Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of Gut Microbiota.

Diet, especially with respect to consumption of dietary fibers, is well recognized as one of the most important factors shaping the colonic microbiota composition. Accordingly, many studies have been conducted to explore dietary fiber types that could predictably manipulate the colonic microbiota for improved health. However, the majority of these studies underappreciate the vastness of fiber structures in terms of their microbial utilization and omit detailed carbohydrate structural analysis. In some cases, this causes conflicting results to arise between studies using (theoretically) the same fibers. In this investigation, by performing in vitro fecal fermentation studies using bran arabinoxylans obtained from different classes of wheat, we showed that even subtle changes in the structure of a dietary fiber result in divergent microbial communities and metabolic outputs. This underscores the need for much higher structural resolution in studies investigating interactions of dietary fibers with gut microbiota, both in vitro and in vivo.

A lthough plant carbohydrates are composed of a relatively limited set of different monosaccharides, astronomical structural diversity arises from the multiplicity of anomeric configurations, linkage types, backbone lengths, branching units, and reducing terminal attachments that occur in these often-branched polymers (1)(2)(3)(4)(5). Further, as biosynthetic enzymes generating plant cell wall polysaccharides are sometimes imprecise, these reactions can be viewed to generate a family of related structural features that can vary significantly among plant species or even different tissues within a plant (1). Conversely, microbial hydrolases are often quite structure specific in their degradative activities (6), requiring a large complement of distinct enzymes to degrade complex polysaccharides and limiting microbial access to such carbohydrates (7). However, this structural diversity is often overlooked when examining the effects of fiber carbohydrates on the community structure and metabolic function of human gut microbiota, raising the question of whether distinct structural variants might interact differently. Recently, the fine structure of insoluble starch molecules was found to influence gut microbiome structural and functional responses in a dose-dependent way in a human feeding study (8). This suggests tight interrelationships between physical and chemical structuring and the organisms most competitive in exploiting these differences (8). In this study, we tested the hypothesis that subtle variation in a soluble fiber carbohydrate's chemical structure would govern the outcome of microbial competition, using arabinoxylan (AX) hemicelluloses extracted from brans of three different commonly consumed classes of wheat (Triticum aestivum)-hard red spring (AX HRS ), hard red winter (AX HRW ), and soft red winter (AX SRW )-as model fiber carbohydrates.
We observed no significant differences in the starch content, molecular weight, or dispersity values of the extracted AXs (P Ͼ 0.05) (see Fig. S1 in the supplemental material). AX HRS and AX HRW were almost identical in sugar composition, displaying no significant differences in any of their acidic and neutral monosaccharides (Fig. 1a). However, AX SRW exhibited a significantly higher abundance of arabinose and a lower abundance of xylose (P Ͻ 0.05) (Fig. 1a). Xylose and arabinose are the main building blocks of AX; the former composes the linear backbone and the latter the major branches of the AX. Thus, the arabinose-to-xylose ratio provides an estimate of an AX's branching density. The arabinose-to-xylose ratios of AX HRS and AX HRW were not distinguishable, whereas that of AX SRW was significantly higher (Fig. 1b), indicating an increasingly branched structure compared to those of AX HRS and AX HRW . Examination of the glycosyl linkages (Table S1) further supports significant differences in branch structures. AX HRS and AX HRW exhibited a significantly higher proportion of 4-xylose linkages (Fig. 1c), which join the xylose units in the linear backbone of AXs. Conversely, a greater abundance of the branch-associated 2-3-4-linked xylose was observed in AX SRW (P Ͻ 0.05) (Fig. 1d). Collectively, these data indicate that AX SRW has a shorter backbone and increased branch density compared to those of AX HRS and AX HRW (Fig. 1e). It should be noted that we did not quantify the protein contents of the AXs, as extensive enzyme (proteases pepsin and pancreatin) treatments applied during the extraction and mimic upper gastrointestinal tract digestion are considered to be sufficient to remove proteins (Text S1). Similarly, ferulic acid contents of the AXs were not quantified, as alkali-extracted wheat bran AXs have been shown to possess no detectable ferulic acid (9). However, as the polysaccharides were extracted from intact wheat brans, it cannot be ruled out that retained traces of these or other components may have influenced the observed fermentation dynamics.
To investigate how these differences in branch densities of AXs impact the structure and metabolism of gut microbiota, we performed an in vitro fermentation study using fecal microbiota obtained from three healthy donors. Microbial composition was assayed with 16S rRNA amplicon sequencing and metabolism with respect to shortchain fatty acid (SCFA) production using gas chromatography. Communities fermenting AX SRW were significantly different in structure than those fermenting AX HRS or AX HRW based upon Bray-Curtis dissimilarity (analysis of molecular variance [AMOVA], P Ͻ 0.001), with AX cultures from the hard varieties not distinguishable from one another ( Fig. 2a and Fig. S2). These data aligned with the significant structural differences between AX SRW and  Table S1). (e) Schematic of proposed generalized structures of the AX samples drawn based on monosaccharide compositions and linkage profiles. Arabinoxylan extracted from hard red spring wheat (AX HRS ) and arabinoxylan extracted from hard red winter wheat (AX HRW ) have longer backbones and fewer branching points than arabinoxylan extracted from soft red winter wheat (AX SRW ). Statistical analyses were done using two-tailed Student's t test (P Ͻ 0.05). Error bars represent the standard errors of three separate replicates.  