Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut

Interbacterial warfare in the human gut: insights from Bacteroidales' perspective

Competition and cooperation are fundamental to the stability and evolution of ecological communities. The human gut microbiota, a dense and complex microbial ecosystem, plays a critical role in the host's health and disease, with competitive interactions being particularly significant. As a dominant and extensively studied group in the human gut, Bacteroidales serves as a successful model system for understanding these intricate dynamic processes. This review summarizes recent advances in our understanding of the intricate antagonism mechanisms among gut Bacteroidales at the biochemical or molecular-genetic levels, focusing on interference and exploitation competition. We also discuss unresolved questions and suggest strategies for studying the competitive mechanisms of Bacteroidales. The review presented here offers valuable insights into the molecular basis of bacterial antagonism in the human gut and may inform strategies for manipulating the microbiome to benefit human health.

mKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data

The advanced single-microbe RNA sequencing (smRNA-seq) technique addresses the pressing need to understand the complexity and diversity of microbial communities, as well as the distinct microbial states defined by different gene expression profiles. Current analyses of smRNA-seq data heavily rely on the integrity of reference genomes within the queried microbiota. However, establishing a comprehensive collection of microbial reference genomes or gene sets remains a significant challenge for most real-world microbial ecosystems. Here, we developed an unbiased embedding algorithm utilizing K-mer signatures, named mKmer, which bypasses gene or genome alignment to enable species identification for individual microbes and downstream functional enrichment analysis. By substituting gene features in the canonical cell-by-gene matrix with highly conserved K-mers, we demonstrate that mKmer outperforms gene-based methods in clustering and motif inference tasks using benchmark datasets from crop soil and human gut microbiomes. Our method provides a reference genome-free analytical framework for advancing smRNA-seq studies.

Inference of functional differentiation of intestinal microbes between two wild zokor species based on metagenomics

BACKGROUND

Currently, there are fewer studies on the intestinal microbes of wild zokors, and it is unclear how zokors adapt to special underground environments by regulating their intestinal microbes. Here, we explored the function of intestinal microbes of Eospalax cansus and Eospalax rothschildi based on metagenomics.

RESULTS

Both zokor species have similar intestinal microbial composition, but E. cansus has a higher proportion of bacteria involved in carbohydrate degradation. Functional analysis based on KEGG and CAZy databases indicated that the intestinal microbes of E. cansus harboured stronger carbohydrate degradation ability, mainly in starch and sucrose metabolism, and further in cellulose degradation. Furthermore, the cellulase activity was significantly higher in E. cansus than that in E. rothschildi. Eospalax cansus has a stronger microbial fermentation ability due to an increase in fibre-degrading bacteria like unclassified_f_Lachnospiraceae, Ruminococcus, and Clostridium. In addition, the dominant bacteria isolated from zokor were Bacillus, some of which could degrade both cellulose and hemicellulose.

CONCLUSION

Metagenomic analysis and bacterial isolation experiments indicate that E. cansus has a stronger microbial cellulose-degrading capacity, possibly as an adaptation to its limited food resources underground. © 2024 Society of Chemical Industry.

Dynamic Impacts of Stock Enhancement on Kaluga Sturgeon (Huso dauricus): Novel Conservation Strategy Insights from the Gut Microbe Composition and Gene Expression Mode

The sturgeon population has experienced strict threats due to inordinate human activities in the last decade and has been classified into the Red List of Threatened Species in recent years. Stock enhancement is one effective practice for the conservation of wild sturgeons. However, the survival conditions for sturgeon were not satisfactory after they were directly restocked into their natural habitat. Huso dauricus is an important protected sturgeon species, and finding an appropriate conservation strategy for the wild population is urgent. To clarify the dynamic adaptability of Huso dauricus to its wild environment, 1000 individuals were released into a natural river. On the 0th, 7th, 14th, and 30th days, five recaptured individuals were used to evaluate the dynamic trends in biochemical biomarkers, intestinal histomorphology, gut microbe taxon composition, and transcription profile over 30 days of stock enhancement. Our results indicated that Huso dauricus individuals still had a physiological stress status on the seventh day and then gradually adapted to the wild habitat 14 days after reintroduction based on the serum cortisol level. Meanwhile, the feeding habitat, organ function indicators, and growth performance showed similar dynamic changes within 30 days. Interestingly, their gut bacterial diversity and taxon structure also fluctuated over the 30 days after restocking, and they were accompanied by dynamic changes in intestinal pathological injury and tight junction protein expression in this period. The transcriptome analysis revealed the dynamic adaptability of Huso dauricus to wild habitats associated with the expression modes of genes related to the FoxO family, immune system, cytochrome family, and ATP metabolism. Taken together, the findings of the present research demonstrated that artificial reintroduction had dynamic impacts on the health condition of Huso dauricus and that 14 days of wilderness training might be essential for sturgeon restocking practices. Our study revealed the adaption mechanism of Huso dauricus at the molecular level during the restocking period and shed light on the theoretical guidelines for wild sturgeon conservation.

Multi-omics analysis explore the mechanism of deoxynivalenol inhibiting rabbit appetite through microbial-gut-brain axis

Deoxynivalenol (DON) is one of the most prevalent mycotoxins and can induce weight loss and vomiting in animals. This study aimed to elucidate the molecular mechanisms underlying DON-induced anorexia in rabbits through the microbial-gut-brain axis. A total of forty rabbits were randomly divided into a DON group and a control group, receiving 1.5 mg/kg.BW of DON and an equivalent volume of saline daily via intragastric administration, respectively. The pre-treatment period lasted for 7 days, followed by a formal experimental period of 24 days. The findings revealed that DON exposure significantly reduced daily food intake and weight gain, leading to intestinal apoptosis and barrier injuries. 16S rRNA sequencing data indicated that DON exposure decreased the diversity and richness of cecal microflora, suppressed probiotic populations, and disrupted host lipid metabolism. RNA-Seq and iTRAQ data were used to cross-analyze the shared differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in the hypothalamus and jejunum, along with their shared enrichment pathways, indicating that TNF-α, NF-κB, and NPY may play pivotal roles in DON-induced anorexia. qRT-PCR and Western blotting results confirmed significant increases in mRNA and protein expression levels of TNF-α, NF-κB and 5-HT2A in both the hypothalamus and jejunum. In conclusion, DON ingestion in rabbits can disrupt the intestinal barrier, up-regulate the expression of IFN-γ, TNF-α, NF-κB, and 5-HT2A in the intestine, and trigger an immuno-inflammatory response in the hypothalamus via the microbial-gut-brain axis, ultimately resulting in appetite suppression and weight loss.

