Fig 1 - uploaded by Andrew Tolonen
Content may be subject to copyright.
Analytical pipeline and description of glycan compositions and fermentation dynamics. a Schematic representation of the analytical pipeline. b-f Monosaccharide compositions and fermentation dynamics of 653 SGs and 110 reference glycans. b Percentages of SGs (yellow) and reference glycans (indigo) containing various monosaccharide types. c Number of monosaccharide types composing each SG or reference glycan. d Distribution of weight average molecular weights of SGs measured by SEC. e-g Growth (OD 600 ) and pH dynamics of triplicate fecal cultures fermenting 5 g l −1 of a single SG or reference glycan in MM29 medium. e Hierarchical clustering of glycans into five fermentation groups based on twelve growth and pH parameters. Bars below the dendrogram show compound class: SG (yellow), reference glycan (indigo), or no glycan (magenta). Mean (f) growth and (g) pH curves (±SD) for each glycan fermentation group shown in e. Source data are provided as a Source Data file. SGs Synthetic Glycans, SEC size exclusion chromatography, OD 600 optical density at 600 nm, SD standard deviation, kDa kilodalton.
Source publication
Relative abundances of bacterial species in the gut microbiome have been linked to many diseases. Species of gut bacteria are ecologically differentiated by their abilities to metabolize different glycans, making glycan delivery a powerful way to alter the microbiome to promote health. Here, we study the properties and therapeutic potential of chem...
Contexts in source publication
Context 1
... profiles and glycosidic linkages. As some reference glycans have been shown to alleviate intestinal inflammation and improve barrier function, as well as reduce colitis from infection, we compare the effects of SG and reference glycan treatment in mouse models of these intestinal pathologies 20,21 . Together, this experimental pipeline (Fig. 1a) evaluates the function and therapeutic potential of SGs as microbiome modulators and demonstrates additional benefits of SGs compared to reference glycans, including compounds currently marketed as ...
Context 2
... and fermentation dynamics. We selected a set of 653 SGs and 110 commercially available, reference glycans that are compositionally diverse and sufficiently soluble for culture-based growth and metabolite assays (Supplementary Data 1, Supplementary Table 1). Both SGs and reference glycans are composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 ...
Context 3
... glycans that are compositionally diverse and sufficiently soluble for culture-based growth and metabolite assays (Supplementary Data 1, Supplementary Table 1). Both SGs and reference glycans are composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 kDa-77.5 kDa), corresponding to a polymerization of approximately ten monosaccharides. We profiled these ...
Context 4
... composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 kDa-77.5 kDa), corresponding to a polymerization of approximately ten monosaccharides. We profiled these SGs and reference glycans in a panel of ex vivo assays and highlighted the performance of two SGs with different compositions, BRF (glucose) and BQM (galactose and glucose), which were ...
Context 5
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and ...
Context 6
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and FOS; group 4 included XOS. Group 5, which included BQM and ...
Context 7
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and FOS; group 4 included XOS. Group 5, which included BQM and BRF, was enriched ...
Context 8
... GOS, and FOS; group 4 included XOS. Group 5, which included BQM and BRF, was enriched in SGs (p = 6.0 × 10 −17 ) that were well-fermented at controlled rates with gradual reductions in pH. Thus, SG composition affects fermentability and SGs are generally fermented more slowly than reference glycans, likely due to their compositional complexity (Fig. 1c). In addition, these fermentation parameters were well correlated between fecal samples from two different donors ( Supplementary Fig. 1c-n). While more data is needed to establish that SG effects are conserved across populations, these data suggest SGs have similar fermentation dynamics between ...
Context 9
... SG composition affects fermentability and SGs are generally fermented more slowly than reference glycans, likely due to their compositional complexity (Fig. 1c). In addition, these fermentation parameters were well correlated between fecal samples from two different donors ( Supplementary Fig. 1c-n). While more data is needed to establish that SG effects are conserved across populations, these data suggest SGs have similar fermentation dynamics between individuals. ...
Context 10
... of reference glycans in patients with gastrointestinal disorders such as irritable bowel syndrome 29 . As the volume and rate of gas produced depend on diet and microbiome composition 30 , we measured gas production rates by fecal communities growing on BRF, BQM, and randomly selected glycans from each of the five fermentation groups in Fig. 1e-g (Supplementary Data 2). The rate of gas production varied widely among groups (Fig. 2b) and reflected fermentation dynamics. Glycans in fermentation groups 1 and 4, mostly reference glycans that are rapidly fermented, had the most rapid gas production. SGs in group 5, which included BRF and BQM, produced gas more moderately, potentially improving ...
