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mRNA expression of all 171 CAZymes during growth on pectins A–C, hemicelluloses D–E, glucans F–H, and raw corn stover I relative to expression on glucose. Expression was quantified as log2(RPKM) with significantly differentially expressed genes on a given polysaccharide shown as triangles and unchanged genes as circles. The 56 purified CAZymes are red and others are blue.
Source publication
Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequ...
Similar publications
Polysaccharides are macromolecules of monosaccharides linked by glycosidic bonds. Non-starch polysaccharides (NSP) are principally non-α-glucan polysaccharides of the plant cell wall. They are a heterogeneous group of polysaccharides with varying degrees of water solubility, size, and structure. The water insoluble fiber fraction include cellulose,...
Citations
... Thousands of enzymes are required to break down chemically diverse dietary components, including variable linkages found within complex polysaccharides. 32 Encoding the enzymes required to digest these compounds would require the host to dedicate an impractical fraction of its genome to this process. By making the large intestine a near-perfect environment for microbial fermentation, evolution arrived at a clever solution to the digestive challenge posed by the chemical complexity in food. ...
The increasing prevalence of immune‐mediated non‐communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co‐evolved host–microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome‐based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.
... The peptidase domain of ClbP (ClbP-pep), as defined in (13), was PCR amplified with a C-terminal His tag using primers clbP_F (5-AAAGAAGGAGATAGGATCATGACAATAATGG AACACGTTAG-3) and clbP_R (5-GTGTAATGGATAGTGATCTTAATGGTGATGGTGATGATGATAT TTGCCAATGCGCAGA-3). The PCR product was cloned by ligation-independent cloning into pET-22B(+) (61,62) and the forward and reverse sequences were confirmed by sequencing. Plasmids were transformed into E. coli BL21(DE3) (Novagen 70235). ...
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.
... 83 It was mentioned that Clostridiales act as a digestive booster due to most of the Clostridium genera playing roles in polysaccharide plants fermentation. 84 Yet a species, Clostridium difficile is accountable for causing various diseases ranging from simple diarrhea to fatal pseudomembranous colitis. 85 Primate gut microbiome functions can vary in mutualistic, commensal or pathogenic. ...
Background
The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus.
Methods
This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high‐throughput sequencing, and 16S rRNA as the targeted region.
Results
A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria‐2 is the dominant phyla found across all samples. Meanwhile, { Unknown Phylum } Bacteria‐2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut.
Conclusions
This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.
... TS-4.15%; TSP4-1.33%) are involved in the degradation of lignocellulosic materials, ferment polysaccharides into shortchain fatty acids (butyrate, acetate) and alcohols [57] and Ruminococcaceae can release hydrolytic enzymes capable of breaking down complex polysaccharides such as cellulose, hemicellulose, and pectin into compounds such as cow rumen, sludge and digestate [58]. These groups of microorganisms with cellulolytic capabilities were favored in the enzymatic pretreatment with cellulase (TSC4). ...
Turkey litter waste is lignocellulosic and keratinous, requiring prior enzymatic treatment to facilitate fiber hydrolysis and utilization by microorganisms in anaerobic digestion (AD) process. The understanding of the performance of microorganisms in AD can be facilitated through molecular biology and bioinformatics tools. This study aimed to determine the taxonomic profile and functional prediction of microbial communities in the AD of turkey litter waste subjected to enzymatic pretreatment and correlate it with operational parameters. The tests involved the use of turkey litter (T) at 25 g L⁻¹ of volatile solids, a granular inoculum (S) (10% m/v), and the addition of cellulase (C), and pectinase (P) enzymes at four concentrations. The use of enzymes increased methane production by 19% (turkey litter, inoculum, and cellulase—TSC4) and 15% (turkey litter, inoculum, and enzymatic pectinase—TSP4) compared to the control (turkey litter and inoculum—TS), being more effective in TSC4 (667.52 mLCH4), where there was consumption of acetic, butyric, and propionic acids. The pectinase assay (TSP4) showed a methane production of 648 mLCH4 and there was the accumulation of metabolites. Cellulolytic microorganisms Bacteroides, Ruminofilibacter, Lachnospiraceae, Ruminococcaceae, and Methanosaeta were favored in TSC4. In TSP4, the predominant genus was Macellibacteroides and Methanosarcina, and genes involved in methylotrophic methanogenesis were also found (mtaB, mtmB, and mtbB). Enzymes involved in hydrogenotrophic methanogenesis were identified in both assays (TSC4 and TSP4). Molecular tools helped to understand the metabolic routes involved in AD with enzymatic treatment, allowing the elaboration of strategies to improve the sustainable degradation of turkey litter waste.