Wheat arabinoxylans: Insight into structure-function relationships

Arabinoxylan (AX), a key non-starch polysaccharide found in the cell walls of cereals like wheat, holds significant importance in the food industry. Recently, it has attracted attention due to its numerous health benefits. While the benefits of wheat arabinoxylans are well-established, a more comprehensive understanding of the relationship between their structure and functional properties is essential. This knowledge will be instrumental in addressing potential concerns in future research focusing on food products containing wheat arabinoxylan. Previous reviews predominantly focused on cereal arabinoxylans, and only a few have addressed wheat arabinoxylan. This review aims to consolidate recent research findings on wheat arabinoxylans, highlighting their health benefits and potential links to structural variations. This will aid future studies in this area. Feruloylated arabinoxylans and arabinoxylan oligosaccharides stand out as the most known for their health benefits. Modifying the chemical structure of arabinoxylans to yield low molecular weight oligosaccharides enhances their immunomodulatory and antioxidant activities, as well as promotes the growth and availability of beneficial gut microbes. The antioxidant activity is positively correlated with the ferulic acid content, whereas it has a negative correlation with arabinose substitution. Nevertheless, additional research using final products is necessary to delve into the potential underlying mechanisms.

Alleviating Clostridium perfringens-Induced Intestinal Lesions in Chickens Using the Xylanase CbXyn10C and Its Binary Cocktail with a Protease

Clostridium perfringens infection can induce necrotic enteritis and lead to significant economic loss to the chicken industry. In this study, a xylanase (CbXyn10C), which effectively promotes the growth of probiotics, and a protease, which degrades the biofilm of C. perfringens, were analyzed for their ability to alleviate C. perfringens-induced necrotic enteritis in broiler chickens. A total of 300 male AA chickens were divided into five treatment groups (control, no enzyme and no C. perfringens challenge; Cp, no enzyme, C. perfringens challenge; Xyn, CbXyn10C plus C. perfringens challenge; Xyn+Am, CbXyn10C+Amylase plus C. perfringens challenge; Xyn+Ap, CbXyn10C+Alkaline protease plus C. perfringens challenge). The C. perfringens CVCC 60102 was administered orally on a daily basis to the chickens from 14 to 20 days. In comparison with Cp, Xyn+Ap significantly reduced intestinal damage in the duodenum, jejunum, and ileum of chickens challenged with C. perfringens (p < 0.05). The enzymes, and particularly Xyn+Ap, notably enhanced the expression of key intestinal barrier genes, reduced the IL-6 level, and decreased the DAO (diamine oxidase) level. Not unexpectedly, feeding enzymes influenced the abundance of Lactobacillus and Butyricicoccus bacteria in the intestine. These results indicated that CbXyn10C and protease can be used to alleviate intestinal damage caused by C. perfringens infection.

A novel CBM serving as a module for efficiently decomposing xanthan by modifying the processivity of hydrolase

The inefficient decomposition of polysaccharides, particularly branched polysaccharides limits their large-scale industrial applications. Further understanding and modification of glycoside hydrolases (GHs) processivity is expected to overcome this limitation. Here, a novel xanthan-binding CBM (MiXBM), which was supposed to alter the processivity of GHs, was systematically characterized. Phylogeny and structure analyses indicated that MiXBM is closely related to putative polysaccharide side chain-binding modules. Quantitative binding assays further revealed that MiXBM probably has a high affinity for xanthan side chain via a variable loop site. Moreover, catalytic performance demonstrated that xanthanase chimeras containing MiXBM promote highly efficient hydrolysis of xanthan because of improved substrate accessibility. Notably, MiXBM was observed to enhance the processivity of xanthanase, owing to its high substrate affinity to the repeating unit xanthan. Furthermore, sequential hydrolysis of xanthan by xanthanases with varying processivity resulted in significantly increased hydrolytic efficiency and focused oligoxanthans array. These results expand understanding of CBM-substrate recognition and shed light on efficient degradation of other regularly branched polysaccharides using modified GHs.

Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model

The macronutrient composition of a host's diet shapes its gut microbial community, with dietary fiber in particular escaping host digestion to serve as a potent carbon source for gut microbiota. Despite widespread recognition of fiber's importance to microbiome health, nutritional research often fails to differentiate hyper-processed fibers from cell-matrix-derived intrinsic fibers, limiting our understanding of how individual polysaccharides influence the gut community. We use the American cockroach (Periplaneta americana) as a model system to dissect the response of complex gut microbial communities to dietary modifications that are difficult to test in traditional host models. Here, we designed synthetic diets from lab-grade, purified ingredients to identify how the cockroach microbiome responds to six different carbohydrates (chitin, methylcellulose, microcrystalline cellulose, pectin, starch, and xylan) in otherwise balanced diets. We show via 16S rRNA gene profiling that these synthetic diets reduce bacterial diversity and alter the phylogenetic composition of cockroach gut microbiota in a fiber-dependent manner, regardless of the vitamin and protein content of the diet. Comparisons with cockroaches fed whole-food diets reveal that synthetic diets induce blooms in common cockroach-associated taxa and subsequently fragment previously stable microbial correlation networks. Our research leverages an unconventional microbiome model system and customizable lab-grade artificial diets to shed light on how purified polysaccharides, as opposed to nutritionally complex intrinsic fibers, exert substantial influence over a normally stable gut community.

Current models in bacterial hemicellulase-encoding gene regulation

The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.

Production of cello-oligosaccharides from corncob residue by degradation-synthesis reactions

The cellulose-rich corncob residue (CCR) is an abundant and renewable agricultural biomass that has been under-exploited. In this study, two strategies were compared for their ability to transform CCR into cello-oligosaccharides (COS). The first strategy employed the use of endo-glucanases. Although selected endo-glucanases from GH9, GH12, GH45, and GH131 could release COS with degrees of polymerization from 2 to 4, the degrading efficiency was low. For the second strategy, first, CCR was efficiently depolymerized to glucose and cellobiose using the cellulase from Trichoderma reesei. Then, using these simple sugars and sucrose as the starting materials, phosphorylases from different microorganisms were combined to generate COS to a level up to 100.3 g/L with different patterns and degrees of polymerization. Using tomato as a model plant, the representative COS obtained from BaSP (a sucrose phosphorylase from Bifidobacterium adolescens), CuCbP (a cellobiose phosphorylase from Cellulomonas uda), and CcCdP (a cellodextrin phosphorylase from Clostridium cellulosi) were shown to be able to promote plant growth. The current study pointed to an approach to make use of CCR for production of the value-added COS. KEY POINTS: • Sequential use of cellulase and phosphorylases effectively generated cello-oligosaccharides from corncob residue. • Cello-oligosaccharides patterns varied in accordance to cellobiose/cellodextrin phosphorylases. • Spraying cello-oligosaccharides promoted tomato growth.

