Navigating the Gut Buffet: Control of Polysaccharide Utilization in Bacteroides spp

The interaction between various food components and intestinal microbiota improves human health through the gut-X axis: independently or synergistically

Food contains various components that improve health by affecting the gut microbiota, primarily by modulating its abundance or altering its diversity. Active substances in food have different effects on the gut microbiota when they act alone or in synergy, resulting in varying impacts on health. The bioactive compounds in food exert different effects on various gut microbiota through multiple pathways, thereby delaying or preventing different kinds of disease. The combination of two or more active compounds may have a synergistic effect, which can more effectively alter the gut microbiota and alleviate diseases through the microbiota-gut-organ axis. According to reports, multiple different food components have similar effects, some of which have been shown to have a synergistic effect on the gut microbiota to promote health. However, there is currently no systematic review of its synergistic effects and mechanisms. There may be more compounds with synergistic effects that have not yet been discovered, while their mechanisms of synergy and ways of impacting host health through the gut microbiota deserve further investigation. The purpose of this review is to systematically summarize the effects of different food components on intestinal flora and health, and further analyze the potential synergies between different food components. PubMed and Google Scholar databases were searched in this review.

Bridging dietary polysaccharides and gut microbiome: How to achieve precision modulation for gut health promotion

Dietary polysaccharides function not only as indispensable nutrients and energy sources for the host organism but also as critical substrates for the gut microbiota. Gut microorganisms possess the ability to selectively degrade and metabolize specific dietary polysaccharides, thus fostering their proliferation and yielding crucial bioactive metabolites that potentially influence host metabolic and immune pathways. Dysbiosis of the gut microbiota has been extensively documented to be closely linked with the onset and progression of various diseases; in this regard, the precision modulation strategy of the gut microbiome via dietary polysaccharides holds substantial potential to enhance human health. Here, we delve into the therapeutic potential of dietary polysaccharides for the precision modulation of specific gut microorganisms via dietary interventions, with particular emphasis on their implications for the prevention and management of metabolic and inflammatory disorders. Given the complexity of the human gut microbiome and the varying degrees to which different bacterial members utilize carbohydrates, we conduct an in-depth analysis of the differential utilization of dietary polysaccharides by key gut microbiome, with particular emphasis on the role of carbohydrate-active enzymes in these processes. Furthermore, we elucidate the pivotal role of carbohydrate utilization within microbial cross-feeding networks and its significance in maintaining gut homeostasis. In summary, this review investigates the precision modulation of gut microbiota through dietary polysaccharides, with the aim of establishing a theoretical foundation for the development of personalized nutritional interventions. These strategies hold substantial potential for enhancing human health and offer valuable opportunities for the prevention and treatment of microbiota-associated diseases.

Differences in utilization and metabolism of Ulva lactuca polysaccharide by human gut Bacteroides species in the in vitro fermentation

Ulva lactuca polysaccharide (ULP), a sulfated polysaccharide, has been widely used in Asia. However, its digestion process and utilization by gut microbiota remain poorly understood. In this study, the in vitro simulated digestion and fermentation were used to analyze the digestibility of ULP. The results showed that ULP was not degraded during simulated digestion, but was utilized by human fecal microbiota. 16S rRNA sequencing revealed that ULP significantly increased the abundance of Bacteroides. Further evaluation of seven Bacteroides species showed that only B. thetaiotaomicron and B. vulgatus could utilize ULP. Interestingly, these two species exhibited different utilization patterns. B. vulgatus preferentially utilized rhamnose of ULP over glucuronic acid to promote growth. Metabolite profiles of B. thetaiotaomicron and B. vulgatus during in vitro fermentation with ULP as the sole carbon source were different. Although both B. thetaiotaomicron and B. vulgatus utilized ULP to produce various metabolites such as acetic acid, propionic acid, cysteic acid and riboflavin, B. thetaiotaomicron accumulated metabolites, such as linoleic acid, that were not accumulated by B. vulgatus. The effects of ULP on the metabolic pathways of B. thetaiotaomicron and B. vulgatus differed. These findings provide a new perspective on the utilization of ULP by human gut microbiota.

A Nitrate/Nitrite Biosensor Designed with an Antiterminator for In Vivo Diagnosis of Colitis Based on Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a common microorganism in the human gut that has been linked to health benefits. Furthermore, it is an emerging synthetic biology chassis with the potential to be modified into diagnostic or therapeutic engineered probiotics. However, the absence of biological components limits its further applications. In this study, we developed an antiterminator microbial whole-cell biosensor (MWCB) based on B. thetaiotaomicron. The antiterminator-based element allows the chassis to detect colitis in mice by responding to nitrate and nitrite in an inflammatory environment. In particular, the nitrate/nitrite-inducible promoter was obtained by combining the constitutive promoter with the inducible terminator. Subsequently, the promoter and RBS were replaced to optimize a sensitive and specific response to nitrate/nitrite. A preliminary in vitro assessment was conducted to ascertain the functionality of the biosensor. Its in vivo sensing ability was evaluated in a chemically induced mouse model of ulcerative colitis (UC). The results demonstrated that the MWCB exhibited a robust response to colitis, with a notable positive correlation between the intensity of the response and the level of inflammation. This novel sensing element may provide a new avenue for the development of components for unconventional chassis, like B. thetaiotaomicron. It will also facilitate the development of engineered probiotics based on B. thetaiotaomicron, thereby providing patients with a wider range of medical treatment options.

Harnessing the polysaccharide production potential to optimize and expand the application of probiotics

Certain probiotic microorganisms can synthesize important bioproducts, including polysaccharides as components of cellular structure or extracellular matrix. Probiotic-derived polysaccharides have been widely applied in food, pharmaceutical, and medical fields due to their excellent properties and biological activities. The development of polysaccharide production potential has become a driving force for facilitating biotechnological applications of probiotics. Based on technical advances in synthetic biology, significant progress has recently been made in engineering probiotics with efficient biosynthesis of polysaccharides. Herein, this review summarizes probiotics chassis and genetic tools used for polysaccharide production. Then, probiotic polysaccharides and relevant biosynthesis mechanisms are also clearly described. Next, we introduce strategies for preparing high-yield, controllable molecular weight or non-native polysaccharides by adjusting metabolic pathways and integrating expression elements in probiotics. Finally, some prospective and well-established contributions of exogenous and in situ polysaccharides in probiotics' stability, bioactivity, and therapeutic effects are presented. Our viewpoints on advancing the efficient biomanufacturing of valuable biopolymers in probiotics and engineering probiotics with customized features are provided to exploit probiotics' industrial and biomedical applications.

