at the later stage of fermentation, while the proportions of rare species changed drastically with the treatments. Furthermore, shifts in the Firmicutes/Bacteriodetes (F/B) ratios were observed after 24 h with an increase in the relative abundance of Firmicutes species and a decrease in Bacteroidetes in all fermentation cultures. The co-exposure to AgNPs and BS led to the lowest F/B ratio. Fluorescent in-situ hybridization analyses indicated that non-lethal concentration of AgNPs negatively affected the relative percentage of Faecalibacterium prausnitzii and Clostridium coccoides/Eubacterium rectales taxa in the fermentation cultures after 24 h. However, exposure to single and combined treatments of AgNPs and BS did not change the overall diversity of the fecal microflora. Functional differences in cell motility, translation, transport, and xenobiotics degradation occurred in AgNPs-treated fermentation cultures but not in AgNPs+BS-treated samples. Compared to the control samples, treated fecal cultures showed no significant statistical differences in terms of short-chain fatty acids profiles, cytotoxic and genotoxic effects on Caco-2 cell monolayers. Overall, AgNPs did not affect the composition and diversity of the core fecal microflora and its metabolic and toxic profiles. This work indicated a chemopreventive role of probiotic on fecal microflora against AgNPs, which were shown by the decrease of F/B ratio and the unaltered state of some key metabolic pathways.

Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut

Chronic disruption of the intestinal microbiota in adult cystic fibrosis (CF) patients is associated with local and systemic inflammation, and has been linked to the risk of serious comorbidities. Supplementation with high amylose maize starch (HAMS) might provide clinical benefit by promoting commensal bacteria and the biosynthesis of immunomodulatory metabolites. However, whether the disrupted CF gut microbiota has the capacity to utilise these substrates is not known. We combined metagenomic sequencing, in vitro fermentation, amplicon sequencing, and metabolomics to define the characteristics of the faecal microbiota in adult CF patients and assess HAMS fermentation capacity. Compared to healthy controls, the faecal metagenome of adult CF patients had reduced bacterial diversity and prevalence of commensal fermentative clades. In vitro fermentation models seeded with CF faecal slurries exhibited reduced acetate levels compared to healthy control reactions, but comparable levels of butyrate and propionate. While the commensal genus Faecalibacterium was strongly associated with short chain fatty acid (SCFA) production by healthy microbiota, it was displaced in this role by Clostridium sensu stricto 1 in the microbiota of CF patients. A subset of CF reactions exhibited enterococcal overgrowth, resulting in lactate accumulation and reduced SCFA biosynthesis. The addition of healthy microbiota to CF faecal slurries failed to displace predominant CF taxa, or substantially influence metabolite biosynthesis. Despite significant microbiota disruption, the adult CF gut microbiota retains the capacity to exploit HAMS. Our findings highlight the potential for taxa associated with the altered CF gut microbiotato mediate prebiotic effects in microbial systems subject to ongoing perturbation, irrespective of the depletion of common commensal clades.

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure

This study investigated the effect of various prebiotics (indigestible dextrin, α-cyclodextrin, and dextran) on human colonic microbiota at a dosage corresponding to a daily intake of 6 g of prebiotics per person (0.2% of dietary intake). We used an in vitro human colonic microbiota model based on batch fermentation starting from a faecal inoculum. Bacterial 16S rRNA gene sequence analysis showed that addition of 0.2% prebiotics did not change the diversity and composition of colonic microbiota. This finding coincided with results from a clinical study showing that the microbiota composition of human faecal samples remained unchanged following administration of 6 g of prebiotics over seven days. However, compared to absence of prebiotics, their addition reduced the pH and increased the generation of acetate and propionate in the in vitro system. Thus, even at such relatively low amounts, prebiotics appear capable of activating the metabolism of colonic microbiota.

Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.

Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline

Quinoline is biodegradable under anaerobic conditions, but information about the degradation kinetics and the involved microorganisms is scarce. Here, the dynamics of a quinoline-degrading bacterial consortium were studied in anoxic batch cultures containing nitrate. The cultures removed 83.5% of the quinoline during the first 80 hours, which were dominated by denitrification, and then switched to methanogenesis when the nitrogen oxyanions were depleted. Time-resolved community analysis using pyrosequencing revealed that denitrifiying bacteria belonging to the genus Thauera were enriched during the denitrification stage from 12.2% to 38.8% and 50.1% relative abundance in DNA and cDNA libraries, respectively. This suggests that they are key organisms responsible for the initial attack on quinoline. Altogether, 13 different co-abundance groups (CAGs) containing 76 different phylotypes were involved, directly or indirectly, in quinoline degradation. The dynamics of these CAGs show that specific phylotypes were associated with different phases of the degradation. Members of Rhodococcus and Desulfobacterium, as well as Rhodocyclaceae- and Syntrophobacteraceae-related phylotypes, utilized initial metabolites of the quinoline, while the resulting smaller molecules were used by secondary fermenters belonging to Anaerolineae. The concerted action by the different members of this consortium resulted in an almost complete anaerobic mineralization of the quinoline.

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota

The gut microbiota of individuals are dominated by different fiber-utilizing bacteria, which ferment dietary fiber into short chain fatty acids (SCFAs) known to be important for human health. Here, we show that the dominance of Prevotella versus Bacteroides in fecal innocula, identified into two different enterotypes, differentially impacts in vitro fermentation profiles of SCFAs from fibers with different chemical structures. In a microbiome of the Prevotella enterotype, fructooligosaccharides, and sorghum and corn arabinoxylans significantly promoted one single Prevotella OTU with equally high production of total SCFAs with propionate as the major product. Conversely, in the Bacteroides-dominated microbiota, the three fibers enriched different OTUs leading to different levels and ratios of SCFAs. This is the first report showing how individual differences in two enterotypes cause distinctly different responses to dietary fiber. Microbiota dominated by different fiber-utilizing bacteria may impact host health by way of producing different amounts and profiles of SCFAs from the same carbohydrate substrates.

Challenges in simulating the human gut for understanding the role of the microbiota in obesity

There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.

In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics

Intestinal microbiota is emerging as one of the key environmental factors influencing or causing the development of numerous human diseases. Metaproteomics can provide invaluable information on the functional activities of intestinal microbiota and on host-microbe interactions as well. However, the application of metaproteomics in human microbiota studies is still largely limited, in part due to the lack of accurate quantitative intestinal metaproteomic methods. Most current metaproteomic microbiota studies are based on label-free quantification, which may suffer from variability during the separate sample processing and mass spectrometry runs. In this study, we describe a quantitative metaproteomic strategy, using in vitro stable isotopically ((15)N) labeled microbiota as a spike-in reference, to study the intestinal metaproteomes. We showed that the human microbiota were efficiently labeled (>95% (15)N enrichment) within 3 days under in vitro conditions, and accurate light-to-heavy protein/peptide ratio measurements were obtained using a high-resolution mass spectrometer and the quantitative proteomic software tool Census. We subsequently employed our approach to study the in vitro modulating effects of fructo-oligosaccharide and five different monosaccharides on the microbiota. Our methodology improves the accuracy of quantitative intestinal metaproteomics, which would promote the application of proteomics for functional studies of intestinal microbiota.