Impacts of ectoparasite flea infestation on gut microbiota of the Meriones unguiculatus in a rodent-flea system

Fleas, along with one of their host species, Meriones unguiculatus, possess the capability to act as vectors in the transmission of plague. Parasitism by fleas may markedly influence the physiology and immune system of their hosts. Gut microbiota plays an important role in the growth and development of rodents. However, few studies have explored the impacts of ectoparasitic flea on the gut microbiome of rodents. This study investigated the immunological responses and changes in the gut microbial diversity and composition in both wild and laboratory rodents infested with fleas and laboratory rodents infested with Ctenocephalides felis. We measured immune reactions post-infestation by enzyme-linked immunosorbent assay (ELISA) and explored the effects of ectoparasitic infestation on the diversity and composition of the rodent gut microbiota in microbiome studies by 16S rRNA gene sequencing techniques. After flea infestation, results from 16S rRNA gene sequencing techniques indicated a significant increase in alpha diversity, affecting the composition of the gut microbiota. At the genus level, the abundance of the harmful bacterium Desulfovibrio increased. Beta diversity analyses showed significant differences between the gut microbiota of the experimental and control groups. ELISA results revealed significantly elevated levels of IgG in parasitized mice, while the differences in IgA levels were not significant. Flea infections affect the composition and diversity of the gut microbiota in the M. unguiculatu, and it has been found that the biomarker Desulfovibrio increases following flea infection in these rodents. Our results indicate that the gut microbiota can regulate the stability of the rodent-flea system. These findings may provide a foundation for exploring preventive measures against plague and aid in developing more effective treatments for the infection.

Elaeagnus angustifolia L. fruit alleviates diarrhea via regulating intestinal microbiota and short chain fatty acids

Fruits of Elaeagnus angustifolia L. have been used as Uyghur medicine due to the properties of treating spleen and stomach weakness, indigestion, enteritis, diarrhea, lung heat, and cough. However, the anti-diarrhea mechanism was still not clear. This study explored the mechanism of E. angustifolia fruit alleviated diarrhea from the perspective of gut microbiota. Diarrhea model was established with Folium sennae in mice. Then, the levels of diarrhea rate and diarrhea index of mice were evaluated. Hematoxylin eosin (HE) staining was employed to detect pathological sections of colon tissue. 16S rRNA sequencing analysis was researched to confirm the gut microbiota in mice. Diversity and differential analysis were adopted to analyze the intestinal microflora. Furthermore, Gas chromatography-quadrupole time-of-flight tandem mass spectrometry (GC-Q-TOF-MS) was used to detect the concentrations of short chain fatty acids (SCFAs) in intestine. The high-dose group (3.2 g/kg) of E. angustifolia fruit could significantly reduce the diarrhea rate and diarrhea index of mice caused by Folium sennae (p < 0.01). We also found that E. angustifolia fruit enhanced the diversity of gut microbiota while ameliorating diarrhea. Alpha diversity revealed that the microbial composition of E. angustifolia fruit group tended to be more similar to that of the CON group (no significant difference at p < 0.05). E. angustifolia fruit also induced structural changes of gut microbiota in mice. In addition, the concentrations of SCFAs increased after administration of E. angustifolia fruit. This study demonstrated that E. angustifolia fruit could ameliorate diarrhea by regulating the composition and abundance of intestinal microbiota, together with the levels of SCFAs.

Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model

The macronutrient composition of a host's diet shapes its gut microbial community, with dietary fiber in particular escaping host digestion to serve as a potent carbon source for gut microbiota. Despite widespread recognition of fiber's importance to microbiome health, nutritional research often fails to differentiate hyper-processed fibers from cell-matrix derived intrinsic fibers, limiting our understanding of how individual polysaccharides influence the gut community. We use the American cockroach (Periplaneta americana) as a model system to dissect the response of complex gut microbial communities to diet modifications that are impossible to test in traditional host models. Here, we designed synthetic diets from lab-grade, purified ingredients to identify how the cockroach microbiome responds to six different carbohydrates (chitin, methylcellulose, microcrystalline cellulose, pectin, starch, xylan) in otherwise balanced diets. We show via 16S rRNA gene profiling that these synthetic diets reduce bacterial diversity and alter the phylogenetic composition of cockroach gut microbiota in a fiber-dependent manner, regardless of the vitamin and protein content of the diet. Comparisons with cockroaches fed whole-food diets reveal that synthetic diets induce blooms in common cockroach-associated taxa and subsequently fragment previously stable microbial correlation networks. Our research leverages an unconventional microbiome model system and customizable lab-grade artificial diets to shed light on how purified polysaccharides, as opposed to nutritionally complex intrinsic fibers, exert substantial influence over a normally stable gut community.

3D printed spiral tube-like cellulose scaffold for oral delivery of probiotics

Introducing specific strains of probiotics into the gut microbiome is a promising way to modulate the intestinal microbiome to treat various health conditions clinically. However, oral probiotics typically have a temporary or limited impact on the gut microbiome and overall health benefits. Here, we reported a 3D printed cellulose-derived spiral tube-like scaffold that enabled high efficacy of the oral delivery of probiotics. Benefiting from the unique surface pattern, this system can effectively extend the retention time of loaded probiotics in the gut without invading nearby tissues, provide a favorable environment for the survival and long-term colonization of loaded probiotics, and influence the intestinal ecosystem as a dietary fiber after degradation. We demonstrate Roseburia intestinalis-loaded scaffold exerts noticeable impacts on the regulation of the gut microbiome to treat various gut-related diseases, including obesity and inflammatory bowel disease; thus, we provide a universal platform for oral delivery of probiotics.

The effect of dietary supplementation of Lycium barbarum leaves on the growth performance, organ indexes and intestinal microflora of rats

This study was conducted to investigate both fruit and different levels of leaf supplementation on the growth performance, organ indices and intestinal microflora of rats. Twenty-five healthy male Sprague-Dawley rats were randomly divided into five groups. The rats in the control (NC) and positive control (PC) groups were fed by gavage a basal diet and a basal diet with 4 g/kg of L. barbarum fruit homogenate, respectively. The test (LD, MD, and HD) groups were fed basal diets with additional 2, 4, and 8 g/kg of L. barbarum leaf homogenate, respectively. The feeding period was 35 d. The result revealed that the rats in the LD group had the highest average weight gain (p < 0.05). The cardiac and renal indexes in the LD and MD groups were significantly higher than in NC group, respectively (p < 0.05). Diversity analysis revealed that adding low concentrations of L. barbarum leaf homogenates markedly reduced the Shannon index of the rats cecum (p < 0.05). The relative abundance of Verrucomicrobiota was higher in the LD group than those in other groups (p < 0.05). The relative abundance of Actinobacteriota was found significantly higher in PC group than others (p < 0.05). The relative abundance of Akkermansia in LD group was the highest (p < 0.05). The relative abundance of Romboutsia in the PC group was considerably higher than that in other groups. The relative abundance of Candidatus_Saccharimonas in the supplementation groups was appreciably lower than those found in other groups. The relative abundance of Alloprevotella was significantly lower in PC, LD, and MD groups than in NC and HD groups (p < 0.05). The relative abundance of Oscillibacter was significantly higher in HD group than in other groups (p < 0.05). Thus, L. barbarum leaf homogenate fed to rats could increase their growth performance, internal organ weights and additionally enhance the relative abundance of beneficial bacteria. Therefore, based on the obtained data in the current study, a dose of L. barbarum leaf homogenate supplemented with 2 g/kg in diet is recommended, however, further studies are required to confirm, especially in animals.