Fig. S2). Dissimilarity was also calculated using ThetaYC; the result was not substantially different from that visualized by Bray-Curtis dissimilarity. (b) Relative abundances (percentage of sequences) based on the top 50 OTUs in each sample. The top 50 OTUs accounted for more than 90% of the total sequences of all AX treatment groups at all time points (relative abundances at the 12-and 24-h time points are given in Fig. S4, and relative abundances displayed in a bar graph are provided in Fig. S5). (c) Cladogram (obtained as a result of linear discriminant analysis) depicting taxa that are overrepresented in the AX samples obtained from hard and soft wheat classes compared with abundances in the initial inoculum and substrate-free blank (Continued on next page) AX HRS/HRW , though not between the hard varieties. The structural variants also differentially affected community richness and evenness, with AX SRW resulting in greater ␣-diversity indices (number of species observed, Simpson evenness, and inverse Simpson, Chao, and Shannon indices); AX HRS and AX HRW treatments were not distinguishable ( Fig. 2d and Fig. S3). We hypothesize that the higher ␣-diversity values observed in AX SRW -fermenting cultures arose from its more complex branching structure, requiring a greater number of glycoside hydrolases for complete consumption and potentially affording more microbial niches.
AX fine structure strongly governed the relative abundances of operational taxonomic units (OTUs), such that the less branched AX HRS and AX HRW promoted OTU2 (Prevotella) and the more branched AX SRW favored OTUs within genus Bacteroides (Fig. 2b and Fig. S4 and S5). Specifically, after 24 h of fermentation, AX SRW elicited a 9.8-fold increase in the relative abundance of OTU2 but 30-and 29-fold increases in AX HRS and AX HRW cultures, respectively. Conversely, although fermentation of AX HRS and AX HRW resulted in Ͻ2.4-fold increases in the relative abundance of OTU5 (Bacteroides), we observed a 12.3-fold increase with AX SRW . AX SRW also significantly increased the abundance of OTU1 (Bacteroides) compared with that obtained with AX HRS and AX HRW . Linear discriminant analysis effect size (LEfSe) identified the members of family Prevotellaceae and subordinate taxa as discriminators for hard wheat AXs, and Bacteroidales and subordinate taxa were discriminators of AX SRW (Fig. 1c). Both Bacteroides and Prevotella species are known to be very well equipped for the degradation of (arabino)xylans (10)(11)(12)(13)(14). Our findings further add to this that the structural complexity of xylans determines which of these taxa outcompete the other; Prevotella species seemed to better compete for less densely branched AXs but Bacteroides species, in general, for the more densely branched one. Moreover, in addition to Bacteroides and Prevotella species, AX consumption was shown to promote Roseburia species (10,12). Our findings reveal that increases in Roseburia relative abundances on AX are structure dependent; neither AX HRS nor AX HRW significantly changed Roseburia relative abundances after 48 h of fermentation, whereas the fermentation of highly branched AX SRW resulted in 3.2-fold increases in the abundance of Roseburia spp. (OTU20) (Fig. 2b and Fig. S4, S5, and S6). Collectively, these findings support the idea that soluble polysaccharides can act as "discrete fiber structures," such that unique fiber chemical structures specifically promote particular microbial taxa in the colon (2,8,15).
Accordingly, structure-specific SCFA formations were observed; compared to AX HRS and AX HRW , AX SRW treatment resulted in formation of significantly higher propionate but lower acetate and butyrate concentrations (P Ͻ 0.05) (Fig. 2e). As both the genera Bacteroides and Prevotella are regarded to increase community propiogenesis, differences in other SCFAs may stem from altered abundance or activity of acetate-consuming, butyrate-producing members of Lachnospiraceae. Moreover, total SCFA production occurred at a lower rate in AX SRW than in hard varieties (Fig. S7a), indicating that AX SRW was more slowly fermented. This was further supported by the slower decrease in pH in fermentations of AX SRW than for AX HRW/HRS (Fig. S8). We hypothesize that the increased branch density in AX SRW may limit enzyme access to the xylan backbone until branches are partially removed, potentially allowing coordinated activity of multiple species.
Overall, our results demonstrate that although the general polysaccharide chemical structures obtained from closely related plant sources may seem similar, subtle structural differences significantly alter their effects on the structure and metabolic function  Fig. S3). (e) Short-chain fatty acid (SCFA; namely, propionate, acetate, and butyrate) production by fecal microbiota at the end of the fermentation (the amounts of SCFAs produced after in vitro fermentation for 12 and 24 h are given in Fig. S6a; the proportions of all SCFAs produced after in vitro fermentation for 12, 24, and 48 h are given in Fig. S6b). Fructooligosaccharide (FOS) was used as a fast-fermenting, butyrate-producing positive control. The blank did not contain any substrate. Statistical analyses were done using two-tailed Student's t test. Error bars represent the standard errors of three separate replicates.
Fine Fiber Structure Effects on Gut Microbiota of colonic microbiota. We submit that studies focusing on interactions among dietary fiber carbohydrates, gut microbiota, and health outcomes should include much more extensive characterization of the carbohydrate structures employed. Further, we propose that use of fibers in general categories (e.g., high-or low-fiber diets or arabinoxylan of unspecified or poorly characterized origin) without such structural data may confuse the conflicting effects of subtle structural variants, which may elicit different microbial responses.
Data availability. Sequence data described in this study are available in the National Center for Biotechnology Information's Sequence Read Archive under BioProject PRJNA628680 as BioSamples SAMN14749672 to SAMN14749719.

SUPPLEMENTAL MATERIAL
Supplemental material is available online only. TEXT S1, DOCX file, 0.03 MB.