Search Results (79)

Berberine (BBR), a protoberberine alkaloid with a long history of medicinal use, has consistently demonstrated benefits in glucose–lipid metabolism and inflammatory balance across both preclinical and human studies. These diverse effects are not mediated by a single molecular target but by BBR’s capacity to restore network coordination among metabolic, immune, and microbial systems. At the core of this regulation is an AMP-activated Protein Kinase (AMPK)-centered mechanistic hub, integrating signals from insulin and nutrient sensing, Sirtuin 1/3 (SIRT1/3)-mediated mitochondrial adaptation, and inflammatory pathways such as nuclear Factor Kappa-light-chain-enhancer of Activated B cells (NF-κB) and NOD-, LRR- and Pyrin Domain-containing Protein 3 (NLRP3). This hub is dynamically regulated by system-level inputs from the gut, mitochondria, and epigenome, which in turn strengthen intestinal barrier function, reshape microbial and bile-acid metabolites, improve redox balance, and potentially reverse the epigenetic imprint of metabolic stress. These interactions propagate through multi-organ axes, linking the gut, liver, adipose, and vascular systems, thus aligning local metabolic adjustments with systemic homeostasis. Within this framework, BBR functions as a negentropic modulator, reducing metabolic entropy by fostering a coordinated balance among these interconnected systems, thereby restoring physiological order. Combination strategies, such as pairing BBR with metformin, Sodium-Glucose Cotransporter 2 (SGLT2) inhibitors, and agents targeting the microbiome or inflammation, have shown enhanced efficacy and substantial translational potential. Berberine ursodeoxycholate (HTD1801), an ionic-salt derivative of BBR currently in Phase III trials and directly compared with dapagliflozin, exemplifies the therapeutic promise of such approaches. Within the hub–axis paradigm, BBR emerges as a systems-level modulator that recouples energy, immune, and microbial circuits to drive multi-organ remodeling. Full article

Outcomes of influenza virus infection vary widely across individuals, reflecting not only viral genetics and host factors but also the composition and function of the airway microbiome. Over the past few years, mechanistic work has clarified how specific commensals (for example, Staphylococcus epidermidis and Streptococcus oralis) restrict influenza replication by priming epithelial interferon-λ programs, reshaping intracellular metabolite pools (notably polyamines), dampening host protease activity, and maintaining barrier integrity; meanwhile, pathobionts (notably Staphylococcus aureus and Streptococcus pneumoniae) can enhance viral fitness via secreted proteases and neuraminidases that activate hemagglutinin and remodel sialylated glycoconjugates and mucus, setting the stage for secondary bacterial disease. Recent studies also highlight the gut–lung axis: gut microbiota-derived short-chain fatty acids (SCFAs), especially acetate, protect tight junctions and modulate antiviral immunity in influenza models. Together, these insights motivate translational strategies—from intranasal live biotherapeutics (LBPs) to metabolite sprays and decoy/dual neuraminidase approaches—that complement vaccines and antivirals. We synthesize recent evidence and outline a framework for leveraging the airway microbiome to prevent infection, blunt severity, and reduce transmission. Key priorities include strain-level resolution of commensal effects, timing/dosing windows for metabolites and LBPs, and microbiome-aware clinical pathways for anticipating and averting bacterial coinfection. Overall, the airway microbiome emerges as a tractable lever for influenza control at the site of viral entry, with several candidates moving toward clinical testing. Full article

