Biology subjects

Lindemann, S. R.

Publications and source records attributed to Lindemann, S. R..

7 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

Interindividual Diversity of Human Gut Mucin-Degrading Microbial Consortia

Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While diverse mucin degrading bacteria have been identified, the individual host microbial community differences capable of metabolizing this complex polymer are not well described. To determine whether individuals have taxonomically distinct but functionally similar mucin-degrading communities, we used a ten-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. Although two of the final communities had genus-level taxonomic differences signified by the presence of Desulfovibrio and Akkermansia, other members, such as Bacteroides, were shared between all three final communities. Metabolic output differences were most notable for one of the donors communities, with significantly less production of acetate and propionate than the other two communities. These findings reinforce the concept of a taxonomically distinct and, at broad levels, a functionally redundant gut microbiome. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.

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↗

bioRxiv2021

Fine carbohydrate structure governs the structure and function of human gut microbiota independently of variation in glycosyl residue composition

Increased dietary fiber consumption has been shown to increase human gut microbial diversity, but the mechanisms driving this effect remain unclear. One possible explanation is that microbes are able to divide metabolic labor in consumption of complex carbohydrates, which are composed of diverse glycosidic linkages that require specific cognate enzymes for degradation. However, as naturally derived fibers vary in both sugar composition and linkage structure, it is challenging to separate out the impact of each of these variables. We hypothesized that fine differences in carbohydrate linkage structure would govern microbial community structure and function independently of variation in glycosyl residue composition. To test this hypothesis, we fermented commercially available soluble resistant glucans, which are uniformly composed of glucose linked in different structural arrangements, in vitro with fecal inocula from each of three individuals. We measured metabolic outputs (pH, gas, and short-chain fatty acid production) and community structure via 16S rRNA amplicon sequencing. We determined that community metabolic outputs from identical glucans were highly individual, emerging from divergent initial microbiome structures. However, specific operational taxonomic units responded similarly in growth responses across individuals microbiota, though in context-dependent ways; these data suggested that certain taxa were more efficient in competing for some structures than others. Together, these data support the hypothesis that variation in linkage structure, independent of sugar composition, governs compositional and functional responses of microbiota. ImportancePrevious studies have reported how physical and chemical structures of carbohydrates influence the gut microbiota, however, variability across dietary fibers in monosaccharide composition and linkage structure obscures the relationship between fine polysaccharide linkage structure and microbial fitness. Revealing connections between subtle differences in glucan structure and microbial composition and metabolic responses, this study suggests much greater attention to substrate structure in the design of experiments to test fiber-microbiome responses in vitro and in vivo. Further, it underscores that, although microbiome responses to distinct fibers are individual and vary among specific glucans, similar carbohydrate structure-microbe relationships occur across individual donor communities. Together, these data may help explain why some individuals may respond (while others do not) to fiber treatments in human feeding trials and support the long-term goal of rational inclusion of specific fibers in dietary patterns to modulate the gut microbiome in support of health.

microbiology↗

bioRxiv2020

Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

Dietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individuals fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates. IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fibers structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

microbiology↗

bioRxiv2019

MetFish: A Metabolomics Platform for Studying Microbial Communities in Chemically Extreme Environments

Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exo-metabolomics analysis in sample matrices containing up to 2 molar total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5-6 orders of magnitude) with excellent linearity, and low median inter-day reproducibility (e.g. 2.6%). MetFish was successfully applied in targeted and untargeted exo-metabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exo-metabolome during community succession; in situ in a native prairie soil, whose exo-metabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exo-metabolome over time in the well.

microbiology↗