Sulfated Polysaccharides from Sea Cucumber Cooking Liquid Prevents Obesity by Modulating Gut Microbiome, Transcriptome, and Metabolite Profiles in Mice Fed a High-Fat Diet

We aimed to explore the anti-obesity mechanism from the microbiome, metabolome, and transcriptome viewpoints, focusing on the sulfated polysaccharides found in the cooking liquid of Apostichopus japonicus (CLSPAJ) to explore the potential mediators of the anti-obesity effects in mice fed a high-fat diet (HFD). The mice treated with CLSPAJ showed a decrease in obesity and blood lipid levels. Gut microbiome dysbiosis caused by the HFD was reversed after CLSPAJ supplementation, along with increased levels of indole-3-ethanol, N-2-succinyl-L-glutamic acid 5-semialdehyde, and urocanic acid. These increases were positively related to the increased Akkermansia, Lactobacillus, Roseburia, and Phascolarctobacterium. Transcriptome analysis showed that B cell receptor signaling and cytochrome P450 xenobiotic metabolism were the main contributors to the improvement in obesity. Metabolome-transcriptome analysis revealed that CLSPAJ reversal of obesity was mainly due to amino acid metabolism. These findings suggest that CLSPAJ could be a valuable prebiotic preparation for preventing obesity-related diseases.

Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health

Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.

Intracellular removal of acetyl, feruloyl and p-coumaroyl decorations on arabinoxylo-oligosaccharides imported from lignocellulosic biomass degradation by Ruminiclostridium cellulolyticum

BACKGROUND

Xylans are polysaccharides that are naturally abundant in agricultural by-products, such as cereal brans and straws. Microbial degradation of arabinoxylan is facilitated by extracellular esterases that remove acetyl, feruloyl, and p-coumaroyl decorations. The bacterium Ruminiclostridium cellulolyticum possesses the Xua (xylan utilization associated) system, which is responsible for importing and intracellularly degrading arabinoxylodextrins. This system includes an arabinoxylodextrins importer, four intracellular glycosyl hydrolases, and two intracellular esterases, XuaH and XuaJ which are encoded at the end of the gene cluster.

RESULTS

Genetic studies demonstrate that the genes xuaH and xuaJ are part of the xua operon, which covers xuaABCDD'EFGHIJ. This operon forms a functional unit regulated by the two-component system XuaSR. The esterases encoded at the end of the cluster have been further characterized: XuaJ is an acetyl esterase active on model substrates, while XuaH is a xylan feruloyl- and p-coumaryl-esterase. This latter is active on oligosaccharides derived from wheat bran and wheat straw. Modelling studies indicate that XuaH has the potential to interact with arabinoxylobiose acylated with mono- or diferulate. The intracellular esterases XuaH and XuaJ are believed to allow the cell to fully utilize the complex acylated arabinoxylo-dextrins imported into the cytoplasm during growth on wheat bran or straw.

CONCLUSIONS

This study reports for the first time that a cytosolic feruloyl esterase is part of an intracellular arabinoxylo-dextrin import and degradation system, completing its cytosolic enzymatic arsenal. This system represents a new pathway for processing highly-decorated arabinoxylo-dextrins, which could provide a competitive advantage to the cell and may have interesting biotechnological applications.

Role of Natural Binding Proteins in Therapy and Diagnostics

This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.

Next-generation probiotics: the upcoming biotherapeutics

Recent and continuing advances in gut microbiome research have pointed out the role of the gut microbiota as an unexplored source of potentially beneficial probiotic microbes. Along the lines of these advances, both public awareness and acceptance of probiotics are increasing. That's why; academic and industrial research is dedicated to identifying and investigating new microbial strains for the development of next-generation probiotics (NGPs). At this time, there is a growing interest in NGPs as biotherapeutics that alter the gut microbiome and affect various diseases development. In this work, we have focused on some emergent and promising NGPs, specifically Eubacterium hallii, Faecalibacterium prausnitzii, Roseburia spp., Akkermansia muciniphila, and Bacteroides fragilis, as their presence in the gut can have an impact on the development of various diseases. Emerging studies point out the beneficial roles of these NGPs and open up novel promising therapeutic options. Interestingly, these NGPs were found to enhance gastrointestinal immunity, enhance immunotherapy efficacy in cancer patients, retain the intestinal barrier integrity, generate valuable metabolites, especially short-chain fatty acids, and decrease complications of chemotherapy and radiotherapy. Although many of these NGPs are considered promising for the prevention and treatment of several chronic diseases, research on humans is still lacking. Therefore, approval of these microbes from regulatory agencies is rare. Besides, some issues limit their wide use in the market, such as suitable methods for the culture and storage of these oxygen-sensitive microbes. The present review goes over the main points related to NGPs and gives a viewpoint on the key issues that still hinder their wide application. Furthermore, we have focused on the advancement in NGPs and human healthiness investigations by clarifying the limitations of traditional probiotic microorganisms, discussing the characteristics of emerging NGPs and defining their role in the management of certain ailments. Future research should emphasize the isolation, mechanisms of action of these probiotics, safety, and clinical efficacy in humans.

Effects of acetyl groups on the prebiotic properties of glucomannan extracted from Artemisia sphaerocephala Krasch seeds

This study explores the structural modification of glucomannan extracted from Artemisia sphaerocephala Krasch seeds (60S) to assess the impact of acetyl groups on its prebiotic characteristics. The structural changes were examined, with a focus on the degree of acetyl group substitution (DS). Both deacetylation and acetylation had limited influence on the molecular properties of 60S. Despite these modifications, the apparent viscosity of all samples remained consistently low. In vitro fermentation experiments revealed that Escherichia-Shigella decreased as DS increased, while Bacteroides ovatus was enriched. Acetylation had no significant impact on the utilization rate of 60S but led to a reduction in the production of propionic acid. Furthermore, untargeted metabolomics analysis confirmed the changes in propionic acid levels. Notably, metabolites such as N-acetyl-L-tyrosine, γ-muricholic acid, and taurocholate were upregulated by acetylated derivatives. Overall, acetyl groups are speculated to play a pivotal role in the prebiotic properties of 60S.

Deciphering the nutritional strategies for polysaccharides effects on intestinal barrier in broilers: Selectively promote microbial ecosystems

The gut microbiota, a complex and dynamic microbial ecosystem, plays a crucial role in regulating the intestinal barrier. Polysaccharide foraging is specifically dedicated to establishing and maintaining microbial communities, contributing to the shaping of the intestinal ecosystem and ultimately enhancing the integrity of the intestinal barrier. The utilization and regulation of individual polysaccharides often rely on distinct gut-colonizing bacteria. The products of their metabolism not only benefit the formation of the ecosystem but also facilitate cross-feeding partnerships. In this review, we elucidate the mechanisms by which specific bacteria degrade polysaccharides, and how polysaccharide metabolism shapes the microbial ecosystem through cross-feeding. Furthermore, we explore how selectively promoting microbial ecosystems and their metabolites contributes to improvements in the integrity of the intestinal barrier.