... Another set of genera were depleted in lower BMF categories, such as Bacteroides, Lachnoclostridium, Lach-nospiraceae_ND3007_group, Lachnospiraceae_UCG-004, and Veillonella, which are all important contributors to SCFA production. [43][44][45][46] This reduction in SCFA producers is consistent with the switch away from saccharolytic fermentation toward proteolytic fermentation in the case of constipation. 10 Reduced SCFA production is known to weaken smooth muscle contractions that drive peristalsis, [47][48][49] acting as a positive feedback on constipation. ...
Bowel movement frequency (BMF) directly impacts the gut microbiota and is linked to diseases like chronic kidney disease or dementia. In particular, prior work has shown that constipation is associated with an ecosystem-wide switch from fiber fermentation and short-chain fatty acid production to more detrimental protein fermentation and toxin production. Here, we analyze multi-omic data from generally healthy adults to see how BMF affects their molecular phenotypes, in a pre-disease context. Results show differential abundances of gut microbial genera, blood metabolites, and variation in lifestyle factors across BMF categories. These differences relate to inflammation, heart health, liver function, and kidney function. Causal mediation analysis indicates that the association between lower BMF and reduced kidney function is partially mediated by the microbially derived toxin 3-indoxyl sulfate (3-IS). This result, in a generally healthy context, suggests that the accumulation of microbiota-derived toxins associated with abnormal BMF precede organ damage and may be drivers of chronic, aging-related diseases.
... We hypothesized that RS2 would reduce serum TG levels by reducing the levels of Coriobacteriaceae_UCG-002, thereby inhibiting cholesterol absorption. Notably, Lachnospiraceae NK4A136 group is a butyrate-producing bacterium [63], which was decreased in obese mice and subsequently increased by the IPA intervention. This group was previously reported to maintain gut barrier integrity in mice and is negatively correlated with intestinal permeability [64]. ...
Owing to the interplay of genetic and environmental factors, obesity has emerged as a significant global public health concern. To gain enhanced control over obesity, we examined the effects of type 2 resistant starch (RS2) and its promoted microbial-derived metabolite, indole-3-propionic acid (IPA), on hepatic steatosis, antioxidant activity, and gut microbiota in obese mice. Neither RS2 nor low-dose IPA (20 mg kg−1) exhibited a reduction in body weight or improved glucose and lipid metabolism in post-obesity state mice continuously fed the high-fat diet (HFD). However, both interventions improved hepatic steatosis, with RS2 being more effective in all measured parameters, potentially due to changes in gut microbiota and metabolites not solely attributed to IPA. LC-MS/MS analysis revealed increased serum IPA levels in both RS2 and IPA groups, which positively correlated with Bifidobacterium and Clostridium. Moreover, RS2 exhibited a more significant restoration of gut dysbiosis by promoting the abundance of health-promoting bacteria including Faecalibaculum and Bifidobacterium. These findings suggest that the regulatory role of RS2 on tryptophan metabolism only partially explains its prebiotic activity. Future studies should consider increasing the dose of IPA and combining RS2 and IPA to explore their potential interventions in obesity.
... Lachnospiraceae possesses the capability to convert plant polysaccharides into short-chain fatty acids, such as butyric acid, via the process of fermentation (Boutard et al., 2014). The Lachnospiraceae_NK4A136_group genus, belonging to the family of Lachnospiraceae, is considered as a potential producer of butyrate to treat dementia (Dou et al., 2020;Stadlbauer et al., 2020). ...