Transcriptional delineation of polysaccharide utilization loci in the human gut commensal Segatella copri DSM18205 and co-culture with exemplar Bacteroides species on dietary plant glycans

There is growing interest in members of the genus Segatella (family Prevotellaceae) as members of a well-balanced human gut microbiota (HGM). Segatella are particularly associated with the consumption of a diet rich in plant polysaccharides comprising dietary fiber. However, understanding of the molecular basis of complex carbohydrate utilization in Segatella species is currently incomplete. Here, we used RNA sequencing (RNA-seq) of the type strain Segatella copri DSM 18205 (previously Prevotella copri CB7) to define precisely individual polysaccharide utilization loci (PULs) and associated carbohydrate-active enzymes (CAZymes) that are implicated in the catabolism of common fruit, vegetable, and grain polysaccharides (viz. mixed-linkage β-glucans, xyloglucans, xylans, pectins, and inulin). Although many commonalities were observed, several of these systems exhibited significant compositional and organizational differences vis-à-vis homologs in the better-studied Bacteroides (sister family Bacteroidaceae), which predominate in post-industrial HGM. Growth on β-mannans, β(1, 3)-galactans, and microbial β(1, 3)-glucans was not observed, due to an apparent lack of cognate PULs. Most notably, S. copri is unable to grow on starch, due to an incomplete starch utilization system (Sus). Subsequent transcriptional profiling of bellwether Ton-B-dependent transporter-encoding genes revealed that PUL upregulation is rapid and general upon transfer from glucose to plant polysaccharides, reflective of de-repression enabling substrate sensing. Distinct from previous observations of Bacteroides species, we were unable to observe clearly delineated substrate prioritization on a polysaccharide mixture designed to mimic in vitro diverse plant cell wall digesta. Finally, co-culture experiments generally indicated stable co-existence and lack of exclusive competition between S. copri and representative HGM Bacteroides species (Bacteroides thetaiotaomicron and Bacteroides ovatus) on individual polysaccharides, except in cases where corresponding PULs were obviously lacking.

IMPORTANCE

There is currently a great level of interest in improving the composition and function of the human gut microbiota (HGM) to improve health. The bacterium Segatella copri is prevalent in people who eat plant-rich diets and is therefore associated with a healthy lifestyle. On one hand, our study reveals the specific molecular systems that enable S. copri to proliferate on individual plant polysaccharides. On the other, a growing body of data suggests that the inability of S. copri to grow on starch and animal glycans, which dominate in post-industrial diets, as well as host mucin, contributes strongly to its displacement from the HGM by Bacteroides species, in the absence of direct antagonism.

Preventive potential of chitosan self-assembled coconut residue dietary fiber in hyperlipidemia: Mechanistic insights into gut microbiota and short-chain fatty acids

Hyperlipidemia is a metabolic disorder resulted from unhealthy dietary and lifestyle habits. Its pathogenesis is possibly linked to gut microbiota dysbiosis. This study investigates the preventive effects of chitosan self-assembled coconut residue dietary fiber (CRFSC) on hyperlipidemia induced by a high-fat diet (HFD) and gut microbiota. CRFSC resulted in a significant weight loss of 7.9% in HFD rats and had a preventive effect on all four lipid parameter abnormalities. HFD supplemented with oat group resulted in a weight loss of 3.8% in HFD rats and had no preventive effect on low-density lipoprotein cholesterol (LDL-C) abnormalities. Prevention was achieved not only through the modulation of gut microbiota composition and the increase of short-chain fatty acids (SCFAs) levels, but also through the activation of superoxide dismutase enzyme and the inhibition of malondialdehyde accumulation, all of which are the factors leading to the controlling of lipid abnormalities and oxidative damage. The prevention of lipid parameters by chitosan self-assembled coconut residue dietary fiber (CRFSC) may be attributed to its richness in chitosan and insoluble dietary fiber, as well as its ability to enrich beneficial bacteria such as Akkermansia, Roseburia, and Ruminococcus. Correlation analysis demonstrated that key bacterial species producing SCFAs, which are rich in the CRFSC diet, had a positive impact on controlling hyperlipidemia. Hence, consumption of a CRFSC diet could serve as an effective strategy for preventing and controlling the development of hyperlipidemia due to its potential ability to regulate gut microbiota and SCFAs. PRACTICAL APPLICATION: This study showed that dietary fiber from coconut residue after chitosan self-assembly had preventive effects on overweight, dyslipidemia, and oxidative damage in rats. In addition, CRFSC also increased the content of short-chain fatty acids in the gut. And improve gut health by affecting gut microbiota. This finding suggests that CRFSC can be used as a dietary strategy to prevent hyperlipidemia and has practical significance in developing new healthy foods.

The antibacterial activity of a prophage-encoded fitness factor is neutralized by two cognate immunity proteins

The human gastrointestinal tract is a competitive environment inhabited by dense polymicrobial communities. Bacteroides, a genus of Gram-negative anaerobes, are prominent members of this ecological niche. Bacteroides spp. uses a repertoire of mechanisms to compete for resources within this environment such as the delivery of proteinaceous toxins into neighbouring competitor bacteria and the ability to consume unique metabolites available in the gut. In recent work, Bacteroides stercoris gut colonization was linked to the activity of a prophage-encoded ADP-ribosyltransferase, which was found to stimulate the release of the metabolite inosine from host epithelial cells. This fitness factor, termed Bxa, shares a similar genomic arrangement to bacterial toxins encoded within interbacterial antagonism loci. Here, we report that Bxa also possesses antibacterial ADP-ribosyltransferase activity, raising the question of how Bxa-producing bacteria resist intoxication prior to Bxa's release from cells. To this end, we identify two cognate immunity proteins, Bsi and BAH, that neutralize Bxa's antibacterial activity using distinct mechanisms. BAH acts as an enzymatic immunity protein that reverses Bxa ADP-ribosylation whereas Bsi physically interacts with Bxa and blocks its ADP-ribosylation activity. We also find that the N-terminal domain of Bxa is dispensable for toxicity and homologous domains in other bacteria are fused to a diverse array of predicted toxins found throughout the Bacteroidaceae, suggesting that Bxa belongs to a broader prophage encoded polymorphic toxin system. Overall, this work shows that Bxa is a promiscuous ADP-ribosyltransferase and that B. stercoris possesses mechanisms to protect itself from the toxic activity of this prophage encoded fitness factor.

The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization

The bacterium Segatella copri is a prevalent member of the human gut microbiota associated with health and disease states. However, the intrinsic factors that determine its ability to colonize the gut effectively remain largely unknown. By extensive transcriptome mapping of S. copri and examining human-derived samples, we discover a small RNA, which we name Segatella RNA colonization factor (SrcF), and show that SrcF is essential for S. copri gut colonization in gnotobiotic mice. SrcF regulates genes involved in nutrient acquisition, and complex carbohydrates, particularly fructans, control its expression. Furthermore, SrcF expression is strongly influenced by human microbiome composition and by the breakdown of fructans by cohabitating commensals, suggesting that the breakdown of complex carbohydrates mediates interspecies signaling among commensals beyond its established function in generating energy. Together, this study highlights the contribution of a small RNA as a critical regulator in gut colonization.

