When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.

Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.

Protein combined with certain dietary fibers increases butyrate production in gut microbiota fermentation.

The modern diet delivers nearly equal amounts of carbohydrates and protein into the colon representing an important protein increase compared to past higher fiber diets. At the same time, plant-based protein foods have become increasingly popular, and these sources of protein are generally less digestible than animal protein sources. As a result, a significant amount of protein is expected to reach the colon and be available for fermentation by gut microbiota. While studies on diet-microbiota interventions have mainly focused on carbohydrate fermentation, limited attention has been given to the role of protein or protein-fiber mixtures as fermentation substrates for the colonic microbiota. In this study, we aimed to investigate: (1) how changing the ratio of protein to fiber substrates affects the types and quantities of gut microbial metabolites and bacteria; and (2) how the specific fermentation characteristics of different types of fiber might influence the utilization of protein by gut microbes to produce beneficial short chain fatty acids. Our results revealed that protein fermentation in the gut plays a crucial role in shaping the overall composition of microbiota communities and their metabolic outputs. Surprisingly, butyrate production was maintained or increased when fiber and protein were combined, and even when pure protein samples were used as substrates. These findings suggest that indigestible protein in fiber-rich substrates may promote the production of microbial butyrate perhaps including the later stages of fermentation in the large intestine.

(1 → 3),(1 → 6) and (1 → 3)-ß-D-glucan physico-chemical features drive their fermentation profile by the human gut microbiota.

Mushroom polysaccharides consist of a unique set of polymers that arrive intact in the human large intestine becoming available for fermentation by resident gut bacteria with potential benefits to the host. Here we have obtained four glucans from two mushrooms (Pholiota nameko and Pleurotus pulmonarius) under different extraction conditions and their fermentation profile by human gut bacteria in vitro was evaluated. These glucans were isolated and characterized as (1 â†’ 3),(1 â†’ 6)-ß-D-glucans varying in branching pattern and water-solubility. An aliquot of each (1 â†’ 3),(1 â†’ 6)-ß-D-glucan was subjected to controlled smith degradation process in order to obtain a linear (1 â†’ 3)-ß-D-glucan from each fraction. The four ß-D-glucans demonstrated different water solubilities and molar mass ranging from 2.2 × 105 g.mol-1 to 1.9 × 106 g.mol-1. In vitro fermentation of the glucans by human gut microbiota showed they induced different short chain fatty acid production (52.0-97.0 mM/50 mg carbohydrates), but an overall consistent high propionate amount (28.5-30.3 % of total short chain fatty acids produced). All glucans promoted Bacteroides uniformis, whereas Anaerostipes sp. and Bacteroides ovatus promotion was strongly driven by the ß-D-glucans solubility and/or branching pattern, highlighting the importance of ß-D-glucan discrete structures to their fermentation by the human gut microbiota.

Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber.

Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.

An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson's disease participants.

A pro-inflammatory intestinal microbiome is characteristic of Parkinson's disease (PD). Prebiotic fibers change the microbiome and this study sought to understand the utility of prebiotic fibers for use in PD patients. The first experiments demonstrate that fermentation of PD patient stool with prebiotic fibers increased the production of beneficial metabolites (short chain fatty acids, SCFA) and changed the microbiota demonstrating the capacity of PD microbiota to respond favorably to prebiotics. Subsequently, an open-label, non-randomized study was conducted in newly diagnosed, non-medicated (n = 10) and treated PD participants (n = 10) wherein the impact of 10 days of prebiotic intervention was evaluated. Outcomes demonstrate that the prebiotic intervention was well tolerated (primary outcome) and safe (secondary outcome) in PD participants and was associated with beneficial biological changes in the microbiota, SCFA, inflammation, and neurofilament light chain. Exploratory analyses indicate effects on clinically relevant outcomes. This proof-of-concept study offers the scientific rationale for placebo-controlled trials using prebiotic fibers in PD patients. ClinicalTrials.gov Identifier: NCT04512599.

Matrix-entrapped fibers create ecological niches for gut bacterial growth.