Cherry tomatoes are highly appreciated for their nutritional value but remain highly perishable due to rapid respiration and senescence. This study evaluated a multi-hurdle strategy combining plasma-activated water (PAW), sodium caseinate-based edible coating, and antioxidant active packaging to preserve minimally processed (MP) cherry tomatoes stored at 1 °C, 4 °C, and 8 °C for 15 days. Quality evolution was monitored through physical, chemical, nutritional, and microbiological parameters and described using pseudo-zero- and first-order kinetic models, with temperature dependence expressed by the Arrhenius equation. The combined treatment (prototype) slowed the degradation rates of pH, titratable acidity, total polyphenols, and antioxidant capacity, as reflected by consistently lower kinetic rate constants across all temperatures. Prototype samples showed better retention of polyphenols and antioxidant capacity, particularly at 1 °C and 4 °C, without detrimental effects on visual appearance. Metagenomic analysis revealed that the multi-hurdle treatment reshaped the microbial community, reducing the relative abundance of potentially problematic taxa such as Acinetobacter johnsonii and limiting the occurrence of antimicrobial resistance (AMR) genes at the end of storage. This study provides the first integrated assessment of PAW, edible coating, and antioxidant active packaging as a synergistic multi-hurdle strategy, demonstrating their combined ability to extend shelf life while modulating the microbiome and resistome of minimally processed cherry tomatoes. Full article

Continuous cropping (CC) poses serious challenges to the sustainable production of Dioscorea opposita Thunb. cv. Tiegun yam. The aim of this study is to illustrate the formation mechanisms of CC obstacles by analyzing rhizosphere soil from yam fields with 0 to 2 years of replanting. Metabolomic and microbiome sequences were used to assess variations in yam yield, underground tuber traits, soil properties, metabolite profiles, and microbial communities. The results show that CC significantly reduced tuber yield, shortened stalk length, and altered tuber morphology, leading to the accumulation of soil available phosphorus and potassium and a notable decrease in pH. A total of 38 differentially expressed metabolites, including organoheterocyclic compounds, lipids, and benzenoids, were identified and linked to pathways such as starch and sucrose metabolism, linoleic acid metabolism, and ABC transporters. Microbial alpha diversity increased with CC duration, and both bacterial and fungal community structures were notably reshaped. Metabolite profiles correlated more strongly with fungal than bacterial communities. Partial least squares path modeling revealed that CC years had a negative indirect impact on tuber yield and morphology (the path coefficient was −0.956), primarily through direct effects on soil properties (p < 0.01) and metabolites (p < 0.001), which, in turn, influenced microbial diversity. These findings emphasize the vital role of soil properties in reshaping the rhizosphere environment under CC and provide a theoretical basis for mitigating CC obstacles through rhizosphere regulation. Full article

Soil-borne pathogens cause devastating root rot diseases in forest ecosystems, often by inducing dysbiosis in the rhizosphere microbiome. While antagonistic bacteria can suppress disease, their effects frequently extend beyond direct inhibition to include ecological restructuring of resident microbial communities. However, the causal relationships between such microbiome restructuring and disease suppression in tree species remain poorly understood. Here, we show that the antagonistic bacterium B. mojavensis dxk33 effectively suppresses F. solani-induced root rot in C. lanceolata, and that this disease suppression coincides with a partial reversal of pathogen-associated dysbiosis in the rhizosphere. Inoculation with dxk33 significantly promoted plant growth and reduced the disease index by 72.19%, while concurrently enhancing soil nutrient availability and key C-, N- and P-cycling enzyme activities. High-throughput sequencing revealed that dxk33 inoculation substantially reshaped the rhizosphere microbiome, counteracting the pathogen’s negative impact on microbial diversity and coinciding with a shift toward a more stable community structure. Under pathogen stress, dxk33 enriched beneficial bacterial taxa such as Pseudomonas and Sphingomonas and suppressed pathogenic fungi while promoting beneficial fungi such as Mortierella. Linear discriminant analysis and functional prediction further indicated that dxk33 remodeled ecological guilds enriched for mycorrhizal and saprotrophic fungi, and reactivated bacterial metabolic pathways and signaling networks that were suppressed by the pathogen. Taken together, our findings are consistent with a multi-tiered mode of action in which direct antagonism by B. mojavensis dxk33 operates alongside associated changes in the rhizosphere microbiome that resemble a disease-suppressive state, although the present experimental design does not allow a strictly causal role for microbiome reconfiguration in disease suppression to be established. This study provides a mechanistic framework for understanding how microbiome engineering may mitigate soil-borne diseases in perennial trees and highlights the potential of targeted microbial interventions for sustainable forest management. Full article

Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera and Pterocarpus macrocarpus (JD); and a composite mixed plantation of D. odorifera, P. macrocarpus, and Clinacanthus nutans (JDY). Using amplicon sequencing technology for soil microbial analysis and combining soil physical and chemical properties with disease severity, we comprehensively analyzed changes in soil microbial community structure and function across different planting modes. The results showed that the diverse mixed mode (JD, JDY) significantly improved soil physicochemical properties and promoted soil nutrient cycling. Redundancy analysis (RDA) indicated that soil organic matter (SOM) and disease severity, quantified by the area under the disease progress curve (AUDPC), were the primary environmental drivers of microbial community variation. Genera positively correlated with SOM and negatively correlated with AUDPC were significantly enriched in JDY and JD, whereas genera showing opposite relationships were predominantly enriched in J. Functional predictions revealed enhanced nutrient-cycling capacities in JD and JDY, with JDY uniquely harboring functional groups such as Arbuscular Mycorrhizal, Epiphyte, and Lichenized taxa. In contrast, microbial functions in the J plantation were mainly limited to environmental amelioration. Co-occurrence network analysis further showed that as planting patterns shifted from J to JDY, microbial communities evolved from competition-dominated networks to cooperative defensive networks, integrating efficient decomposition with strong pathogen suppression potential. The study demonstrates that complex mixed planting systems regulate soil properties, enhance the enrichment of key functional microbial taxa, reshape community structure and function, and ultimately enable ecological control of anthracnose disease. This study provides new perspectives and theoretical foundations for ecological disease management in plantations of rare tree species and for microbiome-based ecological immunization strategies. Full article

Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function. Full article

Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips’ body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips’ body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus–symbiont association contributes to thrips vector competence. Full article

The effectiveness of microbial inoculants in agriculture is often limited by their unstable colonization in dynamic soil environments. We investigated the impact of application timing and continuity of a four-member synthetic microbial community (SynCom) on pepper (Capsicum annuum L.) productivity and rhizosphere microbiome dynamics under greenhouse conditions. Four treatments were included: no inoculation (control), single inoculation at the seedling stage (T1; 5 days post-emergence), single inoculation at the potting stage (T2; 14 days post-transplant), and sustained inoculation at both stages (T3). T3 significantly enhanced plant dry weight (113.4%), root activity (267.8%), fruit sugar (43.9%), and yield (29.0%) relative to the control; and profoundly reshaped the rhizosphere microbiome, enriching functional pathways for nutrient cycling (e.g., phosphorus, nitrogen, and potassium metabolism) and phytohormone synthesis (e.g., indoleacetic acid pathway). Co-occurrence network analysis indicated a significant alteration in microbial interaction patterns, revealing a new community architecture with key taxa such as Neocosmospora, Dyella and the Rhizobium group emerging as central hubs in the T3 network. Our findings underscore that application continuity is a critical factor for optimizing bio-inoculant efficacy, providing a strategy to enhance crop productivity through microbiome engineering in sustainable agriculture. Full article

Allergic rhinitis (AR) is a common heterogeneous chronic disease characterized by high prevalence, complex pathogenesis, and susceptibility to multiple contributing factors. Currently, its prevalence ranges from 20% to 30% in adults and reaches up to 40% in children. Extensive research has confirmed significant differences in nasal microbiota composition between AR patients and healthy individuals, most notably alterations in the abundance of four dominant phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Among these, the most striking abundance alterations occur in Staphylococcus aureus and Streptococcus salivarius within the nasal mucosa of AR patients, suggesting a critical role of nasal microbiota in AR initiation and progression. In response, researchers have proposed microbiome-targeted therapeutic strategies. For example, nasal local administration of probiotics (e.g., Lactobacillus and Bifidobacterium) aims to reshape the nasal microbiota. Additionally, protective bacteria such as Corynebacterium accolens and Dolosigranulum pigrum can inhibit pathogenic bacteria, thereby correcting microbial dysbiosis and alleviating AR symptoms. This review summarizes the composition of the nasal microbiota, the latest research progress on its association with AR, and the underlying potential mechanisms. It provides novel insights and potential therapeutic strategies for the prevention and treatment of AR. Full article