Screening and Functional Prediction of Rumen Microbiota Associated with Methane Emissions in Dairy Cows

Agricultural activities are a significant contributor to global greenhouse gas emissions, accounting for 14.5% of total anthropogenic emissions. Specifically, greenhouse gas emissions from beef cattle and dairy cattle constitute 35% and 30% of total global livestock emissions, respectively. This study focuses on dairy cattle, exploring the complex relationships between rumen microbiota and methane emission. The methane emissions of 968 lactating Holstein cows were measured using a laser methane detector (LMD, Shanghai Hesai Technology Co., Ltd., Shanghai, China). Among the measured cows, 107 individuals were further selected into high (HME) and low methane-emitting (LME) groups, including 50 cows in the HME group and 57 in the LME group. This study analyzed differences in rumen microbiota and microbial functions between cows with varying levels of methane emissions. The results showed significant differences in the Simpson and Pielou indices of rumen bacterial communities between the HME and LME groups. Beta diversity analysis revealed significant differences in microbial community structure between the two groups. It was found that the abundance of Bacteroidales and Prevotellaceae in the rumen of cows in the HME group cows was significantly higher than that of cows in the LME group (LDA > 3, p < 0.05). Additionally, bacterial functions related to biosynthesis and carbohydrate metabolism were more active in the HME group. This study revealed distinct differences in the rumen bacterial communities between HME and LME cow in Chinese Holstein cattle, and identified specific bacteria and their functional differences in the HME group. The microbial characteristics and metabolic pathways provide new insights for developing strategies to reduce methane emissions, supporting the sustainable development of the dairy industry.

Determinants of raffinose family oligosaccharide use in Bacteroides species

Bacteroides species are successful colonizers of the human colon and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in polysaccharide utilization loci (PULs). While recent work has uncovered the PULs required for the use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under the control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in a subset and showed that representative strains of species with a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.

IMPORTANCE

The gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the microbiota in the colon since they remain undigested by the host. Here, we study how the model commensal organism, Bacteroides thetaiotaomicron utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.

Fucoidan modulates gut microbiota and immunity in Peyer's patches against inflammatory bowel disease

Although fucoidan has potential use as an anti-inflammatory agent, the specific mechanisms by which it influences signaling and immunomodulatory pathways between gut microbiota and Peyer's patches remain unclear. Therefore, the aim of this study was to investigate the therapeutic potential of fucoidan in a dextran sulfate sodium (DSS)-induced mouse model of inflammatory bowel disease (IBD) by examining the effects on gut microbiota and the underlying anti-inflammatory mechanisms. Purified fucoidan, which upon characterization revealed structural fragments comprising →3)-β-D-Galp-(1→, →4)-α-L-Fucp-(1→, and →3)-α-L-Fucp-(1→ residues with a sulfation at position C2 was used. Treatment of the mice with fucoidan significantly alleviated the symptoms of IBD and restored the diversity of gut microbiota by enhancing the abundance of Bacteroidetes and reducing the proportion of Firmicutes. The administration of fucoidan also elevated levels of short-chain fatty acids while reducing the levels of pro-inflammatory cytokines, including interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and interferon (IFN)-γ. Most importantly, fucoidan attenuated the expression of integrin α4β7/MAdCAM-1 and CCL25/CCR9, which are involved in homing intestinal lymphocytes within Peyer's patches. These findings indicate that fucoidan is a promising gut microbiota modulator and an anti-inflammatory agent for IBD.

Didymin Ameliorates Dextran Sulfate Sodium (DSS)-Induced Ulcerative Colitis by Regulating Gut Microbiota and Amino Acid Metabolism in Mice

Background: Didymin is a dietary flavonoid derived from citrus fruits and has been shown to have extensive biological functions, especially anti-inflammatory effects, but its mechanism is unclear. The purpose of this study was to investigate the potential mechanism of didymin that alleviates ulcerative colitis. Methods and Results: Our results indicated that didymin could alleviate the symptoms of ulcerative colitis, as it inhibited the expressions of interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α). Didymin also promoted the expressions of claudin-1 and zona occludens-1(ZO-1), which are closely related with restoring colon barrier function. Didymin also increased the abundance of Firmicutes and Verrucomicobiota, while decreasing the abundance of Bacteroidota and Proteobacteria. Meanwhile, didymin significantly altered the levels of metabolites related to arginine synthesis and metabolism, and lysine degradation in the colitis mice. Utilizing network pharmacology and molecular docking, our results showed that the metabolites L-ornithine and saccharin could interact with signal transducer and activator of transcription 3 (STAT3) and nuclear factor kappa-B (NF-κB). In this in vitro study, L-ornithine could reduce the expressions of transcription factors STAT3 and NF-κB, and it also inhibited the expressions of IL-6 and IL-1β in the lipopolysaccharides (LPS) induced in RAW264.7 cells, while saccharin had the opposite effect. Conclusions: Taken together, didymin can regulate gut microbiota and alter metabolite products, which can modulate STAT3 and NF-κB pathways and inhibit the expressions of inflammatory factors and inflammatory response in the DSS-induced colitis mice.

In vivo absorption and fecal excretion of polysaccharides from the fruits of Lycium barbarum L. in rats through fluorescence labeling

In the present study, the in vivo absorption and fecal excretion of a purified fraction of polysaccharides from the fruits of Lycium barbarum L. (LBPs-4) in rats were investigated by labelling LBPs-4 with fluorescein isothiocyanate (FITC). It was found that the fluorescent labeled LBPs-4 (LBPs-4-FITC) was not detected in the plasma within 24 h following the administration of a single dose of LBPs-4-FITC (100 mg/kg of body weight) to rats, indicating that LBPs-4 was hardly absorbed in its prototype form. Instead, a smaller fragment dissociated from LBPs-4-FITC was observed in feces and was accumulated in a time-dependent manner, suggesting that LBPs-4 was excreted into the feces with a form of degradation. Meanwhile, we observed that LBPs-4-FTIC could modulate the fecal bacterial community profile via increasing the relative abundances of Bacteroides ovatus and Alistipes and promote the production of acetic acid. Furthermore, the monoculture experiment confirmed that LBPs-4 could be metabolized into smaller fragment by B. ovatus, producing acetic acid. Collectively, our study provides information on the destiny of LBPs-4 after oral administration: non-absorbed but moved to the large intestine and catabolized by gut microbiota, especially B. ovatus.