Background
Sepsis is commonly associated with a sudden impairment of brain function, thus leading to significant rates of illness and mortality. The objective of this research was to integrate microbiome and metabolome to reveal the mechanism of microbiota-hippocampus-metabolites axis dysfunction in a mouse model of sepsis.
Methods
A mouse model of sepsis was established via cecal ligation and puncture. The potential associations between the composition of the gut microbiota and metabolites in the hippocampus of mice with sepsis were investigated by combining 16S ribosomal RNA gene sequencing and ultra-high-performance liquid chromatography tandem mass spectrometry.
Results
A total of 140 differential metabolites were identified in the hippocampal tissues of mice with sepsis when compared to those of control mice. These differential metabolites in mice with sepsis were not only associated with autophagy and serotonergic synapse, but also involved in the metabolism and synthesis of numerous amino acids. At the phylum level, the abundance of Bacteroidota was increased, while that of Firmicutes (Bacillota) was decreased in mice with sepsis. At the genus level, the abundance of Alistipes was increased, while that of Lachnospiraceae_NK4A136_group was decreased in mice with sepsis. The Firmicutes (Bacillota)/Bacteroidota (F/B) ratio was decreased in mice with sepsis when compared to that of control mice. Furthermore, the F/B ratio was positively correlated with 5′-methylthioadenosine, PC (18:3(9Z,12Z,15Z)/18:0) and curdione, and negatively correlated with indoxylsulfuric acid, corticosterone, kynurenine and ornithine.
Conclusion
Analysis revealed a reduction in the F/B ratio in mice with sepsis, thus contributing to the disturbance of 5′-methylthioadenosine, curdione, PC (18:3(9Z,12Z,15Z)/18:0), corticosterone, ornithine, indoxylsulfuric acid and kynurenine; eventually, these changes led to hippocampus dysfunction. Our findings provide a new direction for the management of sepsis-induced hippocampus dysfunction.
... Clostridium has shown agroecological benefits including nitrogen fixation and phosphate solubilization making these nutrients more available to plants (Figueiredo et al. 2020). Another clostridial member enriched in R/TR was Lachnospiraceae NK4A136 which are gut/rumen microbes and can ferment plant polysaccharides to fatty acids and ethanol (Boutard et al. 2014;Wu et al. 2020). Clostridial species are butanediol producers, as are lactobacilli (O. ...
Rafflesia is an endangered endophytic holoparasitic plant that lives the majority of its life inside the tissues of its sole plant host, Tetrastigma. Rafflesia floral buds emerge to produce the world’s largest single flower. Like other plants, holoparasites harbor a diverse microbiome, the role(s) of which has remained largely unstudied. We characterized the bacterial microbiome of seeds of Rafflesia speciosa and cuttings of its host. We found evidence that R. speciosa seed has similar bacterial profiles to its infected host, which suggests that seeds sequester certain host bacteria, as well as acquire unique bacterial taxa from biotic associates of the fruit. We did not find evidence of mycorrhizal taxa in the microbiome. This is the first study of the microbial endophytes associated with any Rafflesia species and its host, a tripartite holobiont, and provides insights on its cryptic microbial partners. We discuss how this may aid horticultural propagation of Rafflesia.
... Species of Lachnospiraceae collectively metabolize plant biomass through the assimilation of polysaccharides, peptides, and aromatics as well as subsequent transformation of the fermentation products by acetogens and cross-feeding species ( Figure 3). As primary degraders of plant biomass, many Lachnospiraceae ferment a variety of complex polysaccharides including glucans, mannans, xylans, galactans, pectins, and arabinans (Boutard et al., 2014). Biomass-fermenting species sometimes grow faster on polysaccharides than on the constituent monosaccharides (Boutard 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.
... Both Lachnospiraceae NK4A136 group and Lachnospiraceae_UCG-006 belong to the Lachnospiraceae family which is characterized by its ability to convert polysaccharides into SCFAs. Previous studies have shown that enriching Lachnospiraceae with fiber polysaccharides can increase SCFA production, particularly acetate and butyrate, while reducing inflammation [45,46]. Desulfovibrio can produce hydrogen (H 2 S) sulfide to activate the AKT pathway to improve insulin resistance [47]. ...