Search Results (2,090)

Autoimmune and immune-mediated inflammatory diseases (IMIDs) develop when genetically and environmentally susceptible hosts lose stable immune tolerance. The gut ecosystem is increasingly recognized as a biologically active interface in this process. Its bacterial, fungal, and viral components may shape mucosal and systemic immunity through antigenic stimulation, barrier regulation, and metabolite-dependent signaling, although the strength of evidence is uneven: bacteriome data are currently the most mature, whereas mycobiome, virome, and phageome findings remain more disease-specific and emerging. Dysbiosis may influence autoimmunity through overlapping routes, including epithelial barrier failure, altered short-chain fatty acid, bile acid, and tryptophan metabolism, molecular mimicry, and cross-kingdom microbial interactions. Nutrition is central to this network because dietary substrates determine microbial growth, metabolic output, epithelial integrity, and immune-cell differentiation. In this narrative review, we integrate evidence on disease-associated bacteriome, mycobiome, and virome patterns in systemic autoimmune diseases, with emphasis on rheumatoid arthritis, systemic lupus erythematosus, Sjögren’s syndrome, systemic sclerosis, spondyloarthritis, vasculitides, and idiopathic inflammatory myopathies. COVID-19 is considered not as a proven causal driver of autoimmunity, but as an example of an environmental and infectious insult capable of perturbing microbiome–barrier–immune communication. Finally, we discuss diet-based and microbiome-targeted approaches, including probiotics, prebiotics, synbiotics, and postbiotics, as adjunctive strategies that may help restore microbial resilience and immune balance. A better understanding of the diet–microbiome–host immunity axis may support more personalized preventive and therapeutic concepts in autoimmune disease. Full article

Background/Objectives: Bitter taste receptors (T2Rs), specifically T2R38, are present in the respiratory epithelium and react with bacterial quorum-sensing molecules to induce an innate immunity response. Although TAS2R38 polymorphisms have been correlated with susceptibility to chronic rhinosinusitis (CRS), they have not yet been explored in odontogenic rhinosinusitis (ORS), a distinct form of CRS with particular microbial and inflammatory features. We aim to establish a proof-of-concept methodology for investigating TAS2R38 genetic variants in ORS using direct maxillary sinus tissue analysis and demonstrate the feasibility of this translational approach. Methods: We conducted a prospective pilot case–control study of 36 ORS patients and 37 controls undergoing septoplasty without sinonasal disease. Maxillary sinus mucosal biopsies were obtained intraoperatively with informed consent. Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit and quantified via NanoDrop spectrophotometry. TAS2R38 haplotypes were determined and classified as taster (PAV/PAV), non-taster (AVI/AVI), or intermediate (PAV/AVI) phenotype. Results: Among fully classifiable canonical TAS2R38 phenotypes (32 ORS patients, 28 controls), distributions were: tasters 12.5% vs. 25.0%, non-tasters 31.3% vs. 25.0%, and intermediate 56.3% vs. 50.0%. AVI/AVI non-taster status was not significantly associated with ORS susceptibility (OR = 1.36, 95% CI: 0.44–4.25; Fisher’s exact p = 0.775). Conclusions: This proof-of-concept study demonstrates that genotyping-grade genomic DNA can be recovered from acutely inflamed maxillary sinus mucosa, validating this substrate for future tissue-based expression, functional, and microbiome analyses not obtainable from peripheral samples; germline genotyping itself does not require sinus tissue. The observed difference in non-taster prevalence (31.3% vs. 25.0%) did not reach statistical significance and is reported descriptively. This directional trend is hypothesis-generating only and, given the limited statistical power, does not constitute evidence for an association. The demonstrated feasibility, together with the established biological rationale, supports an adequately powered confirmatory study and lays the foundation for future investigation of taste receptor genetics in ORS pathogenesis, and potentially personalized therapeutic strategies. Full article

The growing demand for sustainable energy carriers has intensified interest in hydrogen production from renewable resources and waste-derived substrates. In this context, microbial electrolysis cells (MECs) have emerged as a promising technology for the simultaneous treatment of organic waste and biohydrogen generation. This review provides an overview of recent advances in MEC systems, focusing on reactor configurations, performance indicators such as hydrogen production rate, coulombic efficiency, and chemical oxygen demand removal. Attention is given to the valorization of real waste streams, including municipal and agro-industrial effluents, highlighting the differences between laboratory- and pilot-scale applications. While numerous studies have demonstrated the technical feasibility of MECs, several bottlenecks still limit their large-scale implementation, including challenges associated with the use of complex substrates. In particular, untreated wastewater often leads to reduced process efficiency due to its variable composition and the occurrence of competing microbial pathways. To overcome these limitations, integrated approaches are also discussed, with emphasis on the coupling of dark fermentation, capable of enhancing substrate biodegradability through the production of volatile fatty acids, with MEC systems. Overall, MEC technology represents a promising pathway for sustainable hydrogen production within circular waste management frameworks, although further advancements are required to enable its practical application. Full article

