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Scope: There is a lack of research comparing how different protein isolates influence the microbiome, especially when carbohydrate (CHO) availability is varied. The objective is to determine changes in gut microbiota composition and function during fermentation of digested protein isolates under high and low CHO conditions., Methods and Results: Protein isolates from beef, egg white, milk, pea, and soy are subjected to in vitro digestion and fermentation with human fecal microbiota. Under low CHO conditions, the microbiota is primarily proteolytic with decreased concentrations of peptides and increased variance among microbial taxa and production of ammonia and branched chain fatty acids by the microbiota. Milk protein not only results in the highest production of butyrate and p-hydroxyphenylacetate but also has high concentrations of deleterious fermentation metabolites. Amino acid composition of the protein isolates is significantly correlated with abundances of many microbial taxa and metabolites, but the correlations are stronger in the low CHO medium., Conclusion: This study shows that low CHO conditions increase proteolytic fermentation and result in increased differences in microbiota response to protein isolates. It also showed that amino acid composition is highly associated with microbiota composition and function especially under low CHO conditions., (© 2024 The Author(s). Molecular Nutrition & Food Research published by Wiley‐VCH GmbH.)

Background: Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders., Results: Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial., Conclusions: Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders., (© 2024. The Author(s).)

Whole grains are generally low in nondigestible carbohydrates that are available for fermentation by the gut microbiota, or microbiota-accessible carbohydrates (MAC). However, there is potential to increase MAC in whole grains through food processing. Five processing methods: boiling, extrusion, sourdough bread, unleavened bread, and yeast bread, were applied to whole wheat flour and then subjected to in vitro digestion followed by fermentation using fecal microbiomes from 10 subjects. The microbiomes separated into 2 groups: those that showed high carbohydrate utilization (CU) and those that exhibited low CU. The former exhibited not only enhanced CU but also increased butyrate production (MAC, 31.1 ± 1.1% versus 19.3 ± 1.2%, P  < 0.001; butyrate, 5.26 ± 0.26 mM versus 3.17 ± 0.27 mM, P  < 0.001). Only the microbiomes in the high-CU group showed significant differences among processing methods: extrusion and sourdough bread led to dichotomous results for MAC and short-chain fatty acid production, where extrusion resulted in high MAC but low butyrate production while sourdough bread resulted in low MAC but high butyrate production. Extrusion led to a noticeable decrease in α-diversity and some members of the families Ruminococcaceae and Lachnospiraceae , with increases in Acinetobacter , Enterococcus , and Staphylococcaceae This study demonstrated that only microbiomes that exhibited high CU responded to the effects of processing by showing significant differences among processing methods. In these microbiomes, extrusion was able to increase accessibility of the cell wall polysaccharides but did not increase butyrate production. In contrast, sourdough bread led to high butyrate production by supporting important butyrate-producers in the families Lachnospiraceae and Ruminococcaceae Dietary nondigestible carbohydrates, or dietary fiber, have long been recognized for their beneficial health effects. However, recent studies have revealed that fermentation of nondigestible carbohydrates by gut bacteria is critical in mediating many of the health-promoting properties of dietary fibers. Whole grains are excellent candidates to supply the microbiome with a plentiful source of nondigestible carbohydrates, although unfortunately a majority of these carbohydrates in whole grains are not available to gut bacteria for fermentation. Processing is known to alter the structural characteristics of nondigestible carbohydrates in whole grains, yet the relationship between these effects and gut microbial fermentation is unknown. This research aimed to address this important research gap by identifying interactions between whole-grain processing and gut bacteria, with the ultimate goal of increasing the availability of nondigestible carbohydrates for fermentation to enhance host health.IMPORTANCE Dietary nondigestible carbohydrates, or dietary fiber, have long been recognized for their beneficial health effects. However, recent studies have revealed that fermentation of nondigestible carbohydrates by gut bacteria is critical in mediating many of the health-promoting properties of dietary fibers. Whole grains are excellent candidates to supply the microbiome with a plentiful source of nondigestible carbohydrates, although unfortunately a majority of these carbohydrates in whole grains are not available to gut bacteria for fermentation. Processing is known to alter the structural characteristics of nondigestible carbohydrates in whole grains, yet the relationship between these effects and gut microbial fermentation is unknown. This research aimed to address this important research gap by identifying interactions between whole-grain processing and gut bacteria, with the ultimate goal of increasing the availability of nondigestible carbohydrates for fermentation to enhance host health., (Copyright © 2020 American Society for Microbiology.)