Context 11
... composition. a Yields of two SCFAs, butyrate and propionate, from fecal cultures fermenting either an SG (yellow circles, n = 653), reference glycan (indigo triangles, n = 110), or no glycan (magenta square). b Maximum gas production rate (psi h −1 ) during fecal culture fermentation of glycans from each of the five fermentation groups in Fig. 1e-g. c Shannon diversity and d species richness of fecal cultures fermenting SGs (yellow, n = 190) versus reference glycans (indigo, n = 40). e Shannon diversity of fecal cultures fermenting BRF or BQM (yellow) is higher than reference glycans (indigo) for all comparisons except BQM versus XOS (Kruskal-Wallis followed by Dunn's ...
Context 12
... (2D-NMR). The 2D-NMR profiles of BRF versus pullulan ( Supplementary Fig. 6a) and BQM versus GOS ( Supplementary Fig. 6b) support that these SGs contain a greater diversity of glycosidic bonds with distinct stereo-and regiochemistries. The structural complexity of SGs likely contributes to their comparatively slow fermentation by commensals (Fig. 1f, ...
Context 13
... pH was calculated relative to a standard curve of media at known pH by fitting a sigmoidal curve using four parameter logistic regression. The R package, phgrofit (version 1.0.2) 57 , was developed to extract physiological descriptors from the kinetic pH and OD 600 curves ( Supplementary Fig. 1). Glycans were clustered based on twelve fermentation parameters that were transformed into Z-scores by subtracting the mean across all glycans and dividing by the standard deviation. ...
Context 14
... profiles and glycosidic linkages. As some reference glycans have been shown to alleviate intestinal inflammation and improve barrier function, as well as reduce colitis from infection, we compare the effects of SG and reference glycan treatment in mouse models of these intestinal pathologies 20,21 . Together, this experimental pipeline (Fig. 1a) evaluates the function and therapeutic potential of SGs as microbiome modulators and demonstrates additional benefits of SGs compared to reference glycans, including compounds currently marketed as ...
Context 15
... and fermentation dynamics. We selected a set of 653 SGs and 110 commercially available, reference glycans that are compositionally diverse and sufficiently soluble for culture-based growth and metabolite assays (Supplementary Data 1, Supplementary Table 1). Both SGs and reference glycans are composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 ...
Context 16
... glycans that are compositionally diverse and sufficiently soluble for culture-based growth and metabolite assays (Supplementary Data 1, Supplementary Table 1). Both SGs and reference glycans are composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 kDa-77.5 kDa), corresponding to a polymerization of approximately ten monosaccharides. We profiled these ...
Context 17
... composed of a similar set of monosaccharides (Fig. 1b), but unlike the reference glycans, most SGs (73%) contain multiple, different monosaccharides (Fig. 1c), demonstrating how SGs can be built to include dietary sugars in novel and complex combinations. SGs were catalytically synthesized 19 and span a wide range of average molecular masses ( Fig. 1d) with a median of 1.7 kDa (range 0.3 kDa-77.5 kDa), corresponding to a polymerization of approximately ten monosaccharides. We profiled these SGs and reference glycans in a panel of ex vivo assays and highlighted the performance of two SGs with different compositions, BRF (glucose) and BQM (galactose and glucose), which were ...
Context 18
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and ...
Context 19
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and FOS; group 4 included XOS. Group 5, which included BQM and ...
Context 20
... investigated variation in fermentation dynamics across the 763 glycans by measuring growth and pH kinetics of anaerobic fecal cultures. Hierarchical clustering of growth and pH parameters ( Fig. 1e, Supplementary Fig. 1) identified groups of glycans with distinct growth (Fig. 1f) and pH (Fig. 1g) profiles. Reference glycans were enriched in group 1 (Fisher exact test p = 7.5 × 10 −26 ) and group 4 (Fisher exact test p = 4.8 × 10 −14 ), which both supported rapid growth resulting in a precipitous pH drop. Group 1 included pullulan, lactulose, GOS, and FOS; group 4 included XOS. Group 5, which included BQM and BRF, was enriched ...