Hypolipidemic Effects of Mesona chinensis Benth Polysaccharides with Different Structures and Molecular Weights

Four novel Mesona chinensis Benth polysaccharides were isolated using aqueous alcohol precipitation. Their molecular weights were determined using high-performance gel permeation chromatography: MA1 (2.3 kDa), MA2 (80.5 kDa), MA3 (180.9 kDa), and MA4 (635.2 kDa), and their compositions were analyzed using GC-MS. The polysaccharides were mainly D-glucose, D-galactose, L-Rhamnose, D-arabinose, D-xylose, and D-mannose. The structural characteristics were further analyzed using infrared spectrophotometry and were identified as a type of pyrrhic sugar. An insulin-induced insulin resistance model of HepG2 cells and oleic acid-induced fat accumulation model of insulin were established to evaluate the hypolipidemic effects. Three Bacteroides spp. [Bacteroides thetaiotaomicron (BT), B. ovatus (BO), and B. cellulosilyticus (BC)] that were negatively correlated with lipid-lowering activity were used to evaluate the lipid-lowering activity of polysaccharides. The Bacteroides metabolites of MA1 and MA2 exhibited hypolipidemic effects and antioxidant activities and could potentially be used as lipid-lowering supplements.

Advancements in gene editing technologies for probiotic-enabled disease therapy

Probiotics typically refer to microorganisms that have been identified for their health benefits, and they are added to foods or supplements to promote the health of the host. A growing number of probiotic strains have been identified lately and developed into valuable regulatory pharmaceuticals for nutritional and medical applications. Gene editing technologies play a crucial role in addressing the need for safe and therapeutic probiotics in disease treatment. These technologies offer valuable assistance in comprehending the underlying mechanisms of probiotic bioactivity and in the development of advanced probiotics. This review aims to offer a comprehensive overview of gene editing technologies applied in the engineering of both traditional and next-generation probiotics. It further explores the potential for on-demand production of customized products derived from enhanced probiotics, with a particular emphasis on the future of gene editing in the development of live biotherapeutics.

Oral Microto-Nano Genome-Editing System Enabling Targeted Delivery and Conditional Activation of CRISPR-Cas9 for Gene Therapy of Inflammatory Bowel Disease

The potent CRISPR-Cas9 technology can correct genes in human mutated cells to achieve the treatment of multiple diseases, but it lacks safe and effective delivery systems. Herein, we proposed an oral microto-nano genome-editing system aiming at the enteric excessive level of TNF-α for specific gene therapy of inflammatory bowel disease (IBD). This editing system facilitated the assembly of Cas9/sgRNA ribonucleoprotein (RNP) into nanoclusters (NCs) through the bridging of disulfide bonds. RNP-NCs were subsequently encapsulated within inflammatory cell-targeted lipopolysaccharide-deleted outer membrane vesicles (dOMVs) sourced from Escherichia coli Nissle 1917, which were further shielded by an outer layer of calcium alginate microspheres (CAMs). By leveraging the protection effect of CAMs, the oral administration system withstood gastric acid degradation upon entry into the stomach, achieving targeted delivery to the intestines with high efficiency. As the pH gradually rose, the microscale CAMs swelled and disintegrated, releasing nanoscale RNP-NCs encapsulated in dOMVs into the intestines. These RNP-NCs@dOMVs could traverse the mucosal barrier and target inflammatory macrophages where conditionally activated Cas9/sgRNA RNPs effectively perform genomic editing of TNF-α within the nucleus. Such oral microto-nano genome-editing systems represent a promising translational platform for the treatment of IBD.

Interplay between traditional Chinese medicine polysaccharides and gut microbiota: The elusive "polysaccharides-bond-bacteria-enzyme" equation

Polysaccharides are one of the most important components of traditional Chinese medicine (TCM) and have been extensively studied for their immunomodulatory properties. The functions and effects of TCM polysaccharides are closely related to the gut microbiota, making the study of their interaction a hot topic in the field of TCM metabolism. This review follows two main inquiries: first, how the gut microbiota breaks down TCM polysaccharides to produce bioactive metabolites; and second, how TCM polysaccharides reshape the gut microbiota as a carbon source. Understanding the interaction mechanism involves a challenging equation of the structural association of TCM polysaccharides with the metabolic activities of the microbiota. This review has meticulously searched, partially organized literature spanning the past decade, that delves into the interaction mechanism between TCM polysaccharides and gut microbiota. It also gives an overview of the complex factors of the elusive "polysaccharides-bond-bacteria-enzyme" equation: the complexity of polysaccharide structures, the diversity of glycosidic bond types, the communal nature of metabolizing microbiota, the enzymes involved in functional degradation by microbiota, and the hierarchical roles of polysaccharide utilization locus and gram-positive PULs. Finally, this review aims to facilitate discussion among peers in the field of TCM microbiota and offers prospects for research in related fields, paving the way for pharmacological studies on TCM polysaccharides and gut microbiota therapeutics, and providing a reference point for further clinical research.

Structural properties of glucan from Russula griseocarnosa and its immunomodulatory activities mediated via T cell differentiation

The polysaccharide, RGP2, was isolated from Russula griseocarnosa and its immunostimulatory effects were confirmed in cyclophosphamide (CTX)-induced immunosuppressed mice. Following purification via chromatography, structural analysis revealed that RGP2 had a molecular weight of 11.82 kDa and consisted of glucose (Glc), galactose (Gal), mannose, glucuronic acid and glucosamine. Bond structure analysis and nuclear magnetic resonance characterization confirmed that the main chain of RGP2 was formed by →6)-β-D-Glcp-(1→, →3)-β-D-Glcp-(1→ and →6)-α-D-Galp-(1→, which was substituted at O-3 of →6)-β-D-Glcp-(1→ by β-D-Glcp-(1→. RGP2 was found to ameliorate pathological damage in the spleen and enhance immune cell activity in immunosuppressed mice. Based on combined multiomics analysis, RGP2 altered the abundance of immune-related microbiota (such as Lactobacillus, Faecalibacterium, and Bacteroides) in the gut and metabolites (uridine, leucine, and tryptophan) in the serum. Compared with immunosuppressed mice, RGP2 also restored the function of antigen-presenting cells, promoted the polarization of macrophages into the M1 phenotype, positively affected the differentiation of helper T cells, and inhibited regulatory T cell differentiation through the protein kinase B (AKT)/mechanistic target of rapamycin (mTOR) pathway, ultimately exerting an immune boosting function. Overall, our findings highlight therapeutic strategies to alleviate CTX-induced immunosuppression in a clinical setting.

Astragalus polysaccharides-induced gut microbiota play a predominant role in enhancing of intestinal barrier function of broiler chickens

BACKGROUND

The intestinal barrier is the first line of defense against intestinal invasion by pathogens and foreign antigens and is closely associated with the gut microbiota. Astragalus polysaccharides (APS) have a long history of use in traditional Chinese medicine owing to its protective properties against intestinal barrier function. The mechanism of APS-induced gut microbiota enhancing intestinal barrier function is urgently needed.