Engineering Saccharomyces cerevisiae for targeted hydrolysis and fermentation of glucuronoxylan through CRISPR/Cas9 genome editing

BACKGROUND

The abundance of glucuronoxylan (GX) in agricultural and forestry residual side streams positions it as a promising feedstock for microbial conversion into valuable compounds. By engineering strains of the widely employed cell factory Saccharomyces cerevisiae with the ability to directly hydrolyze and ferment GX polymers, we can avoid the need for harsh chemical pretreatments and costly enzymatic hydrolysis steps prior to fermentation. However, for an economically viable bioproduction process, the engineered strains must efficiently express and secrete enzymes that act in synergy to hydrolyze the targeted polymers.

RESULTS

The aim of this study was to equip the xylose-fermenting S. cerevisiae strain CEN.PK XXX with xylanolytic enzymes targeting beechwood GX. Using a targeted enzyme approach, we matched hydrolytic enzyme activities to the chemical features of the GX substrate and determined that besides endo-1,4-β-xylanase and β-xylosidase activities, α-methyl-glucuronidase activity was of great importance for GX hydrolysis and yeast growth. We also created a library of strains expressing different combinations of enzymes, and screened for yeast strains that could express and secrete the enzymes and metabolize the GX hydrolysis products efficiently. While strains engineered with BmXyn11A xylanase and XylA β-xylosidase could grow relatively well in beechwood GX, strains further engineered with Agu115 α-methyl-glucuronidase did not display an additional growth benefit, likely due to inefficient expression and secretion of this enzyme. Co-cultures of strains expressing complementary enzymes as well as external enzyme supplementation boosted yeast growth and ethanol fermentation of GX, and ethanol titers reached a maximum of 1.33 g L- 1 after 48 h under oxygen limited condition in bioreactor fermentations.

CONCLUSION

This work underscored the importance of identifying an optimal enzyme combination for successful engineering of S. cerevisiae strains that can hydrolyze and assimilate GX. The enzymes must exhibit high and balanced activities, be compatible with the yeast's expression and secretion system, and the nature of the hydrolysis products must be such that they can be taken up and metabolized by the yeast. The engineered strains, particularly when co-cultivated, display robust growth and fermentation of GX, and represent a significant step forward towards a sustainable and cost-effective bioprocessing of GX-rich biomass. They also provide valuable insights for future strain and process development targets.

In vitro digestion and fecal fermentation of basidiospore-derived exopolysaccharides from Naematelia aurantialba

Mushroom polysaccharides exhibit numerous health-enhancing attributes that are intricately linked to the breakdown, assimilation, and exploitation of polysaccharides within the organism. Naematelia aurantialba polysaccharides (NAPS-A), highly prized polysaccharides derived from mushrooms, remain shrouded in uncertainty regarding their characteristics pertaining to gastrointestinal digestion and gut microbial fermentation. The study aimed to understand the digestion and fecal fermentation patterns of NAPS-A. After simulated digestion, NAPS-A's physicochemical properties remained unchanged. However, during in vitro fecal fermentation, indigestible NAPS-A underwent significant changes in various properties, such as reducing sugar, chemical composition, constituent monosaccharides, Molecular weight, apparent viscosity, FT-IR spectra, and microscopic morphology. Notably, NAPS-A was effectively utilized by the gut microbiota, with unchanged properties after digestion but altered after fermentation. It influenced gut microbe composition by increasing beneficial bacteria (Lactobacillus, Faecalibacterium, and Roseburia), lowering pH, and producing short-chain fatty acids. NAPS-A fermentation enriches carbohydrate, fatty acid, and amino acid metabolic pathways through PICRUSt prediction analysis. Overall, these findings emphasize NAPS-A's role in regulating gut bacteria and their metabolic functions, despite its challenging digestibility.

The catabolic specialization of the marine bacterium Polaribacter sp. Q13 to red algal β1,3/1,4-mixed-linkage xylan

Catabolism of algal polysaccharides by marine bacteria is a significant process of marine carbon cycling. β1,3/1,4-Mixed-linkage xylan (MLX) is a class of xylan in the ocean, widely present in the cell walls of red algae. However, the catabolic mechanism of MLX by marine bacteria remains elusive. Recently, we found that a marine Bacteroidetes strain, Polaribacter sp. Q13, is a specialist in degrading MLX, which secretes a novel MLX-specific xylanase. Here, the catabolic specialization of strain Q13 to MLX was studied by multiomics and biochemical analyses. Strain Q13 catabolizes MLX with a canonical starch utilization system (Sus), which is encoded by a single xylan utilization locus, XUL-Q13. In this system, the cell surface glycan-binding protein SGBP-B captures MLX specifically, contributing to the catabolic specificity. The xylanolytic enzyme system of strain Q13 is unique, and the enzymatic cascade dedicates the stepwise hydrolysis of the β1,3- and β1,4-linkages in MLX in the extracellular, periplasmic, and cytoplasmic spaces. Bioinformatics analysis and growth observation suggest that other marine Bacteroidetes strains harboring homologous MLX utilization loci also preferentially utilize MLX. These results reveal the catabolic specialization of MLX degradation by marine Bacteroidetes, leading to a better understanding of the degradation and recycling of MLX driven by marine bacteria.IMPORTANCERed algae contribute substantially to the primary production in marine ecosystems. The catabolism of red algal polysaccharides by marine bacteria is important for marine carbon cycling. Mixed-linkage β1,3/1,4-xylan (MLX, distinct from hetero-β1,4-xylans from terrestrial plants) is an abundant red algal polysaccharide, whose mechanism of catabolism by marine bacteria, however, remains largely unknown. This study reveals the catabolism of MLX by marine Bacteroidetes, promoting our understanding of the degradation and utilization of algal polysaccharides by marine bacteria. This study also sets a foundation for the biomass conversion of MLX.

Microbiota-accessible fiber activates short-chain fatty acid and bile acid metabolism to improve intestinal mucus barrier in broiler chickens

IMPORTANCE

The intestinal mucus barrier, located at the interface of the intestinal epithelium and the microbiota, is the first line of defense against pathogenic microorganisms and environmental antigens. Dietary polysaccharides, which act as microbiota-accessible fiber, play a key role in the regulation of intestinal microbial communities. However, the mechanism via which dietary fiber affects the intestinal mucus barrier through targeted regulation of the gut microbiota is not clear. This study provides fundamental evidence for the benefits of dietary fiber supplementation in broiler chickens through improvement in the intestinal mucus barrier by targeted regulation of the gut ecosystem. Our findings suggest that the microbiota-accessible fiber-gut microbiota-short-chain fatty acid/bile acid axis plays a key role in regulating intestinal function.

Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics

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.

