Search Results (363)

Background: The human gut microbiome is highly complex, and its composition is strongly influenced by dietary patterns. Alterations in microbiome structure have been associated with a range of diseases, including type 2 diabetes mellitus. However, the underlying mechanisms for this remain poorly understood. In this study, a novel in vitro approach was utilized to investigate the interplay between gut bacteria, dietary metabolites, and metabolic dysfunction. Methods: Two representative gut bacterial species—Bacteroides thetaiotaomicron and Lactobacillus fermentum—were isolated from human faecal samples and subjected to controlled dietary manipulation to mimic eubiotic and dysbiotic conditions. Metabolites produced under these conditions were extracted, characterized, and quantified. To assess the functional impact of these metabolites, we utilized the INS-1 832/3 insulinoma cell line, evaluating insulin sensitivity through glucose-stimulated insulin secretion and ERK1/2 activation. Results: Our findings demonstrate that metabolites derived from high-carbohydrate/high-fat diets exacerbate metabolic dysfunction, whereas those generated under high-fibre conditions significantly enhance insulin secretion and glucose-dependent ERK1/2 activation in co-culture compared to monocultures. Conclusions: This work systematically disentangles the complex interactions between gut microbiota, diet, and disease, providing mechanistic insights into how microbial metabolites contribute to the onset of metabolic disorders. Full article

Pasture-based ruminant systems link nitrogen (N) nutrition with ecosystem N cycling. Grazing ruminants convert fibrous forages into milk and meat but excrete 65 to 80% of ingested N, creating excreta hotspots that drive ammonia volatilization, nitrate leaching, and nitrous oxide (N₂O) emissions. This review synthesizes ecological and ruminant nutrition evidence on N flows, emphasizing microbial processes, biological N₂ fixation, plant diversity, and urine patch biogeochemistry, and evaluates strategies to improve N use efficiency (NUE). We examine rumen N metabolism in relation to microbial protein synthesis, urea recycling, and dietary factors including crude protein concentration, energy supply, forage composition, and plant secondary compounds that modulate protein degradability and microbial N capture, thereby influencing N partitioning among animal products, urine, and feces, as reflected in milk and blood urea N. We also examine how grazing patterns and excreta distribution, assessed with sensor technologies, modify N flows. Evidence indicates that integrated management combining dietary manipulation, forage diversity, targeted grazing, and decision tools can increase farm-gate NUE from 20–25% to over 30% while sustaining performance. Framing these processes within the global N cycle positions pasture-based ruminant systems as critical leverage points for aligning ruminant production with environmental and climate sustainability goals. Full article

The intricate interplay between the human microbiota and the immune system has garnered significant attention in recent years, particularly concerning its implications in cancer biology. Macrophages, pivotal players in the tumor microenvironment (TME), exhibit diverse phenotypes that can either promote tumor progression or inhibit it. This review explores the multifaceted role of the microbiota in modulating macrophage polarization within the TME. We highlight recent findings that demonstrate how specific microbial communities influence macrophage behavior through metabolic pathways, immune signaling, and epigenetic modifications. Furthermore, we discuss the therapeutic potential of manipulating the microbiota to reprogram macrophage phenotypes, thereby enhancing antitumor immunity. By integrating insights from microbiology, immunology, and oncology, this article aims to provide a comprehensive overview of the microbiota’s impact on macrophage dynamics in cancer, paving the way for innovative therapeutic strategies that harness this relationship for improved clinical outcomes. Full article

The global population continues to rise, placing increasing pressure on the agri-food sector and leading to the accelerated generation of urban organic waste, factors that collectively intensify climate stress and environmental instability. Insects are recognised for their remarkable capacity to transform substrates into valuable products, with the black soldier fly larvae (BSFL) emerging as one of the most efficient and widely utilised species for this purpose. Beyond recycling organic matter, BSFL can also mitigate microbial contamination, effectively reducing bacterial and fungal loads in waste substrates. Understanding and manipulating the genome could provide tools to improve BSFL bioconversion process and contribute to sustainability. In this review, we provide an overview of recent advances in black soldier fly genomics and genome-editing technologies. Although research in this subject remains limited, recent studies have clarified its origin, characterised its genome, and established the foundation for targeted genetic improvements to enhance by-product conversion, nutrient recovery, and environmental sustainability. Full article