RESULTS

Dietary polysaccharide deprivation induced intestinal barrier dysfunction, decreased growth performance, altered microbial composition (Faecalibacterium, Dorea, and Coprobacillus), and reduced isobutyrate concentration. The results showed that APS facilitates intestinal barrier function in broiler chickens, including a thicker mucus layer, reduced crypt depth, and the growth of tight junction proteins. We studied the landscape of APS-induced gut microbiota and found that APS selectively promoted the growth of Parabacteroides, a commensal bacterium that plays a predominant role in enhancing intestinal barrier function. An in vitro growth assay further verified that APS selectively increased the abundance of Parabacteroides distasonis and Bacteroides uniformis. Dietary APS supplementation increased the concentrations of isobutyrate and bile acid (mainly chenodeoxycholic acid and deoxycholate acid) and activated signaling pathways related to intestinal barrier function (such as protein processing in the endoplasmic reticulum, tight junctions, and adherens junction signaling pathways).

CONCLUSIONS

APS intervention restored the dietary polysaccharide-induced dysfunction of the intestinal barrier by selectively promoting the abundance of Parabacteroides distasonis, and increasing the concentrations of isobutyrate and bile acids (mainly CDCA and DCA). These findings suggest that APS-induced gut microbiota and metabolic niches are promising strategies for enhancing intestinal barrier function.

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.

Degradation and fermentation of hyaluronic acid by Bacteroides spp. from the human gut microbiota

Bacteroides spp. are prominent members of the human gut microbiota that play critical roles in the metabolism of complex carbohydrates from the daily diet. Hyaluronic acid (HA) is a multifunctional polysaccharide which has been extensively used in the food and biomedical industry. However, how HA is degraded and fermented by Bacteroides spp. has not been fully characterized. Here, we comprehensively investigated the detailed degradation profiles and fermentation characteristics of four different HAs with discrete molecular weight (Mw) by fourteen distinctive Bacteroides spp. from the human gut microbiota. Our results indicated that high-Mw HAs were more degradable and fermentable than low-Mw HAs. Interestingly, B. salyersiae showed the best degrading capability for both high-Mw and low-Mw HAs, making it a keystone species for HA degradation among Bacteroides spp.. Specifically, HA degradation by B. salyersiae produced significant amounts of unsaturated tetrasaccharide (udp4). Co-culture experiments indicated that the produced udp4 could be further fermented and utilized by non-proficient HA-degraders, suggesting a possible cross-feeding interaction in the utilization of HA within the Bacteroides spp.. Altogether, our study provides novel insights into the metabolism of HA by the human gut microbiota, which has considerable implications for the development of new HA-based nutraceuticals and medicines.

Determinants of raffinose family oligosaccharide use in Bacteroides species

Bacteroides species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.

The Utilization by Bacteroides spp. of a Purified Polysaccharide from Fuzhuan Brick Tea

In the present study, four Bacteroides species that could degrade Fuzhuan brick tea polysaccharide-3 (FBTPS-3) were isolated from human feces and identified to be Bacteroides ovatus, B. uniformis, B. fragilis and B. thetaiotaomicron. The four Bacteroides species showed growth on FBTPS-3 as the carbon source, and B. ovatus showed the best capability for utilizing FBTPS-3 among the four species since B. ovatus could utilize more FBTPS-3 during 24 h fermentation. Moreover, the four Bacteroides species could metabolize FBTPS-3 and promote the production of acetic, propionic and isovaleric acids. Transcriptome analysis of B. ovatus revealed that 602 genes were up-regulated by FBTPS-3, including two carbohydrate-active enzyme clusters and four polysaccharide utilization loci (PULs). The PUL 1 contained GH28 family that could hydrolyze rhamnogalacturonan and other pectic substrates, which was in line with our previous work that rhamnose and galacturonic acid were the main component monosaccharides of FBTPS-3. Collectively, the results suggested that FBTPS-3 could be utilized by Bacteroides spp., and it might be developed as a promising prebiotic targeting Bacteroidetes in intestinal environment.

Microbiome Taxonomic and Functional Differences in C3H/HeJ Mice Fed a Long-Term High-Fat Diet with Beef Protein ± Ammonium Hydroxide Supplementation

Studies have suggested that alkalinized foods may reduce the effects of the acidogenic Western diet in promoting obesity, metabolic syndrome, type 2 diabetes, cancer, and coronary heart disease. Indeed, a recent study in mice fed a high-fat diet containing dietary beef supplemented with ammonium hydroxide showed improvement in a suite of metabolic outcomes. However, the effects of dietary protein ammonium supplementation on the microbiome remain unknown. In this study, the effects of ammonium supplementation on beef protein towards microbiome taxa and function in a high-fat diet were analyzed. Fecal microbiomes were characterized using a shotgun metagenomic approach for 16-month-old male and female mice after long-term diet treatments. The results for ammoniated diets showed that several bacteria known to be associated with health benefits increased significantly, including Romboutsia, Oscillospiraceae, and Lactococcus cremoris. The beneficial mucin-degrader Akkermansia was especially abundant, with a high prevalence (~86%) in females. Concurrently, the phyla Actinomycetota (Actinobacteria) and Bacteroidota (Bacteroidetes) were significantly reduced. While sex was a confounding factor affecting microbiome responses to ammonium supplementation in dietary protein, it is worth noting that several putatively beneficial microbiome functions increased with ammonium supplementation, such as glycine betaine transport, xenobiotic detoxification, enhanced defense, and others. Conversely, many disease-associated microbiome functions reduced. Importantly, modifying protein pH alone via ammonium supplementation induced beneficial microbiota changes. Taken together, these results suggest that ammonium-supplemented proteins may mediate some negative microbiome-associated effects of high-fat/Western diets.

Bifidobacterium adolescentis CCFM1285 combined with yeast β-glucan alleviates the gut microbiota and metabolic disturbances in mice with antibiotic-associated diarrhea

Antibiotic-associated diarrhea (AAD) is a self-limiting condition that can occur during antibiotic therapy. Our previous studies have found that a combination of Bacteroides uniformis and Bifidobacterium adolescentis can effectively alleviate AAD. However, the use of B. uniformis is still strictly limited. Therefore, this study attempted to use yeast β-glucan to enrich the abundance of B. uniformis in the intestine and supplement Bifidobacterium adolescentis to exert a synergistic effect. The lincomycin hydrochloride-induced AAD model was administered yeast β-glucan or a mixture of B. adolescentis CCFM1285 by gavage for one week. Subsequently, changes in the colonic histopathological structure, inflammatory factors, intestinal epithelial permeability and integrity, metabolites, and gut microbiota diversity were assessed. We found that yeast β-glucan, alone or in combination with B. adolescentis CCFM1285, can help attenuate systemic inflammation, increase the rate of tissue structural recovery, regulate metabolism, and restore the gut microbiota. Specifically, the combination of yeast β-glucan and B. adolescentis CCFM1285 was more effective in decreasing interleukin-6 levels, improving pathological changes in the colon, and upregulating occludin expression. Therefore, our study showed that the combination of yeast β-glucan and B. adolescentis CCFM1285 is an efficacious treatment for AAD.

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.