Extrusion exposes flour components to high pressure and shear during processing, which may affect the dietary fiber fermentability by human fecal microbiota. The objective of this study was to determine the effect of flour moisture content during extrusion on in vitro fermentation properties of whole grain oats. Extrudates were processed at three moisture levels (15%, 18%, and 21%) at fixed screw speed (300rpm) and temperature (130°C). The extrudates were then subjected to in vitro digestion and fermentation. Extrusion moisture significantly affected water-extractable β-glucan (WE-BG) in the extrudates, with samples processed at 15% moisture (lowest) and 21% moisture (highest) having the highest concentration of WE-BG. After the first 8h of fermentation, more WE-BG remained in fermentation media in samples processed at 15% moisture compared with the other conditions. Also, extrusion moisture significantly affected the production of acetate, butyrate, and total SCFA by the microbiota during the first 8h of fermentation. Microbiota grown on extrudates processed at 18% moisture had the highest production of acetate and total SCFA, whereas bacteria grown on extrudates processed at 15% and 18% moisture had the highest butyrate production. After 24h of fermentation, samples processed at 15% moisture supported lower Bifidobacterium counts than those produced at other conditions, but had among the highest Lactobacillus counts. Thus, moisture content during extrusion significantly affects production of fermentation metabolites by the gut microbiota during the initial stages of fermentation, while also affecting probiotic bacteria counts during extended fermentation., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Unlabelled: Sustained colonic fermentation supplies beneficial fermentative by-products to the distal colon, which is particularly prone to intestinal ailments. Blunted/delayed initial fermentation may also lead to less bloating. Previously, we reported that starch-entrapped alginate-based microspheres act as a slowly fermenting dietary fiber. This material was used in the present study to provide a benchmark to compare to other "slowly fermentable" fibers. Dietary fibers with previous reports of slow fermentation, namely, long-chain inulin, psyllium, alkali-soluble corn bran arabinoxylan, and long-chain β-glucan, as well as starch-entrapped microspheres were subjected to in vitro upper gastrointestinal digestion and human fecal fermentation and measured over 48 h for pH, gas, and short-chain fatty acids (SCFA). The resistant fraction of cooked and cooled potato starch was used as another form of fermentable starch and fructooligosaccharides (FOS) served as a fast fermenting control. Corn bran arabinoxylan and long-chain β-glucan initially appeared slower fermenting with comparatively low gas and SCFA production, but later fermented rapidly with little remaining in the final half of the fermentation period. Long-chain inulin and psyllium had slow and moderate, but incomplete, fermentation. The resistant fraction of cooked and cooled potato starch fermented rapidly and appeared similar to FOS. In conclusion, compared to the benchmark slowly fermentable starch-entrapped microspheres, a number of the purported slowly fermentable fibers fermented fairly rapidly overall and, of this group, only the starch-entrapped microspheres appreciably fermented in the second half of the fermentation period., Practical Application: Consumption of dietary fibers, particularly commercial prebiotics, leads to uncomfortable feelings of bloating and flatulence due to their rapid degradation in our large intestine. This article employs claimed potential slowly fermenting fibers and compares their fermentation rates with a benchmark slow fermenting fiber that we fabricated in an in vitro simulation of the human digestive system. Results show a variety of fermentation profiles only some of which have slow and extended rate of fermentation., (© 2011 Institute of Food Technologists®)

Human fecal fermentation profiles of maize, rice, and wheat bran and their dietary fiber fractions released by alkaline-hydrogen peroxide treatment (principally arabinoxylan) were obtained with the aim of identifying and characterizing fractions associated with high production of short chain fatty acids and a linear fermentation profile for possible application as a slowly fermentable dietary fiber. The alkali-soluble fraction from maize bran resulted in the highest short chain fatty acid production among all samples tested, and was linear over the 24 h fermentation period. Size-exclusion chromatography and (1)H NMR suggested that higher molecular weight and uniquely substituted arabinose side chains may contribute to these properties. Monosaccharide disappearance data suggest that maize and rice bran arabinoxylans are fermented by a debranching mechanism, while wheat bran arabinoxylans likely contain large unsubstituted xylose regions that are fermented preferentially, followed by poor fermentation of the remaining, highly branched oligosaccharides.