Insoluble plant cell walls are a main source of dietary fiber. Both chemical and physical fiber structures create distinct niches for gut bacterial utilization. Here, we have taken key fermentable solubilized polysaccharides of plant cell walls and fabricated them back into cell wall-like film forms to understand how fiber physical structure directs gut bacterial fermentation outcomes. Solubilized corn bran arabinoxylan (Cax), extracted to retain some ferulate residues, was covalently linked using laccase to form an insoluble cell wall-like film (Cax-F) that was further embedded with pectin (CaxP-F). In vitro fecal fermentation using gut microbiota from three donors was performed on the films and soluble fibers. Depending on the donor, CaxP-F led to higher relative abundance of recognized beneficial bacteria and/or butyrate producers-Akkermansia, Bifidobacterium, Eubacterium halii, unassigned Lachnospiraceae, Blautia, and Anaerostipes-than free pectin and Cax, and Cax-F. Thus, physical form and location of fibers within cell walls form niches for some health-related gut bacteria. This work brings a new understanding of the importance of insoluble cell wall-associated fibers and shows that targeted fiber materials can be fabricated to support important gut microbiota taxa and metabolites of health significance.

A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice.

Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.

Corn arabinoxylan has a repeating structure of subunits of high branch complexity with slow gut microbiota fermentation.

Corn arabinoxylan (CAX), a cell wall-derived dietary fiber, was extracted with alkali, partially purified, and treated with hydrolytic enzymes in order to investigate the relationship of fine structure and fermentability by the human gut microbiota. Glycosyl composition and linkage analysis of CAX and two hydrolysates, coupled with molecular size analysis, indicated an organized structural feature of the native polymer, which consists of a repeating structural subunit containing complex branching patterns along the xylan backbone and flanked by regions of less complexity. The two lengths of the highly branched subunit were isolated and were shown to have enhanced slow fermentation property compared to the native structure (3.3 vs. 5.9 mL gas, 4 h), that was related to increasing complexity of the branched structures. Lower molecular size structures with higher branch complexity fermented slower, contrary to a conventional view that small fiber structures approaching the oligosaccharide level are necessarily more rapidly fermented.

Boosting the value of insoluble dietary fiber to increase gut fermentability through food processing.

Insoluble dietary fibers are typically known to be poorly fermented in the large intestine. However, their value may be high as evidence shows that important butyrogenic bacteria preferentially utilize insoluble substrates to support their energy needs. The objective of this study was to increase fermentability of an insoluble bran fiber (pearl millet) while keeping it mostly insoluble to promote bacteria in the community that rely on fermentable insoluble dietary fibers. Following pretests with different processing methods, a combination of microwave and enzymatic treatments were applied to isolated pearl millet fiber to increase its accessibility of gut bacteria. In vitro human fecal fermentation was conducted and analyses were made for short chain fatty acids and microbiota changes. Combined microwave and enzymatic processing increased the amount of insoluble fiber fermented in vitro from 36 to 59% of total dietary fiber, with a minor increase in soluble fiber (8%). Microwave/enzymatic processing doubled butyrate production and almost tripled acetate production at 6 h fermentation compared to the native millet fiber. 16S rRNA gene sequencing showed that the processing promoted a significant increase in Firmicutes/Bacteroidetes ratio compared to the native fiber with relative abundance increases in Blautia and Copprococcus genera and a decrease in Bacteroidetes. Overall, these data show that processing techniques can be used to increase the value of insoluble fiber, presumably by increasing accessibility of the fiber to degrading bacteria, and to support Firmicutes that preferentially compete on insoluble fibers.

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities.

Most dietary fibers used to shape the gut microbiota present different and unpredictable responses, presumably due to the diverse microbial communities of people. Recently, we proposed that fibers can be classified in a hierarchical way where fibers of high specificity (i.e., structurally complex and utilized by a narrow group of gut bacteria) could have more similar interindividual responses than those of low specificity (i.e., structurally simple and utilized by many gut bacteria). To test this hypothesis, we evaluated microbiota fermentation of fibers tentatively classified as low (fructooligosaccharides), low-to-intermediate (type 2 resistant starch), intermediate (pectin), and high (insoluble ß-1,3-glucan) specificity, utilizing fecal inoculum from distinct subjects, regarding interindividual similarity/dissimilarity in fiber responses. Individual shifts in target bacteria (as determined by linear discriminant analysis) confirmed that divergent fiber responses occur when utilizing both of the low-specificity dietary fibers, but fibers of intermediate and high specificity lead to more similar responses across subjects in support of targeted bacteria. The high-specificity insoluble ß-glucan promoted a large increase of the target bacteria (from 0.3 to 16.5% average for Anaerostipes sp. and 2.5 to 17.9% average for Bacteroides uniformis), which were associated with increases in ratios of related metabolites (butyrate and propionate, respectively) in every microbial community in which these bacteria were present. Also, high-specificity dietary fibers promoted more dramatic changes in microbial community structure than low-specificity ones relative to the initial microbial communities. IMPORTANCE In the face of interindividual variability and complexity of gut microbial communities, prediction of outcomes from a given fiber utilized by many microbes would require a sophisticated comprehension of all competitive interactions that occur in the gut. Results presented here suggest that high-specificity fibers potentially circumvent the competitive scope in the gut for fiber utilization, providing a promising path to targeted and predictable microbial shifts in different individuals. These findings are the first to indicate that fiber specificity is related to similarity and intensity of response in distinct human gut microbiota communities.