Caragana sinica (Buc'hoz) Rehd. (jin ji er) polysaccharide regulates the immune function and intestinal microbiota of cyclophosphamide (CTX) induced immunosuppressed mice

ETHNOPHARMACOLOGICAL RELEVANCE

Caragana sinica (Buc'hoz) Rehd. is a plant widely grown in Yunnan, China, for both medicinal and edible purposes. The "National Compilation of Chinese Herbal Medicine" describes its nature as "slightly temperate and sweet". Caragana sinica is usually medicated with whole herbs, the main function is to replenish the kidneys and stop bleeding. Caragana sinica was used in folk medicine in Chuxiong, Yunnan, to treat deficiency colds, fatigue, fever, cough, hypertension, and other diseases.

AIM OF THE STUDY

This article investigates the structural characteristics of Caragana sinica polysaccharide (CSP) and explores its immune-regulatory activity and molecular biological mechanisms in cyclophosphamide-induced immunosuppressed mice, as well as its effects on intestinal bacteria.

METHODS

With the water-extraction and alcohol-precipitation method, Caragana sinica polysaccharide were extracted, obtaining CSP by purification. A variety of methods and techniques have been used to analyze the chemical properties and structural characteristics of CSP. Immunosuppressive mice model was established through intraperitoneal injection of cyclophosphamide (CTX) to study the immune-regulatory effects and mechanisms of CSP.

RESULTS

The data indicated that CSP is a neutral heteropolysaccharide mainly composed of arabinose and galactose. This article uses immunosuppressive mice induced by cyclophosphamide (CTX) as the model. The results showed that CSP can promote the immune function of CTX treated immunosuppressed mice and regulate the diversity and composition of intestinal microbiota. CSP can increase macrophage phagocytosis, NK cell killing activity, and lymphocyte proliferation activity. It can also repair the index and morphological damage of the thymus and spleen. And by binding to the TLR4 receptor, MyD88 was activated and interacted with TRAF6 to promote the transfer of NF-κB into the nucleus. Thereby promoting cytokine release and increasing the production of IL-1β, IL-6, IL-10, TNF-α, IgA, and IgG in the serum. CSP also effectively alleviated the liver damage caused by CTX through antioxidant activity. Furthermore, CSP can dramatically affect the intestinal microbiota and the body's immunity by boosting the relative presence of Bacteroides and Verrucamicrobiota.

CONCLUSIONS

Research results indicated that CSP can regulate the immune function of mice, providing a basis for developing CSP as a potential immune modulator and functional food.

Bacteroides thetaiotaomicron metabolic activity decreases with polysaccharide molecular weight

The human colon hosts hundreds of commensal bacterial species, many of which ferment complex dietary carbohydrates. To transform these fibers into metabolically accessible compounds, microbes often express a series of dedicated enzymes homologous to the starch utilization system (Sus) encoded in polysaccharide utilization loci (PULs). The genome of Bacteroides thetaiotaomicron (Bt), a common member of the human gut microbiota, encodes nearly 100 PULs, conferring a strong metabolic versatility. While the structures and functions of individual enzymes within the PULs have been investigated, little is known about how polysaccharide complexity impacts the function of Sus-like systems. We here show that the activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth. We demonstrate the effect of size-dependent metabolism in the context of dextran metabolism driven by the specific utilization system PUL48. We find that as the molecular weight of dextran increases, Bt growth rate decreases and lag time increases. At the enzymatic level, the dextranase BT3087, a glycoside hydrolase (GH) belonging to the GH family 66, is the main GH for dextran utilization, and BT3087 and BT3088 contribute to Bt dextran metabolism in a size-dependent manner. Finally, we show that the polysaccharide size-dependent metabolism of Bt impacts its metabolic output in a way that modulates the composition of a producer-consumer community it forms with Bacteroides fragilis. Altogether, our results expose an overlooked aspect of Bt metabolism that can impact the composition and diversity of microbiota.

IMPORTANCE

Polysaccharides are complex molecules that are commonly found in our diet. While humans lack the ability to degrade many polysaccharides, their intestinal microbiota contain bacterial commensals that are versatile polysaccharide utilizers. The gut commensal Bacteroides thetaiotaomicron dedicates roughly 20% of their genomes to the expression of polysaccharide utilization loci for the broad range utilization of polysaccharides. Although it is known that different polysaccharide utilization loci are dedicated to the degradation of specific polysaccharides with unique glycosidic linkages and monosaccharide compositions, it is often overlooked that specific polysaccharides may also exist in various molecular weights. These different physical attributes may impact their processability by starch utilization system-like systems, leading to differing growth rates and nutrient-sharing properties at the community level. Therefore, understanding how molecular weight impacts utilization by gut microbe may lead to the potential design of novel precision prebiotics.

Modulating Gastrointestinal Microbiota in Preweaning Dairy Calves: Dose-Dependent Effects of Milk-Based Sodium Butyrate Supplementation

Sodium butyrate (SB), an essential nutritional additive for livestock, has drawn notable interest for its potential for enhancing microbiota development in ruminant animals. This study aimed to assess SB's effects on ruminal and intestinal microbiota when added to milk for preweaning dairy calves nearing 45 days old. We administered SB in the calves' milk at four levels: 0 g/d (control), 4.4 g/d (low), 8.8 g/d (medium), and 17.6 g/d (high). After a six-week trial with ten replicates per group, ruminal fluid and fecal samples were collected for 16S rRNA sequencing, specifically targeting the V3-V4 regions to analyze microbiota. The results indicated an enhancement in ruminal microbiota, particularly in community richness, with low-level SB supplementation but minimal benefits from medium and high levels of supplementation. Increasing the level of SB supplementation had a negative impact on intestinal microbiota, affecting community richness and some potentially beneficial bacterial genera. However, low SB supplementation could positively adjust the communication between ruminal and intestinal microbiota. Overall, this study suggests feeding milk supplemented with a low level of SB to suckling calves close to an older age to promote ruminal microbiota development.

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.

Insoluble/soluble fraction ratio determines effects of dietary fiber on gut microbiota and serum metabolites in healthy mice

Both soluble dietary fiber (SDF) and insoluble dietary fiber (IDF) play pivotal roles in maintaining gut microbiota homeostasis; whether the effects of the different ratios of IDF and SDF are consistent remains unclear. Consequently, we selected SDFs and IDFs from six representative foods (apple, celery, kale, black fungus, oats, and soybeans) and formulated nine dietary fiber recipes composed of IDF and SDF with a ratio from 1 : 9 to 9 : 1 (NDFR) to compare their impact on microbial effects with healthy mice. We discovered that NDFR treatment decreased the abundance of Proteobacteria and the ratio of Firmicutes/Bacteroidetes at the phylum level. The α diversity and relative richness of Parabacteroides and Prevotella at the genus level showed an upward trend along with the ratio of IDF increasing, while the relative abundance of Akkermansia at the genus level and the production of acetic acid and propionic acid exhibited an increased trend along with the ratio of SDF increasing. The relative abundance of Parabacteroides and Prevotella in the I9S1DF group (the ratio of IDF and SDF was 9 : 1) was 1.72 times and 5.92 times higher than that in the I1S9DF group (the ratio of IDF and SDF was 1 : 9), respectively. The relative abundance of Akkermansia in the I1S9DF group was 17.18 times higher than that in the I9S1DF group. Moreover, a high ratio of SDF (SDF reaches 60% or more) enriched the glycerophospholipid metabolism pathway; however, a high ratio of IDF (IDF reaches 80% or more) regulated the tricarboxylic acid cycle. These findings are helpful in the development of dietary fiber supplements based on gut microbiota and metabolites.