Nitrogen (N) deposition poses a multi-pronged threat to the carbon (C)-regulating services of moss understories. For forest C-cycle modeling under increasing N deposition, failure to mechanistically incorporate the moss-mediated processes risks severely overestimating the C sink potential of global forests. To explore whether and how N input affects the moss-mediated CH₄ and carbon dioxide (CO₂) fluxes, a five-year field measurement was performed in the N manipulation experimental plots treated with 22.5 and 45 kg N ha⁻¹ yr⁻¹ as ammonium chloride for nine years under a well-drained temperate forest in northeastern China. In the presence of mosses, the average annual CH₄ uptake and CO₂ emission in all N-treated plots ranged from 0.96 to 1.48 kg C-CH₄ ha⁻¹ yr⁻¹ and from 4.04 to 4.41 Mg C-CO₂ ha⁻¹ yr⁻¹, respectively, with a minimum in the high-N-treated plots, which were smaller than those in the control (1.29–1.83 kg C-CH₄ ha⁻¹ yr⁻¹ and 4.82–6.51 Mg C-CO₂ ha⁻¹ yr⁻¹). However, no significant differences in annual cumulative CO₂ and CH₄ fluxes across all treatments occurred without moss cover. Based on the differences in C fluxes with and without mosses, the average annual moss-mediated CH₄ uptake and CO₂ emission in the control were 0.77 kg C-CH₄ ha⁻¹ yr⁻¹ and 2.40 Mg C-CO₂ ha⁻¹ yr⁻¹, respectively, which were larger than those in the two N treatments. The N effects on annual moss-mediated C fluxes varied with annual meteorological conditions. Soil pH, available N and C contents, and microbial activity inferred from δ¹³C shifts in respired CO₂ were identified as the main driving factors controlling the moss-mediated CH₄ and CO₂ fluxes. The results highlighted that this inhibitory effect of increasing N deposition on moss-mediated C fluxes in the context of climate change should be reasonably taken into account in model studies to accurately predict C fluxes under well-drained forest ecosystems. Full article

The human gut microbiota plays a key role in neurochemical communication, especially through the gut–brain axis. There is growing evidence that the gut microbiota influences dopamine metabolism through both production and consumption mechanisms. Two key bacterial enzymes are central to this process: tyrosine decarboxylase (TDC), which primarily catalyzes the decarboxylation of tyrosine to tyramine but can also act on L-DOPA to produce dopamine in certain bacterial strains, and aromatic L-amino acid decarboxylase (AADC), which can convert precursors such as L-DOPA, tryptophan, or 5-hydroxytryptophan into bioactive amines including dopamine, tryptamine, and serotonin. Identifying the bacterial families corresponding to TDC and AADC enzymes opens new avenues for clinical intervention, particularly in neuropsychiatric and neurodegenerative disorders, such as Parkinson’s disease. Moreover, elucidating strain-specific microbial contribution and host-microbe interactions may enable personalized therapeutic strategies, such as selective microbial enzyme inhibitors or tailored probiotics, to optimize dopamine metabolism. Emerging technologies, including biosensors and organ-on-chip platforms, offer new tools to monitor and manipulate microbial dopamine activity. This article explores the bacterial taxa capable of producing or consuming dopamine, focusing on the enzymatic mechanisms involved and the methodologies available for studying these processes in vivo. Full article

Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant–soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems. Full article

Calcium (Ca²⁺) is a signal messenger for ion flow in and out of microbial, parasitic, and host defense cells. Manipulation of calcium ion signaling with ion blockers and calcineurin inhibitors may improve host defense while decreasing microbial/parasitic resistance to therapy. Ca²⁺ release from intracellular storage sites controls many host defense functions (cell integrity, movement, and growth). The transformation of phospholipids in the erythrocyte membrane is associated with changes in deformability. This type of lipid bilayer defense mechanism helps to prevent attack by Plasmodium. Patients with sickle cell disease (SS hemoglobin) do not have this protection and are extremely vulnerable to massive hemolysis from parasitic infestation. Patients with thalassemia major also lack parasite protection. Alteration of Ca²⁺ ion channels responsive to environmental stimuli (transient receptor potential) results in erythrocyte protection from Plasmodium. Similarly, calcineurin inhibitors (cyclosporine) reduce heart and brain inflammation injury with Trypanosoma and Taenia. Ca²⁺ channel blockers interfere with malarial life cycles. Several species of parasites are known to invade hepatocytes: Plasmodium, Echinococcus, Schistosoma, Taenia, and Toxoplasma. Ligand-specific membrane channel constituents (inositol triphosphate and sphingosine phospholipid) constitute membrane surface signal messengers. Plasmodium requires Ca²⁺ for energy to grow and to occupy red blood cells. A cascade of signals proceeds from Ca²⁺ to two proteins: calmodulin and calcineurin. Inhibitors of calmodulin were found to blunt the population growth of Plasmodium. An inhibitor of calcineurin (cyclosporine) was found to retard population growth of both Plasmodium and Schistosoma. Calcineurin also controls sensitivity and resistance to antibiotics. After exposure to cyclosporine, the liver directs Ca²⁺ ions into storage sites in the endoplasmic reticulum and mitochondria. Storage of large amounts of Ca²⁺ would be useful if pathogens began to occupy both red blood cells and liver cells. We present scientific evidence supporting the benefits of calcium channel blockers and calcineurin inhibitors to potentiate current antiparasitic therapies. Full article