Gut microbiota determines the fate of dietary fiber-targeted interventions in host health

Epidemiological investigation confirmed that the intake of dietary fiber (DF) is closely related to human health, and the most important factor affecting the physiological function of DF, besides its physicochemical properties, is the gut microbiota. This paper mainly summarizes the interaction between DF and gut microbiota, including the influence of DF on the colonization of gut microbiota based on its different physicochemical properties, and the physiological role of gut microbiota in destroying the complex molecular structure of DF by encoding carbohydrate-active enzymes, thus producing small molecular products that affect the metabolism of the host. Taking cardiovascular disease (Atherosclerosis and hypertension), liver disease, and immune diseases as examples, it is confirmed that some DF, such as fructo-oligosaccharide, galactooligosaccharide, xylo-oligosaccharide, and inulin, have prebiotic-like physiological effects. These effects are dependent on the metabolites produced by the gut microbiota. Therefore, this paper further explores how DF affects the gut microbiota's production of substances such as short-chain fatty acids, bile acids, and tryptophan metabolites, and provides a preliminary explanation of the mechanisms associated with their impact on host health. Finally, based on the structural properties of DF and the large heterogeneity in the composition of the population gut microbiota, it may be a future trend to utilize DF and the gut microbiota to correlate host health for precision nutrition by combining the information from population disease databases.

Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem

The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.

Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review

Arabinoxylo-oligosaccharides (AXOS) are non-digestible dietary fibers that potentially confer a health benefit by stimulating beneficial bacteria in the gut. Still, a detailed overview of the diversity of gut bacteria and their specificity to utilize structurally different AXOS has not been provided to date and was aimed for in this study. Moreover, we assessed the genetic information of summarized bacteria, and we extracted genes expected to encode for enzymes that are involved in AXOS hydrolysis (based on the CAZy database). The taxa involved in AXOS fermentation in the gut display a large variety of AXOS-active enzymes in their genome and consequently utilize AXOS to a highly different extent. Clostridia and Bacteroidales are generalists that consume many structurally diverse AXOS, whereas Bifidobacterium are specialists that specifically consume AXOS with a low degree of polymerization. Further complexity is evident from the fact that the exact bacterial species, and in some cases even the bacterial strains (e.g. in Bifidobacterium longum) that are stimulated, highly depend on the specific AXOS molecular structure. Furthermore, certain species in Bifidobacterium and Lactobacillaceae are active as cross-feeders and consume monosaccharides and unbranched short xylo-oligosaccharides released from AXOS. Our review highlights the possibility that (enzymatic) fine-tuning of specific AXOS structures leads to improved precision in targeting growth of specific beneficial bacterial species and strains in the gut.

Gut firmicutes: Relationship with dietary fiber and role in host homeostasis

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human gut. Accumulating evidence suggests that dietary fiber plays a crucial role in host health, yet most studies have focused on how the dietary fiber affects health through gut Bacteroides. More recently, gut Firmicutes have been found to possess many genes responsible for fermenting dietary fiber, and could also interact with the intestinal mucosa and thereby contribute to homeostasis. Consequently, the relationship between dietary fiber and Firmicutes is of interest, as well as the role of Firmicutes in host health. In this review, we summarize the current knowledge regarding the molecular mechanism of dietary fiber degradation by gut Firmicutes and explain the communication pathway of the dietary fiber-Firmicutes-host axis, and the beneficial effects of dietary fiber-induced Firmicutes and their metabolites on health. A better understanding of the dialogue sustained by the dietary fiber-Firmicutes axis and the host could provide new insights into probiotic therapy and novel dietary interventions aimed at increasing the abundance of Firmicutes (such as Faecalibacterium, Lactobacillus, and Roseburia) to promote health.

A pectic polysaccharide isolated from Achyranthes bidentata is metabolized by human gut Bacteroides spp

Achyranthes bidentata (A. bidentata) is a famous traditional Chinese medicine (TGM) for treatment osteoporosis. Polysaccharides, a major factor for shaping the gut microbiota, are the primary ingredients of A. bidentata. However, bioactivity of A. bidentata polysaccharide on human gut microbiota (HGM) remains unknown. Here, a homogeneous pectic polysaccharide A23-1 with average molecular weight of 93.085 kDa was extracted and purified from A. bidentata. And A23-1 was compsed of rhamnose, glucuronic acid, galacturonic acid, glucose, galactose and arabinose in a molar ratio of 7.26: 0.76: 5.12: 2.54: 23.51: 60.81. GC-MS, partial acid hydrolysis and NMR results indicated the backbone of A23-1 was composed of 1, 2, 4-Rhap and 1, 4-GlapA, while the branches were composed of galactose, arabinose, glucose and glucuronic acid. Further, A23-1 was found to be degraded into monosaccharides and fragments. Taking Bacteroides thetaiotaomicron (BT) as a model, we suggested three polysaccharide utilization loci (PULs) might be involved in the A23-1 degradation. Degraded products generated by BO might not support the growth of probiotics. Besides, acetate and propionate as the main end products were generated by Bacteroides spp. and probiotics utilizing A23-1. These findings suggested A23-1 was possible one of food sources of human gut Bacteroides spp.

Degradation of xylan by human gut Bacteroides xylanisolvens XB1A

Although many polysaccharides utilization loci (PULs) have been investigated by genomics and transcriptomics, the detailed functional characterization lags severely behind. We hypothesize that PULs on the genome of Bacteroides xylanisolvens XB1A (BX) dictate the degradation of complex xylan. To address, xylan S32 isolated from Dendrobium officinale was employed as a sample polysaccharide. We firstly showed that xylan S32 promoted the growth of BX which might degrade xylan S32 into monosaccharides and oligosaccharides. We further showed that this degradation was performed mainly via two discrete PULs in the genome of BX. Briefly, a new surface glycan binding protein (SGBP) BX_29290^SGBP was identified, and shown to be essential for the growth of BX on xylan S32. Two cell surface endo-xylanases Xyn10A and Xyn10B cooperated to deconstruct the xylan S32. Intriguingly, genes encoding Xyn10A and Xyn10B were mainly distributed in the genome of Bacteroides spp. In addition, BX metabolized xylan S32 to produce short chain fatty acids (SCFAs) and folate. Taken together, these findings provide new evidence to understand the food source of BX and the BX-directed intervention strategy by xylan.

Combining gut microbiota modulation and chemotherapy by capecitabine-loaded prebiotic nanoparticle improves colorectal cancer therapy

Colorectal cancer (CRC) therapy efficiency can be influenced by the microbiota in the gastrointestinal tract. Compared with traditional intervention, prebiotics delivery into the gut is a more controllable method for gut microbiota modulatory therapy. Capecitabine (Cap), the first-line chemotherapeutic agent for CRC, lacks a carrier that can prolong its half-life. Here, we construct a Cap-loaded nanoparticle using the prebiotic xylan-stearic acid conjugate (SCXN). The oral administration of SCXN delays the drug clearance in the blood and increases the intra-tumoral Cap concentration in the CRC mouse model. SCXN also facilitates the probiotic proliferation and short chain fatty acid production. Compared with free Cap, SCXN enhances the anti-tumor immunity and increases the tumor inhibition rate from 5.29 to 71.78%. SCXN exhibits good biocompatibility and prolongs the median survival time of CRC mice from 14 to 33.5 d. This prebiotics-based nanoparticle provides a promising CRC treatment by combining gut microbiota modulation and chemotherapy.