An overview of microbial enzymatic approaches for pectin degradation

Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.

Direct and Indirect Evidence of Effects of Bacteroides spp. on Obesity and Inflammation

Metabolic disorders present a significant public health challenge globally. The intricate relationship between the gut microbiome, particularly Bacteroides spp. (BAC), and obesity, including their specific metabolic functions, remains partly unresolved. This review consolidates current research on BAC's role in obesity and lipid metabolism, with three objectives: (1) To summarize the gut microbiota's impact on obesity; (2) To assess BAC's efficacy in obesity intervention; (3) To explore BAC's mechanisms in obesity and lipid metabolism management. This review critically examines the role of BAC in obesity, integrating findings from clinical and preclinical studies. We highlight the changes in BAC diversity and concentration following successful obesity treatment and discuss the notable differences in BAC characteristics among individuals with varying obesity levels. Furthermore, we review recent preclinical studies demonstrating the potential of BAC in ameliorating obesity and related inflammatory conditions, providing detailed insights into the methodologies of these in vivo experiments. Additionally, certain BAC-derived metabolites have been shown to be involved in the regulation of host lipid metabolism-related pathways. The enhanced TNF production by dendritic cells following BAC administration, in response to LPS, also positions BAC as a potential adjunctive therapy in obesity management.

Advancing the fitness of gut commensal bacteria

Nutrient starvation of beneficial bacteria helps them colonize the human gut.

Gut microbiota bridges dietary nutrients and host immunity

Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.

Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production

This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.

Regulatory effect of lactulose on intestinal flora and serum metabolites in colitis mice: In vitro and in vivo evaluation

Lactulose is a common component in foods. However, the effect of lactulose on intestinal flora and overall metabolic levels remains unclear. Therefore, this study aims to explore the regulative role of lactulose on intestinal flora and serum metabolites via in vitro simulated colonic fermentation model and in vivo colitis mouse model. The results showed that lactulose significantly enriched beneficial bacteria including Dubosiella and Bifidobacterium, and reduced pathogenic bacteria such as Fusobacterium. Moreover, lactulose significantly inhibited dextran sodium sulfate-induced body weight loss, colon shortening, colonic inflammatory infiltration, and pro-inflammatory cytokines IL-6, TNF-α, IL-17, and IL-1β. Lactulose significantly affected serum metabolome in colitis mice and total 24 metabolites representing a high inter-group difference were obtained. Correlation analysis revealed that the changes in serum metabolites were closely associated with the role of intestinal flora, and thus affected phenotypic indicators. Our study provides a reference for nutritional characteristics and application scenarios of dietary lactulose.

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.

Lifestyle patterns influence the composition of the gut microbiome in a healthy Chinese population

High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study-the Chinese Healthy Gut Project (n = 483)-where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.

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.

A Three-Arm, Randomized, Double-Blind, Placebo-Controlled Study to Evaluate the Safety of Lactobacillus salivarius AP-32 and Bifidobacterium animalis CP-9 Used Individually in Healthy Infants

Probiotics are considered safe and beneficial to human health. However, the safety of Lactobacillus salivarius AP-32 and Bifidobacterium animalis CP-9 in infants has not been confirmed. This study was to assess the safety of long-term oral administration of L. salivarius AP-32 and B. animalis CP-9 in healthy infants compared with placebo. A three-arm, randomized, double-blind, placebo-controlled trial was conducted in healthy, full-term infants. Eighty-eight infants between 7 days and 2 months (60 ± 7 days) of age were selected and randomized to treatment with L. salivarius AP-32, B. animalis CP-9 or placebo for 4 months. The unblinding indicated subjects were randomized to receive B. animalis CP-9 (N = 28), L. salivarius AP-32 (N = 29), or placebo (N = 31). A total of 76 infants completed the 4-month treatment with fully compliance. The primary outcome was weight gain, with no significant difference in infant weight at 4 months when comparing AP-32 or CP-9 group with the placebo group, either. The head circumference and recumbent length of the CP-9 group were not significantly different from those of the placebo group. The recumbent length of the AP-32 group was slightly lower than that in the placebo group at month 4, but there was no difference between the two groups in head circumference. Overall, the growth trend of all treatments was similar without significant difference. Furthermore, there were no apparent differences between each group in digestive tolerance, the occurrence of adverse events, crying/fussing time and episodes, alpha diversity, and beta diversity. The CP-9 group showed a significant increase in the abundance of the Bacteroides genus, while the AP-32 group demonstrated a significant increase in the abundance of the Lactobacillus genus when comparing the two probiotic groups. Our study findings indicate that the oral administration of both AP-32 and CP-9 strains has a positive impact on the maintenance of a healthy gut flora in infants. Long-term use of L. salivarius AP-32 or B. animalis CP-9 is safe for infants from 7 days to 6 months of age.

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression

Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not well understood. Here we developed and applied transposon mutagenesis to identify genes important for intestinal colonization and for the use of mucin. An analysis of transposon mutants indicated that de novo biosynthesis of amino acids was required for A. muciniphila growth on mucin medium and that many glycoside hydrolases are redundant. We observed that mucin degradation products accumulate in internal compartments within bacteria in a process that requires genes encoding pili and a periplasmic protein complex, which we term mucin utilization locus (MUL) genes. We determined that MUL genes were required for intestinal colonization in mice but only when competing with other microbes. In germ-free mice, MUL genes were required for A. muciniphila to repress genes important for cholesterol biosynthesis in the colon. Our genetic system for A. muciniphila provides an important tool with which to uncover molecular links between the metabolism of mucins, regulation of lipid homeostasis and potential probiotic activities.

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.

Integrated microbiota and metabolite profiling analysis of prebiotic characteristics of Phellinus linteus polysaccharide in vitro fermentation

Phellinus linteus polysaccharide (PLP) had received increasing attention due to its multiple biological activities. Herein, the extraction, characterization and in vitro fermentation of PLP were studied to explore its physiochemical properties and the interaction mechanism between the gut microbiota and PLP. The results obtained demonstrated that PLP was mainly composed of 9 monosaccharides, with three gel chromatographic peaks and molecular weights (M_w) of 308.45 kDa, 13.58 kD and 3.33 kDa, respectively. After 48 h fermentation, the M_w, total sugar, reducing sugar, pH and monosaccharides composition were decreased. Furthermore, PLP regulated the composition of gut microbiota, such as promoting the proliferation of beneficial bacteria such as Bacteroides, Prevotella and Butyricimonas, while preventing the growth of pathogenic bacteria such as Escherichia-Shigella, Morganella and Intestinimonas. Gut microbiota metabolites regulated by PLP such as short-chain fatty acids were the main regulators that impact the host health. Bioinformatics analysis indicated that butyrate, bile acid and purine metabolism were the main metabolic pathways of PLP regulating host health, and the Bacteroides was the key genus to regulate these metabolic pathways. In conclusion, our finding suggested that PLP may be used as a prebiotic agent for human health because of its ability to regulate gut microbiota.