To improve cocoa fermentation and the quality of its final products, microbial cultures with potential as starters were investigated. Yeasts were considered a promising option due to their adaptability to biotechnological processes and ease of laboratory manipulation. From 185 strains previously isolated from spontaneous cocoa fermentation, those producing protease, amylase, and cellulase were identified. Strain CII87b (Pichia manshurica) exhibited the most favorable results and was evaluated for cytotoxicity using the MTT assay, showing no adverse effects. This culture was subsequently inoculated into freshly harvested cocoa almonds during the secondary (winter) harvest. The inoculum accelerated and increased the average fermentation temperature from 25 to 50 °C, reduced internal mold incidence, decreased defect rates, increased total fermentation, and resulted in a more desirable pH compared to the control. These findings demonstrate that the use of P. manshurica CII87b as a starter culture in winter harvests can improve fermentation efficiency and product quality, offering a biotechnological tool with potential benefits for cocoa producers and the chocolate industry. Full article

Soil microbial communities face the combined pressures of climate change and biodiversity loss, yet how these stressors interact to shape ecosystem function remains a critical uncertainty. To investigate this, we established a constructed grassland plant community and conducted a fully factorial experiment manipulating plant diversity (1, 3, and 6 species), temperature (ambient, +2 °C), and precipitation (ambient, +50%). High-throughput 16S rRNA gene sequencing revealed that plant diversity exerted a stronger influence on soil bacterial community structure than did warming or precipitation changes. Beta diversity analysis revealed a distinct clustering of bacterial communities corresponding to the plant diversity gradient. This shift was characterized by a consistent enrichment of the metabolically versatile genus Sphingomonas in medium-diversity plots that experienced elevated precipitation, suggesting a predicted potential for enhanced organic matter decomposition. Despite overall stability in alpha diversity, the interaction between plant diversity and warming significantly modulated bacterial diversity and dominance patterns. Our findings highlight that plant diversity plays a key role in mediating soil bacterial responses to simulated climate factors in the short term. Incorporating these plant–soil feedback mechanisms into ecological models appears crucial for advancing predictions of ecosystem dynamics under future climate conditions. Full article

Microbial biofilms in food processing environments pose significant challenges due to their exceptional resistance to conventional sanitation methods, presenting substantial risks to food safety and public health. This review systematically evaluates recent advances in understanding biofilm development across key stages, i.e., initial microbial adhesion, extracellular polymeric substance production, biofilm maturation including resistant phenotypes such as persister cells, and dispersion. Particular emphasis is placed on the molecular mechanisms underlying biofilm formation and the regulatory roles of cyclic-di-GMP and quorum sensing. Crucially, we highlight emerging targeted interventions including enzyme-mediated extracellular polymeric substance disruption, microenvironmental manipulation, quorum sensing inhibitors, metabolic reactivation of persisters (“wake-and-kill”), and controlled biofilm dispersion techniques, clearly outlining their practical applicability and potential limitations in real-world food industry contexts. Moreover, this review uniquely integrates innovative technological developments such as responsive antimicrobial coatings, real-time biosensors, predictive modeling systems, and precision biotechnology approaches. Uniquely, this review integrates molecular mechanisms with practical, stage-specific sanitation strategies and provides actionable insights that can enhance biofilm control, contributing to safer food production practices and im-proved public health outcomes. Full article

HIV-induced apoptosis is a contradictory complicated phenomenon that occurs at the intersection of viral persistence and host defense. HIV primarily affects CD4 T cells during an infection, causing widespread immune cell death through both direct infection and indirect (bystander) mechanisms. This immunopathologic process is caused by viral proteins such as Tat, Nef, Env, and Vpr, which modify host signaling cascades such as the PI3K/Akt, p53, NF-κB, and mitochondrial pathways. Dysregulation of pro- and anti-apoptotic mediators, particularly Bax, Bcl-2, and caspase activation, which results in mitochondrial depolarization, oxidative stress, and cytochrome c release, exacerbates immune depletion. Although apoptosis serves as a host antiviral mechanism to limit viral replication and spread, HIV exploits it to evade immune surveillance and establish chronic infection. HIV pathogenesis, which includes lymphoid tissue destruction, microbial translocation, and persistent inflammation, is significantly influenced by apoptosis of both infected and bystander cells. Furthermore, alterations in death receptor signaling (Fas/FasL and TNF pathways) and mitochondrial dysfunction highlight the delicate balance between immune defense and viral manipulation. Despite considerable progress in antiretroviral therapy, immune restoration is still incomplete due to ongoing apoptotic loss and immune exhaustion. This review examines the biological mechanisms underlying HIV-induced apoptosis, evaluates the dual role of cell death in host defense versus viral persistence, and highlights novel therapeutic targets intended to restore immune homeostasis and reduce HIV-associated immunopathology. Full article

