Biology subjects

Deemer, D. G.

Publications and source records attributed to Deemer, D. G..

3 recordsLinked to original sources

bioRxiv2025

The effect of particle size on wheat bran fermentation by human gut microbiota

0.Dietary fibers within whole grains reach the large intestine where they shape the microbial composition. However, the bioavailability of these dietary nutrients to the microbiota is likely limited due to entrapment within the grain particle and requires liberation by microbial enzymes. Here, we used batch fecal fermentation from mixed donors on a range of sizes of wheat particles generated by cyclone milling from a single source to identify bacterial taxa and genomic signatures that are responsive to differences in wheat bran fine structures. We present evidence that different taxa within the same genus colonize wheat bran particles of different sizes. Further, neutral sugar content varied across wheat bran particles despite originating from the same batch, suggesting different polysaccharide structures and nutritional niches. In line with the taxonomic and compositional differences, specific short chain fatty acids varied across particle sizes; in fine wheat bran particle fermentations propionate was high and butyrate low. To identify relevant genomic features implicated in bran colonization, we took a metagenomic approach. From this, we linked genes associated with polysaccharide fermentation to wheat bran particles independent of size, however, within one well-distributed taxon, Lachnospiraceae, genes related to motility were linked to large and medium wheat bran particles. Overall, these results suggest that differences in fine structures and resource availability, as generated through milling, can drive compositional changes in the gut microbiota in an organism-specific manner, mediated through its genomic capacity. IMPORTANCECereal brans comprise a large fraction of the dietary fiber consumption. Although it is well-known that dietary fibers influence the metabolic output and taxonomic composition of the gut microbiota, relatively little is known regarding whether the fine structures and resource availability of milled whole grains exert any influence on the microbial makeup. Our data suggest that the sugar content varies across bran milled from a single source to different sizes. These differences in composition may result in colonization differences by related, but unique, taxa, mediated by genes related to polysaccharide fermentation, thus leading to differences in metabolic output. Furthermore, our data suggest that genes related to motility might influence the capacity of microorganisms to colonize particles. Taken together, our data suggest that physical context can influence gut microbiota composition in turn impacting metabolic output. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/654185v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1b3b95corg.highwire.dtl.DTLVardef@4e5432org.highwire.dtl.DTLVardef@79d317org.highwire.dtl.DTLVardef@119ba9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Botanicals impact the bifidogenic effect and metabolic outputs of in vitro fiber fermentation by gut-derived microbiota in individual-specific ways

Fortification of products frequently consumed by a large proportion of society provides an attractive strategy to close the "fiber gap" and may have the potential to concomitantly reverse the detrimental health effects exacerbated by our modern diets. Besides prebiotic fibers, products can contain other functional components, e.g. botanicals. However, most studies have investigated functional components in isolation. The impact of other components present in functional product blends on the bifidogenic effect typically exerted by prebiotic fibers are largely unexplored. Here, we investigated the fiber and botanical blends included in OLIPOP, a functional soda, in an in vitro gut fermentation model. Our data revealed that the blend of inulins and resistant dextrins promoted growth of bifidobacteria across gut microbiota from four donors, even those with small initial populations. In addition, botanicals interacted with fiber fermentation in donor-specific ways, in some cases strongly enhancing fermentation rate and production of short-chain fatty acids. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/537114v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@129f0f2org.highwire.dtl.DTLVardef@89bc29org.highwire.dtl.DTLVardef@a03976org.highwire.dtl.DTLVardef@11c724c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

SUBTLE DIFFERENCES IN FINE POLYSACCHARIDE STRUCTURES GOVERN SELECTION AND SUCCESSION OF HUMAN GUT MICROBIOTA

Dietary fibers are fermented in the human gut and are known to modulate microbiome composition and metabolic function, but few studies have explored to what extent the small variations in complex fiber structures impact community assembly, microbial division of labor, and organismal metabolic responses across individuals microbiome structures. To test the hypothesis that subtle linkage variations in chemical structures of polysaccharides afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fermentation with fecal inocula from individual donors and measured microbial responses using an integrated multi-omics approach. We fermented two sorghum arabinoxylans (SAXs) as model complex polysaccharides, with fecal microbiota from three donors and an artificially high diversity mix of all three. Although differences in sugar linkage profiles across SAXs were subtle, surprisingly, consortia fermenting different AXs revealed distinct species-level genomic diversity and metabolic outcomes with nearly-identical strains on each polysaccharide across inocula. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials; however, CAZyme genes enriched in different AX-fermenting consortia were specific to SAX type and displayed various catabolic domain fusions with diverse accessory motifs, suggesting they may be functionally degenerate and this degeneracy may relate to fine substrate structure. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia, which are present amongst unrelated individuals.

microbiology↗