Context 21
... GOS, and FOS; group 4 included XOS. Group 5, which included BQM and BRF, was enriched in SGs (p = 6.0 × 10 −17 ) that were well-fermented at controlled rates with gradual reductions in pH. Thus, SG composition affects fermentability and SGs are generally fermented more slowly than reference glycans, likely due to their compositional complexity (Fig. 1c). In addition, these fermentation parameters were well correlated between fecal samples from two different donors ( Supplementary Fig. 1c-n). While more data is needed to establish that SG effects are conserved across populations, these data suggest SGs have similar fermentation dynamics between ...
Context 22
... SG composition affects fermentability and SGs are generally fermented more slowly than reference glycans, likely due to their compositional complexity (Fig. 1c). In addition, these fermentation parameters were well correlated between fecal samples from two different donors ( Supplementary Fig. 1c-n). While more data is needed to establish that SG effects are conserved across populations, these data suggest SGs have similar fermentation dynamics between individuals. ...
Context 23
... of reference glycans in patients with gastrointestinal disorders such as irritable bowel syndrome 29 . As the volume and rate of gas produced depend on diet and microbiome composition 30 , we measured gas production rates by fecal communities growing on BRF, BQM, and randomly selected glycans from each of the five fermentation groups in Fig. 1e-g (Supplementary Data 2). The rate of gas production varied widely among groups (Fig. 2b) and reflected fermentation dynamics. Glycans in fermentation groups 1 and 4, mostly reference glycans that are rapidly fermented, had the most rapid gas production. SGs in group 5, which included BRF and BQM, produced gas more moderately, potentially improving ...
Context 24
... composition. a Yields of two SCFAs, butyrate and propionate, from fecal cultures fermenting either an SG (yellow circles, n = 653), reference glycan (indigo triangles, n = 110), or no glycan (magenta square). b Maximum gas production rate (psi h −1 ) during fecal culture fermentation of glycans from each of the five fermentation groups in Fig. 1e-g. c Shannon diversity and d species richness of fecal cultures fermenting SGs (yellow, n = 190) versus reference glycans (indigo, n = 40). e Shannon diversity of fecal cultures fermenting BRF or BQM (yellow) is higher than reference glycans (indigo) for all comparisons except BQM versus XOS (Kruskal-Wallis followed by Dunn's ...
Context 25
... (2D-NMR). The 2D-NMR profiles of BRF versus pullulan ( Supplementary Fig. 6a) and BQM versus GOS ( Supplementary Fig. 6b) support that these SGs contain a greater diversity of glycosidic bonds with distinct stereo-and regiochemistries. The structural complexity of SGs likely contributes to their comparatively slow fermentation by commensals (Fig. 1f, ...
Context 26
... pH was calculated relative to a standard curve of media at known pH by fitting a sigmoidal curve using four parameter logistic regression. The R package, phgrofit (version 1.0.2) 57 , was developed to extract physiological descriptors from the kinetic pH and OD 600 curves ( Supplementary Fig. 1). Glycans were clustered based on twelve fermentation parameters that were transformed into Z-scores by subtracting the mean across all glycans and dividing by the standard deviation. ...
Similar publications
Clarification is required when the term “carbohydrate” is used interchangeably with “saccharide” and “glycan.” Carbohydrate classification based on human digestive enzyme activities brings clarity to the energy supply function of digestible sugars and starch. However, categorizing structurally diverse non‐digestible carbohydrates (NDCs) to make die...
Citations
... An exciting area of recent research also suggests synthetic glycans as precision prebiotics, which could be developed to recapitulate features of the chemical complexity of dietary fiber by controlling reaction conditions including types of monosaccharides, bond types, and degrees of polymerization. Tolenen et al. 153 recently showed that fermentation of a range of synthetic glycans resulted in specific shifts in taxonomic and metabolite profiles, which were not observed with natural reference glycans commonly found in diets. Synthetic glycan fermentation specifically enriched abundances of Lachnospiraceae, Parabacteroides, and Roseburia, a key butyrate producer which is depleted in Crohn disease subjects 154 as well as Fusicatenibacter which is depleted in active ulcerative colitis. ...