Disruption of the gut-microbiome-brain axis contributes to the development of chronic inflammation, impaired intestinal barrier integrity, and progressive tissue damage, ultimately reducing quality of life and increasing risk of comorbidities, including neurodegenerative diseases. Current therapies are often limited by adverse effects and insufficient long-term efficacy, highlighting the need for more comprehensive therapeutic approaches. Berberine (BRB), a plant-derived isoquinoline alkaloid, has attracted growing attention due to its pleiotropic immunomodulatory, neuroprotective, and gut-homeostasis-modulating properties, which involve reshaping the gut microbiota and underscore its therapeutic relevance within the gut–microbiome–brain axis. The aim of this review is to synthesize current scientific evidence regarding the anti-inflammatory mechanisms of BRB in inflammatory bowel disease (IBD). We compare its activity with first-line therapies and discuss its impact on microbial composition, including the bidirectional regulation of specific bacterial taxa relevant to intestinal and systemic disorders that originate in the gut. Furthermore, we emphasize that gut bacteria convert BRB into bioactive metabolites, contributing to its enhanced intraluminal activity despite its low systemic bioavailability. By integrating molecular and microbiological evidence, this review fills a critical knowledge gap regarding the comprehensive therapeutic potential of BRB as a promising candidate for future IBD interventions. The novelty of this work lies in unifying fragmented findings into a framework that explains how BRB acts simultaneously at the levels of host immunity, microbial ecology, and neuroimmune communication—thus offering a new conceptual model for its role within the gut–microbiome–brain axis. Full article

Eurotium cristatum (EC), a fungus derived from Fu brick tea, exhibits anti-obesity potential, but its mechanisms regulating intestinal gluconeogenesis (IGN) remain unclear. This study aimed to elucidate whether EC alleviates obesity and glucolipid metabolic disorders by modulating the gut microbiota and activating the IGN pathway. The 8-week EC administration at low (10⁴ CFU/mL), medium (10⁶ CFU/mL), and high doses (10⁸ CFU/mL) ameliorated high-fat-diet (HFD)-induced metabolic abnormalities, including aberrant weight gain, dyslipidemia, glucose intolerance and hepatic injury with effects showing a dose-dependent trend. EC treatment significantly activated IGN, as indicated by increased colonic levels of short-chain fatty acids (SCFAs) and succinate (key IGN substrates) and the upregulation of IGN-key enzymes (PEPCK, FBPase, and G6Pase). In addition, EC treatment significantly alleviated the HFD-induced gut dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and enriching beneficial bacteria such as Lachnospiraece_NK4A136_group, Bacteroidota and Alloprevotella. Non-targeted metabolomics analysis revealed that EC significantly altered the linoleic acid metabolism, specifically decreasing the relative levels of bile acid and chenodeoxycholic acid (p < 0.01) while increasing those of linoleic acid and ricinoleic acid (p < 0.05). EC treatment reshaped the gut microbiome, promoted the production of beneficial metabolites (e.g., SCFAs), and consequently activated the IGN pathway, ultimately ameliorating host glucose and lipid metabolic disorders. Our findings provide mechanistic insights into the anti-obesity effects of EC, suggesting its potential for further investigation as a dietary intervention for metabolic diseases. Full article