This study investigated the interactive effects of different light conditions and weed control methods on the medicinal compound composition and rhizosphere bacterial community structure of Epimedium sagittatum. A completely randomized block design was employed, incorporating four treatments: full light with manual weeding (LN), shade with manual weeding (SN), full light with weed-control fabric mulch (LG), and shade with mulch (SG). Active compound levels in two-year-old plants were quantified using HPLC, and rhizobacterial diversity was assessed via high-throughput sequencing. The results indicated that the SG treatment significantly enhanced the photosynthetic efficiency and yielded the highest levels of epimedin C and total active compounds. In contrast, the SN treatment fostered a beneficial rhizosphere environment—characterized by increased pH, ammonium nitrogen (NH₄⁺-N), bacterial diversity, and the abundance of Flavobacterium—which supported the highest production of epimedin B and icariin. Redundancy analysis confirmed that these microbial shifts were primarily driven by soil pH, nitrate nitrogen (NO₃⁻-N), and shading. Furthermore, while stochastic processes governed bacterial community assembly, deterministic selection intensified across the treatments from LN to SG. Collectively, our findings demonstrate that light and mulching can be strategically tailored to manipulate the plant–soil-microbe system, thereby enabling precise modulation of the medicinal quality of E. sagittatum. Full article

Black soldier fly (BSF) larvae are among the most widely mass-reared insects and develop in moist feed substrates where larvae and microorganisms jointly degrade organic matter but also compete for nutrients. Microbial activity introduces variability and often decreases substrate conversion efficiency (SCE), defined as the ratio of larval biomass produced to substrate consumed. Supplementing feed substrates with antimicrobial agents may suppress microbial activities and thereby enhance the SCE. In this study, BSF larvae were reared on chicken feed supplemented with 0–0.2% benzoic acid at either initial pH = 7.6 or pH ≤ 4, under varying larval densities. Larval weights and CO₂ production from both larvae and substrates were measured periodically. At low pH, benzoic acid lowered the CO₂ evolution from the feed substrate while the substrate reduction rate (SRR) diminished dose dependently, indicating suppressed microbial activity. Despite the lower SRR, larval biomass yield remained unchanged, resulting in a dose-dependent increase in SCE. The effect was most pronounced in feed-sufficient larvae. Benzoic acid had no effect on larval performances in terms of maximal larval weight, specific growth rate, or mortality. Their overall net growth efficiency (larval weight gain relative to assimilated substrate) even increased dose-dependently. However, the low pH needed for benzoic acid to be active did have minor negative effects on larval performances. These findings demonstrate that microbial activity influences SCE during productions of BSF larvae and that substrate conversion efficiency can be manipulated and potentially optimized without harming the larvae through the inclusion of antimicrobial agents such as benzoic acid in their feed substrates. Full article

The proliferation of antibiotic resistance genes (ARGs) in livestock manure has raised growing environmental and public health concerns. Composting is widely recognized as an effective method to mitigate ARG dissemination; however, recent studies have increasingly reported a rebound in ARG abundance during the curing stage of composting, undermining its long-term effectiveness. Here, “rebound” refers to a renewed increase in ARG abundance—either in absolute terms or relative to the 16S rRNA gene—following its decline to a minimum during the thermophilic phase. This review systematically summarizes the dynamic changes in ARGs throughout the composting process, with a particular focus on the mechanisms and drivers underlying ARG rebound. Vertical and horizontal gene transfer, along with microbial succession, are discussed as key contributors to this phenomenon. Current strategies to suppress ARG rebound, including microbial community manipulation, hyperthermophilic composting, and exogenous amendments, are evaluated. Furthermore, the roles of heavy metals and extracellular polymeric substances in promoting ARG persistence are examined, highlighting their potential involvement in ARG rebound. This review aims to provide a comprehensive understanding of ARG rebound in composting and to inform the development of more effective, integrated mitigation strategies. Full article