... 155 Interestingly, synthetic glycans also conferred a selective growth benefit for commensals over gut pathogens potentially increasing their safety for at-risk populations. 153 However, it is important to consider that the development of synthetic glycans still faces several limitations, including insufficient mechanistic evidence, a limited understanding of precise microbial responses, and unresolved regulatory and safety concerns, particularly regarding their long-term effects on Figure 3. Schematic of the hypothetical mechanisms of action of low specificity prebiotics on gut microbiota composition and metabolic activity and related host health benefits. Low-specificity prebiotics such as frucotoligossachirides (FOS) and inulin are easily accessible and can be utilized by a broad range of microbes. ...
In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.
... Ren M et al. [ 112 ] reported that resistant starch from Arenga pinnata mitigated the expression of inflammatory markers and lessened inflammatory lesions in the ileum and colon of aged mice afflicted with disease. The proposed mechanisms include the proliferative effect of RS on probiotic bacteria, which inhibits the production of interferon-gamma by CD4+ T-cells, activates the expression of PPAPγ, and enhances the secretion of anti-inflammatory cytokines, such as IL-10 and IL-4, in the spleen, thereby curbing the intestinal inflammatory response mediated through the cytokine signaling pathway in mice [ 113 ] . Anqi Wang et al. [ 114 ] developed an intestinal fermentation model in mice and discovered that RS not only Dietary supplementation with RS may also demonstrate anti-inflammatory effects in the elderly population [ 115 ] . ...
... https://doi.org/10.1038/s41589-024-01763-6 effects on the relative abundances of bacterial taxa characterized by culture-independent methods 7,14 . In the present study, we examine the mechanisms by which certain human gut Bacteroides respond to a SG preparation in vitro and in gnotobiotic mice. ...
... We selected eight SG pools from a collection of several hundred previously reported pools; selection was based on their occupancy within distinct chemical space as defined by unsupervised clustering of glycosyl linkage data collected from the SGs and natural glycans 7 . The eight SG pools were each generated from one to three monosaccharide building blocks, contained <3% of their monosaccharide starting material and had a median average degree of polymerization (DP) of 12.45 (range 8.09-15.03). ...
... Based on the minimum pH documented (a biomarker of fermentation), we concluded that all of Glycans that are generated synthetically can contain structures and linkage combinations not previously identified in nature. A recently developed and generalizable approach for generating synthetic glycans (SGs) involves monosaccharide building blocks and a zwitterionic resin that catalyzes glycosidic bond formation between the reducing end of a monosaccharide and an acceptor hydroxyl on the growing SG 6,7 . By changing the monosaccharide starting material and reaction conditions, a pool of nonidentical, nonrepetitive oligosaccharides can be obtained in a fashion agnostic to biocatalysis or biocompatibility, but instead driven by principles of thermodynamics (monosaccharide ring conformation and anomer) and kinetics (formation of a given glycosidic bond) 7,8 . ...
Synthetic glycans (SGs) containing glycosidic linkages and structures not identified in nature offer a means for deliberately altering microbial community properties. Here pools of SG oligosaccharides were generated via polymerization of monosaccharides and screened for their ability to increase saccharolytic Bacteroides in ex vivo cultures of human fecal samples. A lead SG preparation was orally administered to gnotobiotic mice harboring a consortium of 56 cultured, phylogenetically diverse human gut bacteria and fed a Western diet. The abundances of 3 of 15 Bacteroides strains increased, most prominently B. intestinalis. Underlying mechanisms were characterized by analyzing in vivo expression of the carbohydrate utilization machinery, using retrievable microscopic paramagnetic particles with bound SG oligosaccharides and assaying SG degradation by individual purified B. intestinalis glycoside hydrolases. The results reveal that SGs can selectively co-opt carbohydrate utilization machinery in different human gut Bacteroides and demonstrate a means for identifying artificial carbohydrate structures for targeted bacterial manipulation.
... Restoring the balanced composition of the gut microbial community to manage diseases such as IBD is gaining interest as an ecological therapy. One possible intervention to reverse dysbiosis and control IBD is supplementation or diet modulation that enriches the abundance of SCFA producers [75]. For example, some diet protocols restrict food implicated in inflammation to control IBD [76]. ...