Exploring the Plasticity of Diet on Gut Microbiota and Its Correlation with Gut Health

Dietary habits have been proven to help alter the composition of gut microbiota, and exploring the impact of nutritional patterns on gut microbiota changes can help protect gut health. However, few studies have focused on the dietary impact on the gut microbiota over an experimental timeframe. In this study, 16S rRNA gene sequencing was employed to investigate the gut microbiota of mice under different dietary patterns, including AIN-93G diet (Control), high protein diet (HPD), high fiber diet (HFD), and switch diet (Switch). The alpha diversity of the HPD group significantly decreased, but HFD can restore this decline. During HPD, some genera were significantly upregulated (e.g., Feacalibaculum) and downregulated (e.g., Parabacteroides). However, after receiving HFD, other genera were upregulated (e.g., Akkermansia) and downregulated (e.g., Lactobacillus). In addition, the interaction between pathogenic bacteria was more pronounced during HPD, while the main effect was probiotics during HFD. In conclusion, the plasticity exhibited by the gut microbiota was subject to dietary influences, wherein disparate dietary regimens hold pivotal significance in upholding the well-being of the host. Therefore, our findings provide new ideas and references for the relationship between diets and gut microbiota.

Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions

The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus, Bifidobacterium, and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus, B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum.

Microbiome and tryptophan metabolomics analysis in adolescent depression: roles of the gut microbiota in the regulation of tryptophan-derived neurotransmitters and behaviors in human and mice

BACKGROUND

Adolescent depression is becoming one of the major public health concerns, because of its increased prevalence and risk of significant functional impairment and suicidality. Clinical depression commonly emerges in adolescence; therefore, the prevention and intervention of depression at this stage is crucial. Recent evidence supports the importance of the gut microbiota (GM) in the modulation of multiple functions associated with depression through the gut-brain axis (GBA). However, the underlying mechanisms remain poorly understood. Therefore, in the current study, we aimed to screen the microbiota out from healthy and depressive adolescents, delineate the association of the targeted microbiota and the adolescent depression, address the salutary effects of the targeted microbiota on anti-depressive behaviors in mice involving the metabolism of the tryptophan (Trp)-derived neurotransmitters along the GBA.

RESULTS

Here, we found the gut microbiota from healthy adolescent volunteers, first diagnosis patients of adolescent depression, and sertraline interveners after first diagnosis displayed significant difference, the relative abundance of Faecalibacterium, Roseburia, Collinsella, Blautia, Phascolarctobacterium, Lachnospiraceae-unclassified decreased in adolescent depressive patients, while restored after sertraline treatment. Of note, the Roseburia abundance exhibited a high efficiency in predicting adolescent depression. Intriguingly, transplantation of the fecal microbiota from healthy adolescent volunteers to the chronic restraint stress (CRS)-induced adolescent depressed mice significantly ameliorated mouse depressive behaviors, in which the Roseburia exerted critical roles, since its effective colonization in the mouse colon resulted in remarkably increased 5-HT level and reciprocally decreased kynurenine (Kyn) toxic metabolites quinolinic acid (Quin) and 3-hydroxykynurenine (3-HK) levels in both the mouse brain and colon. The specific roles of the Roseburia were further validated by the target bacteria transplantation mouse model, Roseburia intestinalis (Ri.) was gavaged to mice and importantly, it dramatically ameliorated CRS-induced mouse depressive behaviors, increased 5-HT levels in the brain and colon via promoting tryptophan hydroxylase-2 (TPH2) or -1 (TPH1) expression. Reciprocally, Ri. markedly restrained the limit-step enzyme responsible for kynurenine (indoleamine2,3-dioxygenase 1, IDO1) and quinolinic acid (3-hydroxyanthranilic acid 3,4-dioxygenase, 3HAO) generation, thereby decreased Kyn and Quin levels. Additionally, Ri. administration exerted a pivotal role in the protection of CRS-induced synaptic loss, microglial activation, and astrocyte maintenance.

CONCLUSIONS

This study is the first to delineate the beneficial effects of Ri. on adolescent depression by balancing Trp-derived neurotransmitter metabolism and improving synaptogenesis and glial maintenance, which may yield novel insights into the microbial markers and therapeutic strategies of GBA in adolescent depression. Video Abstract.

Oligosaccharides as Potential Regulators of Gut Microbiota and Intestinal Health in Post-COVID-19 Management

The COVID-19 pandemic has had a profound impact worldwide, resulting in long-term health effects for many individuals. Recently, as more and more people recover from COVID-19, there is an increasing need to identify effective management strategies for post-COVID-19 syndrome, which may include diarrhea, fatigue, and chronic inflammation. Oligosaccharides derived from natural resources have been shown to have prebiotic effects, and emerging evidence suggests that they may also have immunomodulatory and anti-inflammatory effects, which could be particularly relevant in mitigating the long-term effects of COVID-19. In this review, we explore the potential of oligosaccharides as regulators of gut microbiota and intestinal health in post-COVID-19 management. We discuss the complex interactions between the gut microbiota, their functional metabolites, such as short-chain fatty acids, and the immune system, highlighting the potential of oligosaccharides to improve gut health and manage post-COVID-19 syndrome. Furthermore, we review evidence of gut microbiota with angiotensin-converting enzyme 2 expression for alleviating post-COVID-19 syndrome. Therefore, oligosaccharides offer a safe, natural, and effective approach to potentially improving gut microbiota, intestinal health, and overall health outcomes in post-COVID-19 management.

β-glucans: a potential source for maintaining gut microbiota and the immune system

The human gastrointestinal (GI) tract holds a complex and dynamic population of microbial communities, which exerts a marked influence on the host physiology during homeostasis and disease conditions. Diet is considered one of the main factors in structuring the gut microbiota across a lifespan. Intestinal microbial communities play a vital role in sustaining immune and metabolic homeostasis as well as protecting against pathogens. The negatively altered gut bacterial composition has related to many inflammatory diseases and infections. β-glucans are a heterogeneous assemblage of glucose polymers with a typical structure comprising a leading chain of β-(1,4) and/or β-(1,3)-glucopyranosyl units with various branches and lengths as a side chain. β-glucans bind to specific receptors on immune cells and initiate immune responses. However, β-glucans from different sources differ in their structures, conformation, physical properties, and binding affinity to receptors. How these properties modulate biological functions in terms of molecular mechanisms is not known in many examples. This review provides a critical understanding of the structures of β-glucans and their functions for modulating the gut microbiota and immune system.