At the archeological site of Pompeii, the deterioration of exposed structures is frequently associated with the combined action of microbial colonization and soluble salts, both recognized as major agents of decay affecting ancient surfaces. Although biocides are commonly applied during cleaning procedures to reduce microbial biomass, their incorporation into restoration-oriented formulations for the protection of porous stone substrates requires careful assessment of efficacy, microbiological risks, and sustainability. This study evaluated the performance of 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil) and iodopropynyl butylcarbamate (IPBC) as candidate active ingredients for conservation applications in activated new mortars. Yellow tuff, gray tuff, and brick samples collected from different sectors of Pompeii were investigated through culture-based analyses, ATP quantification, and metabolic profiling. Biocidal treatments were subsequently tested under laboratory conditions. The investigated substrates exhibited variable microbial counts and metabolic activity, generally reflecting different degrees of deterioration. Chlorothalonil showed negligible inhibitory effects, whereas IPBC reduced fungal growth in a dose-dependent manner. However, the highest IPBC concentration induced a red chromatic alteration associated with the selection of a bacterial strain preliminarily identified as Micrococcus roseus. Phenotype microarray analyses revealed broad chemical tolerance. Overall, biocidal treatments may alter microbial communities, favor tolerant microorganisms, and produce undesirable aesthetic effects. Finally, the study also assessed the environmental impact associated with laboratory and field activities, highlighting potential mitigation strategies to support more sustainable conservation research practices. Full article

Per- and polyfluoroalkyl substances (PFASs) are persistent emerging contaminants characterized by high environmental stability and biotoxicity. Ubiquitous detection of these contaminants across aquatic environments poses severe threats to ecosystem stability and human health, while constructed wetlands (CWs) serve as a sustainable low-carbon alternative for the remediation of PFAS-laden wastewater. However, traditional mechanisms such as matrix adsorption, phytoaccumulation, and microbial transformation often suffer from low efficiency, rapid saturation, and incomplete degradation. To overcome the above drawbacks, the arbuscular mycorrhizal fungi (AMF)–plant–microbe synergistic consortium has become a promising remediation candidate, which facilitates PFAS immobilization and biodegradation via symbiotic crosstalk among three components. This paper reviews recent advancements in PFAS remediation within AMF-facilitated systems, examining fundamental synergistic mechanisms, treatment efficiencies, and key influencing factors. We propose several optimization strategies, including substrate modification, operational parameter refinement, and the integration of advanced technologies. Furthermore, we emphasize the necessity of elucidating the molecular pathways governing long-chain PFAS degradation and addressing current bottlenecks in engineering applications. Future research should prioritize molecular interaction level interaction mechanisms, the development of anti-interference systems, and field-scale validation. This review provides a theoretical foundation and technical framework for leveraging AMF–plant–microbe synergism to enhance PFAS removal in CWs. Full article

Rice–fish co-culture is widely promoted for mitigating nitrous oxide (N₂O) emissions from paddy soils, yet how the duration of co-culture reshapes the underlying nitrogen-cycling microbial community under low-nitrogen input remains poorly understood. This study aimed to (i) characterize how co-culture duration alters the rhizosphere microbial functional potential for N₂O production and consumption, and (ii) identify the water and soil variables linking fish activity to that response. The experiment was conducted during the 2024 rice growing season in the Qingtian rice–fish system (Zhejiang Province, China), a traditional agricultural heritage system managed without chemical fertilizer or supplementary feed. Three treatments (i.e., rice monoculture, first-year co-culture, and long-established (~10-year) co-culture) were compared using six independently bunded replicate plots each. Rhizosphere soils were collected at the tillering, heading and maturity stages for shotgun metagenomic profiling of nitrogen-cycling functional genes, with concurrent measurement of N₂O flux and water and soil physicochemical properties. Fluxes were uniformly low and did not differ among treatments (p > 0.05), defining a substrate-limited baseline. Against this baseline, first-year co-culture induced a coordinated shift toward complete denitrification (nosZ increased by 25–33% across all stages; nosZ/(nirK + nirS) rose to 0.99 at heading), associated with a transient water organic carbon pulse and dissolved-oxygen availability. The long-established system resembled monoculture, indicating a non-monotonic, duration-dependent response. Full article