The gut microbiome emerges as an integral component of precision medicine because of its signature variability among individuals and its plasticity, which enables personalized therapeutic interventions, especially when integrated with other multiomics data. This promise is further fueled by advances in next-generation sequencing and metabolomics, which allow in-depth high-precision profiling of microbiome communities, their genetic contents, and secreted chemistry. This knowledge has advanced our understanding of our microbial partners, their interaction with cellular targets, and their implication in human conditions such as inflammatory bowel disease (IBD). This explosion of microbiome data inspired the development of next-generation therapeutics for treating IBD that depend on manipulating the gut microbiome by diet modulation or using live products as therapeutics. The current landscape of artificial microbiome therapeutics is not limited to probiotics and fecal transplants but has expanded to include community consortia, engineered probiotics, and defined metabolites, bypassing several limitations that hindered rapid progress in this field such as safety and regulatory issues. More integrated research will reveal new therapeutic targets such as enzymes or receptors mediating interactions between microbiota-secreted molecules that drive or modulate diseases. With the shift toward precision medicine and the enhanced integration of host genetics and polymorphism in treatment regimes, the following key questions emerge: How can we effectively implement microbiomics to further personalize the treatment of diseases like IBD, leveraging proven and validated microbiome links? Can we modulate the microbiome to manage IBD by altering the host immune response? In this review, we discuss recent advances in understanding the mechanism underpinning the role of gut microbes in driving or preventing IBD. We highlight developed targeted approaches to reverse dysbiosis through precision editing of the microbiome. We analyze limitations and opportunities while defining the specific clinical niche for this innovative therapeutic modality for the treatment, prevention, and diagnosis of IBD and its potential implication in precision medicine.
... In fact, glucosaminesupplemented diet promoted increased expression of tight junction proteins zonulin (ZO)-1 and occludin, and decreased the expression of pro-inflammatory markers, such as TNF-α and IL-1β in the colonic mucosa [131]. Tolonen and colleagues demonstrated, in mouse models of intestinal damage, the therapeutic efficacy of synthetic glycans (SGs) which are metabolized by commensals but not by important pathogens [132]. Interestingly, SGs treatment significantly enhanced faecal microbiota associated with anti-inflammatory properties namely Lachnospiraceae, Ruminiclostridium, and Parabacteroides [132], commonly decreased in IBD patients [133]. ...
... Tolonen and colleagues demonstrated, in mouse models of intestinal damage, the therapeutic efficacy of synthetic glycans (SGs) which are metabolized by commensals but not by important pathogens [132]. Interestingly, SGs treatment significantly enhanced faecal microbiota associated with anti-inflammatory properties namely Lachnospiraceae, Ruminiclostridium, and Parabacteroides [132], commonly decreased in IBD patients [133]. Also, supplementation with SGs displayed therapeutic effect in colitis induced DSS and in context of Clostridium difficile infection by improving survival, impairing weight loss, diarrhoea and decreasing epithelial erosion, mucosal inflammation, or ulceration [132]. ...
... Interestingly, SGs treatment significantly enhanced faecal microbiota associated with anti-inflammatory properties namely Lachnospiraceae, Ruminiclostridium, and Parabacteroides [132], commonly decreased in IBD patients [133]. Also, supplementation with SGs displayed therapeutic effect in colitis induced DSS and in context of Clostridium difficile infection by improving survival, impairing weight loss, diarrhoea and decreasing epithelial erosion, mucosal inflammation, or ulceration [132]. In parallel, administration of FOS (fructo-oligosaccharides) enhanced the expression of Muc2 mucin in rats treated with trinitrobenzenesulphonic acid (TNBS). ...
... Differences in pH during E. coli growth would thus influence fluorescence measurements using ClbP-17. The pH in cultures can be measured in real-time based on the fluorescence of BCECF [2,7-bis-(2-carboxyethyl)5-(and 6)-carboxyfluorescein] (25,26). We confirmed that BCECF does not affect the growth of E. coli ATCC 25922 (Fig. S3) and developed this method to quantify the pH dynamics of ATCC 25922 growing in MS, MM29, and CMG media (Fig. S5). ...
... The pH of cultures was measured using the BCECF method (25,26). BCECF (C3411 Sigma) at 2 µM was added to cultures and fluorescence at the pH-sensitive point (485 nm excitation; 540 nm emission) relative to the pH-insensitive isosbestic point (450 nm excitation; 540 nm emission) was calculated. ...