Previous research has revealed that waxy corn starch which has been entrapped in a matrix of electrostatically cross-linked alginate, shows a slow digestion rate such that much of the starch may reach the colon; thus making this a new type of resistant starch. The purpose of this research was to test the fermentative properties of starch-entrapped microspheres using a batch fecal fermentation method. Fermentation of starch-entrapped microspheres showed significantly lower rates of gas production compared to waxy corn starch, and showed significant increases in total SCFAs during the latter stages of fermentation (24-48 h), whereas waxy corn starch did not. Cooking the starch-entrapped microspheres increased the amount of SCFAs and the molar fraction of butyrate produced during fermentation. Bacterial fingerprinting revealed that uncooked starch-entrapped microspheres have a unique effect on the microbiota that is different from waxy corn starch alone, but cooking causes a shift toward a pattern more closely resembling that of the starch. Starch-entrapped microspheres may deliver slowly fermentable carbohydrate to the colon, with the ability to influence the microbiota. Further human studies are required to determine whether these characteristics occur in vivo.

The benefits of dietary fiber on inflammatory bowel disease may be related to the fermentative production of butyrate in the colon, which appears to decrease the inflammatory response. The benefits of dietary fiber against colon cancer may be related to both fermentative and non-fermentative processes, although poorly fermentable fibers appear more influential. Dietary fiber fermentation profiles are important in determining optimal fibers for colonic health, and may be a function of structure, processing conditions, and other food components. A greater understanding of the relationships between fermentation rate and dietary fiber structure would allow for development of dietary fibers for optimum colonic health.

Diet influences gut microbiota composition. Therefore, we hypothesized that diet would impact the extent of dietary fiber utilization and the types of metabolic end-products produced by the microbiota during in vitro fecal fermentation. By obtaining long-term dietary records from fecal donors, we aimed to determine the correlations between dietary intake variables and dietary fiber degradation and short-/branched-chain fatty acid (BCFA) and ammonia production during in vitro fecal fermentation. Eighteen subjects completed 1-year diet history questionnaires and provided fecal samples that were used for in vitro fermentation of a whole wheat substrate. The percentage of dietary fiber fermented was not correlated with nutrient intakes; however, butyrate production was correlated with fecal donor intake of many nutrients of which principal component analysis revealed were mostly contributed by grain-, nut-, and vegetable-based foods. Negative correlations were found for propionate with intake of total carbohydrate, added sugar, and sucrose and for ammonia and BCFA production with intake of unsaturated fats. Thus, our analysis did not support our first hypothesis: the percentage of dietary fiber fermented during in vitro fermentation was not correlated with dietary records. However, production of butyrate; BCFA; ammonia; and, to a lesser extent, propionate was correlated with the diet records of fecal donors, thus supporting our second hypothesis. These results suggest that diets high in plant-based foods and high in unsaturated fats are associated with microbial metabolism that is consistent with host health. [ABSTRACT FROM AUTHOR]

Abstract: The objective of this research was to determine the conversion efficiency of proso millet to ethanol compared to corn in a bench-scale dry-grind procedure. Seven proso millet cultivars and six advanced breeding lines containing waxy starch were fermented with Saccharomyces cerevisiae and ethanol production was compared with normal corn and “highly fermentable” corn. The highly fermentable corn exhibited the highest fermentation efficiency (97.0±1.4%). Among proso millet lines, those with the highest fermentation efficiencies were: Huntsman (85.9±0.6%), 172-2-9 (90.8±0.2%), 172-2-13 (85.1±2.5%), and 182-4-24 (84.7±2.1). Waxy proso millet lines resulted in higher fermentation efficiencies than the non-waxy proso millet varieties containing normal starch (82.4±5.5% vs. 75.5±7.4%, respectively, p =0.01). Proso millet distiller''s dried grains with solubles (DDGS) contained more protein (26.6–33.4%) than the DDGS from corn (17.2–23.4%). These data indicate that proso millet exhibits promise as a feedstock for ethanol production, especially if breeding programs focus on selecting “highly fermentable” lines for advancement. [Copyright &y& Elsevier]