Potential of Prebiotic Butyrogenic Fibers in Parkinson's Disease.

Parkinson's Disease (PD) is a neurodegenerative disorder characterized by loss of dopaminergic neurons in the substantia nigra. Recent evidence supports the involvement of the gastrointestinal tract in PD pathogenesis, including alterations in microbiota and intestinal permeability. Apart from being the preferred energy source for colonic epithelial cells, butyrate is involved in anti-inflammatory, enteroendocrine and epigenetic mechanisms that influence colonic and systemic health, including brain function. A few studies using oral administration of sodium butyrate indicate beneficial effects in PD animal models; however, prebiotic fibers that generate butyrate locally in the gut may be more effective. The design and selection of butyrogenic prebiotic fibers would allow preclinical studies to evaluate how gut-derived butyrate could affect PD pathophysiology. This review describes potential benefits of increasing gut butyrate production in PD through a prebiotic approach. Moreover, physico-chemical features of prebiotic fibers that target butyrogenic colonic bacteria are discussed.

A Meta-Analysis to Determine the Impact of Restaurant Menu Labeling on Calories and Nutrients (Ordered or Consumed) in U.S. Adults.

A systematic review and meta-analysis determined the effect of restaurant menu labeling on calories and nutrients chosen in laboratory and away-from-home settings in U.S. adults. Cochrane-based criteria adherent, peer-reviewed study designs conducted and published in the English language from 1950 to 2014 were collected in 2015, analyzed in 2016, and used to evaluate the effect of nutrition labeling on calories and nutrients ordered or consumed. Before and after menu labeling outcomes were used to determine weighted mean differences in calories, saturated fat, total fat, carbohydrate, and sodium ordered/consumed which were pooled across studies using random effects modeling. Stratified analysis for laboratory and away-from-home settings were also completed. Menu labeling resulted in no significant change in reported calories ordered/consumed in studies with full criteria adherence, nor the 14 studies analyzed with ≤1 unmet criteria, nor for change in total ordered carbohydrate, fat, and saturated fat (three studies) or ordered or consumed sodium (four studies). A significant reduction of 115.2 calories ordered/consumed in laboratory settings was determined when analyses were stratified by study setting. Menu labeling away-from-home did not result in change in quantity or quality, specifically for carbohydrates, total fat, saturated fat, or sodium, of calories consumed among U.S. adults.

Elevated propionate and butyrate in fecal ferments of hydrolysates generated by oxalic acid treatment of corn bran arabinoxylan.

Previous work in our laboratory showed that alkali-solubilized corn arabinoxylan (CAX) has a slow initial, but later complete, in vitro human fecal fermentation. CAX and a moderately high molecular weight hydrolysate (CH) were propiogenic, and produced low levels of butyrate. Here, we show that oxalic acid-generated hydrolysates from CAX, which include a large xylooligosaccharide, and free arabinose fractions, increased short chain fatty acid (SCFA) production, which included relatively high levels of both propionate and butyrate, an unusual SCFA combination. Hydrolytic degradation of CAX by acid hydrolysis (0.05 M oxalic acid at 100 °C for 2 h) and subsequent graded ethanol precipitations were used to obtain mixtures with different molecular weight ranges. Ethanol-precipitated fractions (F 0-65%, F 65-75%, F 75-85%) were mostly lower than 100 kDa and F > 85% was composed of monosaccharides and oligosaccharides of DP 2-8. Oxalic acid treatment caused the removal of all single arabinose unit branch chains and some di/trisaccharide branch chains, producing lightly substituted xylan backbone fragments, most of which were in the oligosaccharide (DP < 10) size range. In vitro human fecal fermentation analyses showed all oxalic acid-hydrolysate fractions were slower fermenting than fructooligosaccharides (FOS), but produced similar or higher amounts of total SCFAs. Butyrate production in two hydrolyzate fractions was double that of CH, while propionate levels remained relatively high.