Colibactin, a nonribosomal peptide/polyketide produced by pks+ Enterobacteriaceae, is a virulence factor and putative carcinogen that damages DNA by interstrand crosslinking (ICL). While the clb genes for colibactin biosynthesis have been identified, studies are needed to elucidate the mechanisms regulating colibactin production and activity. Here we perform untargeted metabolomics of pks+ Escherichia coli cultures to identify L-tryptophan as a candidate repressor of colibactin activity. When pks+ E. coli is grown in a minimal medium supplemented with L-tryptophan in vitro ICL of plasmid DNA is reduced by >80%. L-tryptophan does not affect the transcription of clb genes but protects from copper toxicity and triggers the expression of genes to export copper to the periplasm where copper can directly inhibit the ClbP peptidase domain. Thus, L-tryptophan and copper interact and repress colibactin activity, potentially reducing its carcinogenic effects in the intestine.
IMPORTANCE
Colibactin is a small molecule produced by pks+ Enterobacteriaceae that damages DNA, leading to oncogenic mutations in human genomes. Colibactin-producing Escherichia coli (pks+) cells promote tumorigenesis in mouse models of colorectal cancer (CRC) and are elevated in abundance in CRC patient biopsies, making it important to identify the regulatory systems governing colibactin production. Here, we apply a systems biology approach to explore metabolite repression of colibactin production in pks+ E. coli. We identify L-tryptophan as a repressor of colibactin genotoxicity that stimulates the expression of genes to export copper to the periplasm where it can inhibit ClbP, the colibactin-activating peptidase. These results work toward an antibiotic-sparing, prophylactic strategy to inhibit colibactin genotoxicity and its tumorigenic effects in the intestine.
... A bacteriophage cocktail has been developed to improve the growth performance and gut microbiome of broiler chickens (57). Interestingly, a mixture of chemically diverse synthetic glycans has shown remarkable effectiveness in altering the microbiome to promote health, surpassing the effects of using pullulan or galactooligosaccharides (58). Despite several studies reporting on the therapeutic effects of mono-GMRC, there hasn't been any research on the GMRC cocktail itself. ...
Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death. Modulating the gut microbiome is a promising therapeutic approach for managing SIRS. This study assesses the therapeutic potential of the Xuanfei Baidu (XFBD) formula in treating SIRS. The results showed that XFBD administration effectively reduced mortality rates and inflammation in SIRS mice. Using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we substantiated that the therapeutic effects of XFBD are partly attributed to gut microbiota modulation. We conducted in vitro experiments to accurately assess the gut microbiome remodeling effects of 51 compounds isolated from XFBD. These compounds exhibited varying abilities to induce a microbial structure that closely resembles that of the healthy control group. By quantifying their impact on microbial structure and clustering their regulatory patterns, we devised multiple gut microbiome remodeling compound (GMRC) cocktails. GMRC cocktail C, comprising aucubin, gentiopicroside, syringic acid, gallic acid, p-hydroxybenzaldehyde, para-hydroxybenzoic acid, and isoimperatorin, demonstrated superior efficacy in treating SIRS compared to a single compound or to other cocktails. Finally, in vitro experiments showcased that GMRC cocktail C effectively rebalanced bacteria composition in SIRS patients. This study underscores XFBD’s therapeutic potential in SIRS and highlights the importance of innovative treatment approaches for this disease by targeting the gut microbiota.
IMPORTANCE
Developing effective treatment strategies for systemic inflammatory response syndrome (SIRS) is crucial due to its severe and often life-threatening nature. While traditional treatments like dexamethasone have shown efficacy, they also come with significant side effects and limitations. This study makes significant strides by demonstrating that the Xuanfei Baidu (XFBD) formula can substantially reduce mortality rates and inflammation in SIRS mice through effective modulation of the gut microbiota. By quantitatively assessing the impact of 51 compounds derived from XFBD on the gut microbiome, we developed a potent gut microbiome remodeling compound cocktail. This cocktail outperformed individual compounds and other mixtures in efficacy against SIRS. These findings highlight the potential of XFBD as a therapeutic solution for SIRS and underscore the critical role of innovative strategies targeting the gut microbiota in addressing this severe inflammatory condition.