Effects of Isaria cicadae on growth, gut microbiota, and metabolome of Larimichthys crocea

The large yellow croaker (Larimichthys crocea) is the most productive mariculture fish in China, and its aquaculture scale is expanding along the southeastern coast of China, but that development is causing environmental damage by increasing the use of antibiotics and other chemicals. How to improve fish immunity through non-antibiotic substances is still a problem facing aquaculture industry. At present, the experiments have shown that Isaria cicadae spent substrate (IC) can improve the growth performance and immunity of Oreochromis niloticus. Therefore, I. cicadae may be a natural alternative to antibiotic for aquaculture. In order to study the effects of IC on growth performance, serum biochemical indices, intestinal microbiota, and intestinal metabolism of large yellow croakers, the fish were divided into three groups with three replicates in each group. Basal diet, basal diet with 2% and 6% IC supplementation (IC2 and IC6 groups), respectively. The results showed that weight gain rate (WG) and specific growth rate (SGR) of large yellow croaker significantly increased (P < 0.05) in IC6 group. The content of triglyceride (TG), low density lipoprotein cholesterol (LDL-C), total protein (TP) and albumin (ALB) increased significantly (P < 0.05), and total cholesterol (T-CHO) decreased significantly (P < 0.05) in IC2 group. Compared to IC0 group, the activity of malondialdehyde (MDA) , superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) increased significantly (P < 0.05) in IC2 group, the activity of total antioxidant capacity (T-AOC) and GSH-Px increased significantly (P < 0.05) in IC6 group, and the activity of lysozyme (LZM) increased significantly in IC2 and IC6 groups. The addition of IC in the diets significantly increased the diversity of the microbial community in the intestine of large yellow croaker (P < 0.05), significantly improved the relative abundance of Acidobacteriota (P < 0.05) at the phylum level, and reduced the relative abundance of Bacteroidota, Desulfobacterota, and Synergistota (P < 0.05). At the genus level, the relative abundance of Bacteroides, Cetobacterium and Mycoplasma, which are dominant bacteria in fish gut, significantly increased (P < 0.05). The relative abundance of Ruminofilibacter, Desulfomicrobium, DMER64, Syntrophomonas, Hydrogenophaga, and Aminobacterium reduced significantly (P < 0.05). Among them, Ruminofilibacter, DMER64, Syntrophomonas and Hydrogenophaga are bacteria that can participate in the hydrolysis and acidification of organic matter, while DMER64 is the hydrogen carrier. The intestinal metabolome analysis showed that IC could improve metabolic composition and function, which was related to host immunity and metabolism. In conclusion, I. cicadae can improve the growth performance, regulate the lipid metabolism and immune and antioxidant capacity of large yellow croakers by regulating intestinal microbiota and intestinal metabolism. This study provides a reference for the application of IC in aquaculture.

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.

A structure defined pectin SA02B from Semiaquilegia adoxoides is metabolized by human gut microbes

Polysaccharide is one of the major factors for shaping the gut microbiota. However, bioactivity of polysaccharide isolated from Semiaquilegia adoxoides on human gut microbiota remains unclear. Thus, we hypothesize gut microbes may act on it. Herein, pectin SA02B from the roots of Semiaquilegia adoxoides with molecular weight 69.26 kDa was elucidated. The backbone of SA02B was composed of alternate 1, 2-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 4-, 1, 3- and 1, 3, 6-linked β-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf and T-, 1, 4-linked-β-Xylp substituted at C-4 of 1, 2, 4-linked α-Rhap. Bioactivity screening showed SA02B promoted the growth of Bacteroides spp. which deconstructed it into monosaccharide. Simultaneously, we observed competition might exist between Bacteroides spp. and probiotics. Besides, we found that both Bacteroides spp. and probiotics could generate SCFAs grown on SA02B. Our findings highlight SA02B may deserve as a prebiotic to be explored to benefit the health gut microbiota.

Sharing of Moonlighting Proteins Mediates the Symbiotic Relationship among Intestinal Commensals

The human gastrointestinal tract is inhabited by trillions of symbiotic bacteria that form a complex ecological community and influence human physiology. Symbiotic nutrient sharing and nutrient competition are the most studied relationships in gut commensals, whereas the interactions underlying homeostasis and community maintenance are not fully understood. Here, we provide insights into a new symbiotic relationship wherein the sharing of secreted cytoplasmic proteins, called "moonlighting proteins," between two heterologous bacterial strains (Bifidobacterium longum and Bacteroides thetaiotaomicron) was observed to affect the adhesion of bacteria to mucins. B. longum and B. thetaiotaomicron were cocultured using a membrane-filter system, and in this system the cocultured B. thetaiotaomicron cells showed greater adhesion to mucins compared to that shown by monoculture cells. Proteomic analysis showed the presence of 13 B. longum-derived cytoplasmic proteins on the surface of B. thetaiotaomicron. Moreover, incubation of B. thetaiotaomicron with the recombinant proteins GroEL and elongation factor Tu (EF-Tu)-two well-known mucin-adhesive moonlighting proteins of B. longum-led to an increase in the adhesion of B. thetaiotaomicron to mucins, a result attributed to the localization of these proteins on the B. thetaiotaomicron cell surface. Furthermore, the recombinant EF-Tu and GroEL proteins were observed to bind to the cell surface of several other bacterial species; however, the binding was species dependent. The present findings indicate a symbiotic relationship mediated by the sharing of moonlighting proteins among specific strains of B. longum and B. thetaiotaomicron. IMPORTANCE The adhesion of intestinal bacteria to the mucus layer is an important colonization strategy in the gut environment. Generally, the bacterial adhesion process is a characteristic feature of the individual cell surface-associated adhesion factors secreted by a particular bacterium. In this study, coculture experiments between Bifidobacterium and Bacteroides show that the secreted moonlighting proteins adhere to the cell surface of coexisting bacteria and alter the adhesiveness of the bacteria to mucins. This finding indicates that the moonlighting proteins act as adhesion factors for not only homologous strains but also for coexisting heterologous strains. The presence of a coexisting bacterium in the environment can significantly alter the mucin-adhesive properties of another bacterium. The findings from this study contribute to a better understanding of the colonization properties of gut bacteria through the discovery of a new symbiotic relationship between them.