[Display omitted] • Processing could be a way to reduce gas production by the microbiome. • Germination reduced gas production the most among six processing methods. • Germination also reduced abundance of Bacteroides and Lachnospiraceae. • Germination also reduced production of beneficial microbial metabolites. Flatulence is one barrier to pulse consumption for many people. Therefore, we examined how processing affects gas production by the microbiome in three classes of pulses. Processing did not affect gas production from Navy beans. However, in Pardina lentils and green peas, (−1.9 ± 0.3 mL/24 h, p < 0.001; −2.3 ± 0.3 mL/24 h, p < 0.001, respectively). In Pardina lentils and green peas, germination diminished carbohydrate utilization by the microbiome compared with unprocessed samples. In Pardina lentils germination reduced abundance germination resulted in the greatest reduction in gas production among six processing methods of amplicon sequence variants (ASVs) from Bacteroides and Lachnospiraceae and reduced propionate production compared with unprocessed samples. In green peas, germination reduced ASVs from Lachnospiraceae, including one from Roseburia , and reduced proportion of butyrate production during fermentation. Three ASVs from Clostridium sensu stricto (cluster 1), Megasphaera elsdenii , and unclassified Veillonellaceae, were strongly associated with increased gas production across all samples (ρ = 0.67–0.69, p < 0.001). This study showed that processing can reduce gas production by the microbiome in some pulses, but also reduces saccharolytic fermentation and production of beneficial microbial metabolites. [ABSTRACT FROM AUTHOR]

The development of dietary fibers with slow fermentation profiles that deliver desirable fermentation products, such as butyrate, to distal regions of the colon may be beneficial for colonic health. The purpose of this study was to determine whether alginate-entrapped starch might be used for such a designed dietary fiber. Alginate-starch microspheres were prepared from 1, 2, or 3% alginate and 10% starch. A blank was also prepared using only alginate. Samples were subjected to in vitro digestion and fermentation. A sample of normal corn starch was included as a control. During fermentation, total gas volume was measured using a graduated syringe, and short chain fatty acids (SCFAs) were quantified by gas chromatography. Alginate entrapment significantly reduced starch digestion to less than 20%. During fermentation, higher alginate concentrations significantly reduced both the total and rate of gas production. This implies that the starch microspheres would not contribute to the uncomfortable bloating experienced with many dietary fibers. Increasing alginate concentration changed the rate of SCFA production from a parabolic to more linear profile, while simultaneously and substantially increasing the proportion of butyrate (of total SCFAs) produced. This suggests than starch entrapment may allow for a significant and constant, slow delivery of butyrate throughout the colon. [ABSTRACT FROM AUTHOR]

Gut bacteria may influence obesity through the metabolites produced by dietary fiber fermentation (mainly, short-chain fatty acids [SCFA]). Five cereal grain samples (wheat, rye, maize [corn], rice, and oats) were subjected to in vitro digestion and fermentation using fecal samples from 10 obese and nine normal weight people. No significant differences in total SCFA production between the normal weight and obese groups were observed [279 (12) vs. 280 (12), mean (standard error), respectively; P=.935]. However, the obese microbiota resulted in elevated propionate production compared with that of normal weight [24.8(2.2) vs. 17.8(1.9), respectively; P=.008]. Rye appeared to be particularly beneficial among grain samples due to the lowest propionate production and highest butyrate production during fermentation. These data suggest that the dietary fibers from cereal grains affect bacterial metabolism differently in obese and normal weight classes and that certain grains may be particularly beneficial for promoting gut health in obese states. [ABSTRACT FROM AUTHOR]