Chinese herbal medicine (CHM) residues represent a promising and sustainable category of silage additives, with the potential to modulate fermentation and enhance nutrient preservation. This study investigated the effects of two CHMs, Astragalus membranaceus L. (Astragali Radix, AR) and Inula helenium L. (Inulae Radix, IR), on the fermentation profile, nutritional composition, and bacterial community structure in barley silage. The forage was ensiled without additive (control, CK), or with 1% or 2% (w/w) of AR or IR for 75 days. The results showed that all additive treatments significantly improved fermentation quality, as evidenced by lower pH and reduced ammonia-nitrogen (NH₃-N) content compared to CK. The 2% IR treatment was most effective in promoting homolactic fermentation, yielding the highest lactic acid content and lactic acid-to-acetic acid ratio. Nutritionally, additives significantly increased dry matter, starch, and water-soluble carbohydrates, while decreasing neutral and acid detergent fiber contents. High-throughput sequencing of the 16S rRNA gene revealed that both herbal additives profoundly reshaped the microbial community. They suppressed undesirable bacteria and significantly enriched beneficial Lactobacillus species. Principal component analysis confirmed a distinct separation in microbial community structure between control and treated silages. These findings underscore the potential of these herbal residues as natural modulators of the silage microbiome for improved forage conservation. Full article

The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological environment. To address this issue, this study developed a novel biochar–urea peroxide composite particle (BC-UP). Batch degradation experiments and electron paramagnetic resonance (EPR) analysis confirmed the synergistic adsorption-oxidation function of BC-UP. A pot experiment demonstrated that application of BC-UP (5.0 g/kg) significantly alleviated phenolic acid stress. Specifically, BC-UP application significantly enhanced shoot biomass by 28.8% and root surface area by 49.3% compared to the phenolic acid-stressed treatment and concurrently reduced the total phenolic acid content in the rhizosphere soil by 37.3%. This growth promotion was accompanied by the enhanced accumulation of key bioactive compounds (volatile oils, pogostone, and patchouli alcohol). BC-UP amendment also improved key soil physicochemical properties (e.g., pH, and organic matter) and enhanced the activities of critical enzymes. Furthermore, BC-UP reshaped the microbial community, notably reducing the fungi-to-bacteria OTU ratio by 49.7% and enriching the relative abundance of Firmicutes and Nitrospirota but suppressing the Ascomycota phylum abundance. Redundancy analysis identified soil sucrase and catalase activity, total phenolic acid content, and Ascomycota abundance as key factors influencing patchouli biomass. In conclusion, BC-UP effectively mitigates phenolic acid stress through combined adsorption and radical oxidation, subsequently improving soil properties and restructuring the rhizosphere microbiome, offering a promising soil remediation strategy for patchouli and other medicinal crops. Full article

Rice cadmium (Cd) contamination is a serious threat to global food security and human health. Plant-associated microbiomes are known to affect Cd accumulation in plants. However, the response of the rice microbiome to Cd contamination and its role in modulating grain Cd accumulation remain poorly understood. In the present study, the responses of the rhizospheric fungi (RF) community and seed endophytic fungi (SEF) community to the soil physiochemical properties of rice from moderately (MC) and severely (SC1 and SC2) Cd-contaminated paddies were investigated. Moreover, the effects of soil physiochemical properties, RF community and SEF community on grain Cd accumulation were analyzed through correlation analysis. The results showed that the Cd concentration in rice grains from SC2 exceeded the food safety standard of China and was higher than that of SC1 and MC. The Cd concentration in rice grains was positively correlated with the soil-available Cd concentration, while being negatively correlated with the available nutrient elements and pH value of soil. In addition, it was found that the diversity of RF increased with the soil-available Cd concentration, while the diversity and richness of SEF decreased with the soil-available Cd concentration. Moreover, the RF community was influenced by soil physiochemical properties. The Spearman correlation analysis showed that the soil-available Cd was positively correlated with RF Sebacina, Clonostachys, Acremonium, Talaromyces and Fusarium, and most of them were related to grain Cd concentration, while unclassified SEF Pleosporales and Xylariales were associated with grain Cd concentration. These results suggested that Cd stress triggered a niche-specific response of the rice fungal microbiome. The fungi related to soil Cd availability and rice grain Cd accumulation may have a great potential application in food safety production in Cd-contaminated soil. Full article