... 18 The success of faecal microbiota transplantation (FMT) for the treatment of recurrent Clostridioides difficile infections, coupled with the expansion of the microbiome field with the advent of next generation sequencing, led to a renewed interest in the potential for microbiota therapeutics to target the gut microbiome in IBD. Microbiotatargeted therapeutics have focused on the alteration of dietary or glycan composition, 19,20 a reduction in the abundance of specific bacteria through the use of bacteriophages, 21 or the addition of new strains or decolonisation of recipient strains through FMT or defined bacterial consortia. [22][23][24] Most IBD microbiota therapeutic clinical studies have been FMT treatments for the induction of clinical remission in ulcerative colitis 25 with the primary endpoint assessed after 8-12 weeks. ...
... Carbohydrates could be broken down into forms by specific CAZymes, allowing the gut microbiota to utilize their production as a source of energy [37,38]. As shown in Fig. 6D, glycoside hydrolases (GHs) were the main difference CAZymes in these three groups. ...
... GHs could catalyze the hydrolysis of glycosidic linkages between sugar molecules to degrade and metabolize carbohydrates. Previous study has shown that the abundances of CAZymes that are active on polysaccharide should increase in the polysaccharide treatment group [38]. Compared with the DSS and TFP group, GH1 family was significantly enriched in the DIP group. ...
Introduction
Over decades, the source-function relationships of bioactive polysaccharides have been progressively investigated, however, it is still unclear how a defined structure may conduce to the bioactivities of polysaccharides.
Objectives
To explore the structure–function relationship of fungus polysaccharides, we employed a dextran sulfate sodium (DSS)‐induced colitis mouse model to compare the anti-inflammatory activity of two fungus polysaccharides from Dictyophora indusiata (DIP) and Tremella fuciformis (TFP), which exhibit distinct glycosidic linkages.
Methods
The structures of DIP and TFP were characterized through molecular weight detection, molecular morphology analysis, methylation analysis, and NMR analysis. Subsequently, we employed a DSS-induced colitis model to assess the anti-inflammatory efficacy of DIP and TFP. The colitis symptoms, histological morphology, intestinal inflammatory cytokines, and the composition and function of gut microbiota before and after polysaccharides treatment in colitis mice were also investigated.
Results
DIP, l,3-β-D-glucan with 1,4-β and 1,6-β-D-Glcp as branched chains, exhibited superior therapeutic effect than that of TFP consisted of a linear 1,3-α-D-mannose backbone with D-xylose and L-fucose in the side chains. Both DIP and TFP relieved DSS-induced colitis in a gut microbiota-dependent manner. Furthermore, metagenomics showed that DIP and TFP could partially reverse the bacterial function in colitis mice. Glycoside Hydrolase 1 (GH1) and GH3 were identified as being involved in hydrolyzing the glucose linkages in DIP, while GH92 and GH29 were predicted to be active in cleaving the α-1,3-linked mannose linkages and the glycosidic bonds of L-fucose residues in TFP.
Conclusion
Our findings highlight the pivotal role of glycosidic linkages in anti-inflammatory activities of fungus polysaccharides and would promote the design and discovery of polysaccharides with designated activity to be used as functional foods and/or therapeutics.
... While typically able to ferment multiple polysaccharides, species of Lachnospiraceae are ecologically differentiated by specializing on certain substrates. As such, addition of different glycans results in compound-specific changes to the relative abundances of Lachnospiraceae in mixed communities (Tolonen et al., 2022). For example, Roseburia intestinalis efficiently metabolizes β-mannans and xylan (Leth et al., 2018;La Rosa et al., 2019), while Roseburia faecis ferments arabinogalactan (Sheridan et al., 2016). ...
The Lachnospiraceae is a family of anaerobic bacteria in the class Clostridia with potential to advance the bio-economy and intestinal therapeutics. Some species of Lachnospiraceae metabolize abundant, low-cost feedstocks such as lignocellulose and carbon dioxide into value-added chemicals. Others are among the dominant species of the human colon and animal rumen, where they ferment dietary fiber to promote healthy gut and immune function. Here, we summarize recent studies of the physiology, cultivation, and genetics of Lachnospiraceae, highlighting their wide substrate utilization and metabolic products with industrial applications. We examine studies of these bacteria as Live Biotherapeutic Products (LBPs), focusing on in vivo disease models and clinical studies using them to treat infection, inflammation, metabolic syndrome, and cancer. We discuss key research areas including elucidation of intra-specific diversity and genetic modification of candidate strains that will facilitate the exploitation of Lachnospiraceae in industry and medicine.