Complex alpha and beta mannan foraging by the human gut bacteria

The human gut microbiota (HGM), a community of trillions of microbes, underscores its contribution by impacting many facets of host health and disease. In the HGM, Bacteroidota and Bacillota represent dominant bacterial phyla, which mainly rely on the glycans recalcitrant to host digestion to meet their energy requirements. Accordingly, the impact of dietary and host-derived glycans in the assembly and operation of these dominant microbial communities continues to be an area of active research. Among various glycans, mannans represent an integral component of the human diet. Apart from their health effects, the diverse and complex mannan structures bears molecular signatures that alter the expression of specific gene clusters in selected Bacteroidota and Bacillota species. Both the phyla possess variable and sophisticated loci of mannan recognition proteins, hydrolytic enzymes, transporters, and other metabolic proteins to sense, capture and utilize mannans as an energy source. The current review summarizes mannan structural diversity, and strategies adopted by select species of the HGM bacteria to forage mannans by focusing primarily on glycoside hydrolases and their effects on host health and metabolism.

Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota

Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid-base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.

Cordyceps militaris extracts and cordycepin ameliorate type 2 diabetes mellitus by modulating the gut microbiota and metabolites

Introduction:Cordyceps militaris, which has many potential medicinal properties, has rarely been reported to alleviate type 2 diabetes mellitus (T2DM).

Methods: The effects of C. militaris extracts (CE) and cordycepin (CCS) on high-fat diet and streptozotocin (STZ) induced T2DM mice were analysed by gut microbiome and metabolomics methods in this study.

Results: The results demonstrated that glucose and lipid metabolism parameters, oxidative stress biomarkers and inflammation cytokines were down-regulated in the CCS and CE groups. A comparative analysis of the fecal samples from mice in the model and experimental groups showed that experimental groups resulted in a higher abundance of Firmicutes/Bacteroidetes.

Conclusion: This study provides evidence that C. militaris can be used as a food supplement to relieve T2DM, which provides a promising prospect for new functional food in it.

Potential of Wood Hemicelluloses and Their Derivates as Food Ingredients

A holistic utilization of all lignocellulosic wood biomass, instead of the current approach of using only the cellulose fraction, is crucial for the efficient, ecological, and economical use of the forest resources. Use of wood constituents in the food and feed sector is a potential way of promoting the global economy. However, industrially established food products utilizing such components are still scarce, with the exception of cellulose derivatives. Hemicelluloses that include xylans and mannans are major constituents of wood. The wood hemicelluloses are structurally similar to hemicelluloses from crops, which are included in our diet, for example, as a part of dietary fibers. Hence, structurally similar wood hemicelluloses have the potential for similar uses. We review the current status and future potential of wood hemicelluloses as food ingredients. We include an inventory of the extraction routes of wood hemicelluloses, their physicochemical properties, and some of their gastrointestinal characteristics, and we also consider the regulatory route that research findings need to follow to be approved for food solutions, as well as the current status of the wood hemicellulose applications on that route.

Association of Plasma Lipopolysaccharide-Binding Protein Concentration with Dietary Factors, Gut Microbiota, and Health Status in the Japanese General Adult Population: A Cross-Sectional Study

The influx of intestinal bacteria-derived lipopolysaccharide (LPS) into the blood has attracted attention as a cause of diseases. The aim of this study is investigating the associations between the influx of LPS, dietary factors, gut microbiota, and health status in the general adult population. Food/nutrient intake, gut microbiota, health status and plasma LPS-binding protein (LBP; LPS exposure indicator) were measured in 896 residents (58.1% female, mean age 54.7 years) of the rural Iwaki district of Japan, and each correlation was analyzed. As the results, plasma LBP concentration correlated with physical (right/left arms' muscle mass [β = -0.02, -0.03]), renal (plasma renin activity [β = 0.27], urine albumin creatinine ratio [β = 0.50]), adrenal cortical (cortisol [β = 0.14]), and thyroid function (free thyroxine [β = 0.05]), iron metabolism (serum iron [β = -0.14]), and markers of lifestyle-related diseases (all Qs < 0.20). Plasma LBP concentration were mainly negatively correlated with vegetables/their nutrients intake (all βs ≤ -0.004, Qs < 0.20). Plasma LBP concentration was positively correlated with the proportion of Prevotella (β = 0.32), Megamonas (β = 0.56), and Streptococcus (β = 0.65); and negatively correlated with Roseburia (β = -0.57) (all Qs < 0.20). Dietary factors correlated with plasma LBP concentration correlated with positively (all βs ≥ 0.07) or negatively (all βs ≤ -0.07) the proportion of these bacteria (all Qs < 0.20). Our results suggested that plasma LBP concentration in the Japanese general adult population was associated with various health issues, and that dietary habit was associated with plasma LBP concentration in relation to the intestinal bacteria.

Butyrate producers, "The Sentinel of Gut": Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics

Gut-microbial butyrate is a short-chain fatty acid (SCFA) of significant physiological importance than the other major SCFAs (acetate and propionate). Most butyrate producers belong to the Clostridium cluster of the phylum Firmicutes, such as Faecalibacterium, Roseburia, Eubacterium, Anaerostipes, Coprococcus, Subdoligranulum, and Anaerobutyricum. They metabolize carbohydrates via the butyryl-CoA: acetate CoA-transferase pathway and butyrate kinase terminal enzymes to produce most of butyrate. Although, in minor fractions, amino acids can also be utilized to generate butyrate via glutamate and lysine pathways. Butyrogenic microbes play a vital role in various gut-associated metabolisms. Butyrate is used by colonocytes to generate energy, stabilizes hypoxia-inducible factor to maintain the anaerobic environment in the gut, maintains gut barrier integrity by regulating Claudin-1 and synaptopodin expression, limits pro-inflammatory cytokines (IL-6, IL-12), and inhibits oncogenic pathways (Akt/ERK, Wnt, and TGF-β signaling). Colonic butyrate producers shape the gut microbial community by secreting various anti-microbial substances, such as cathelicidins, reuterin, and β-defensin-1, and maintain gut homeostasis by releasing anti-inflammatory molecules, such as IgA, vitamin B, and microbial anti-inflammatory molecules. Additionally, butyrate producers, such as Roseburia, produce anti-carcinogenic metabolites, such as shikimic acid and a precursor of conjugated linoleic acid. In this review, we summarized the significance of butyrate, critically examined the role and relevance of butyrate producers, and contextualized their importance as microbial therapeutics.

The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation

A demonstration of cellulose degrading bacterium from human gut changed our view that human cannot degrade the cellulose. However, investigation of cellulose degradation by human gut microbiota on molecular level has not been completed so far. We showed here, using cellobiose as a model that promoted the growth of human gut key members, such as Bacteroides ovatus (BO), to clarify the molecular mechanism. Our results showed that a new polysaccharide utilization locus (PUL) from BO was involved in the cellobiose capturing and degradation. Further, two new cellulases BACOVA_02626GH5 and BACOVA_02630GH5 on the cell surface performed the degradation of cellobiose into glucose were determined. The predicted structures of BACOVA_02626GH5 and BACOVA_02630GH5 were highly homologous with the cellulase from soil bacteria, and the catalytic residues were highly conservative with two glutamate residues. In murine experiment, we observed cellobiose reshaped the composition of gut microbiota and probably modified the metabolic function of bacteria. Taken together, our findings further highlight the evidence of cellulose can be degraded by human gut microbes and provide new insight in the field of investigation on cellulose.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides

Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.