Background: Approximately 42% of breast cancer patients report cannabis use for chemotherapy-related symptom relief, yet its impact on the gut–immune axis remains unexplored. This trial evaluated the feasibility of monitoring short-chain fatty acids (SCFAs) and systemic cytokines as exploratory biomarkers during cannabis oil intervention. Method: In a double-blind, placebo-controlled pilot trial, women with breast cancer (n = 10) receiving chemotherapy were randomized to cannabis oil (n = 6) or placebo (n = 4) for 12 weeks. Fecal SCFAs and plasma cytokines were analyzed in paired samples. Results: Dietary stability was systematically assessed using a food frequency questionnaire, with stability defined as <30% shift in functional protein and fiber indices. High dietary stability was confirmed, with all participants maintaining consistent intake of fermentation substrates. Numerical trends, none reaching statistical significance (all p > 0.05), were observed in both exploratory endpoints. Fecal short-chain fatty acid profiling revealed a descriptive numerical reduction in the proteolytic dysbiosis marker iso-butyric acid within the cannabis arm compared with a marginal increase in placebo. Directionally, the cannabis group demonstrated greater median reductions in inflammatory cytokines such as IL-6, IL-8, IL-1β, and TNF-⍺ whereas the placebo group exhibited persistent or heterogeneous profiles. Conclusions: These directional trends toward reduced proteolytic metabolites and attenuated systemic cytokines suggest possible associations between cannabis oil exposure and exploratory gut microbial and immune biomarkers. Given the small pilot sample size, these hypothesis-generating findings lack formal statistical power but warrant adequately powered confirmatory trials. Full article

The Loess Hilly Region of northern Shaanxi is one of the most erosion-prone areas in the world due to its porous, erodible loess, steep slopes, and seasonal rainfall. To address this, conversion of sloping farmland to terraces has been extensively conducted across China’s loess regions, as terracing can reduce soil and water loss and enhance soil fertility. However, disturbance of soil layers during terracing can also lead to short-term decline in farmland productivity. This study investigates the effects of terracing operations at two sites of different ground substrate configurations in the Loess Hilly Region. Utilizing geochemical and molecular biological analysis methods, we examined the changes in the physicochemical and microbial properties of the ground substrate after terracing, using adjacent sloping farmlands as control sites. The results show that when the ground substrate configuration remained intact, terracing increased the average water content (from 8.44% to 14.34%) and soil organic carbon (from 2.74 g/kg to 5.76 g/kg) by 70% and 110%, respectively, and increased soil microbial α-diversity by 90%. The microbial community structure was also enhanced with an increase in relative abundance of soil- and plant-benefiting genera such as Streptomyces and Nocardioides, thereby promoting plant growth. Conversely, when the ground substrate configuration was altered, terracing led to a decrease in soil nutrient and moisture content, which was detrimental to crop growth. Therefore, maintaining the integrity of the ground substrate configuration is crucial during the terracing process to achieve optimal soil and water conservation outcomes. Full article

Olive mill wastewater (OMW), due to its high organic load and phenolic content, represents both a major environmental challenge and a promising low-cost substrate for microbial bioprocesses. In this study, lipid production by Yarrowia lipolytica using OMW was optimized through a mixed-level Taguchi experimental design. The effects of OMW dilution (%), nitrogen supplementation, NaCl concentration, sterilization, and carbon source (glucose or glycerol) were evaluated in terms of biomass production, lipid accumulation, and fatty acid composition. The results demonstrated a clear inverse relationship between biomass formation and lipid accumulation. The highest lipid content (33.49%) was achieved under nitrogen-limited conditions combined with a high OMW dilution. After 168 h of fermentation, the calculated lipid yield was 0.51 g/L. Biomass and lipid productivities were calculated as 0.22 g/L/day and 0.073 g/L/day, respectively. ANOVA analysis revealed that nitrogen concentration was the dominant factor affecting lipid production (67.71%), followed by NaCl concentration (18.83%). In contrast, OMW dilution, sterilization, and carbon source type were not statistically significant (p > 0.05), indicating that lipid production can be effectively performed under non-sterile conditions with flexible substrate utilization. Fatty acid analysis revealed that the produced lipids were rich in oleic acid (C18:1n9c), reaching up to 57.97%, with unsaturated fatty acids generally accounting for the majority of the total fatty acid composition. Although the carbon source had a limited effect on lipid yield, it contributed to variations in fatty acid composition, suggesting the possibility of tailoring lipid quality through substrate selection. Full article

Anaerobic co-digestion (AcoD) is increasingly applied in sewage-sludge management and organic-waste treatment because it can improve methane recovery, stabilize mixed substrates, and reduce life-cycle greenhouse-gas emissions under appropriate feedstock and operating conditions. However, existing reviews still focus mainly on feedstock types or isolated enhancement measures and less often connect synergistic mechanisms with engineering implementation and carbon outcomes. The specific novelty of this review is to connect functional feedstock classification, mechanism boundaries, engineering controls, and carbon-performance evaluation within one sludge-centered AcoD framework. This review synthesizes recent progress in AcoD of sewage sludge, food waste, livestock manure, crop residues, and industrial organic streams through a chain from feedstock traits to substrate interactions, microbial responses, engineering performance, and carbon benefits. Feedstocks are reorganized by function rather than by waste name, highlighting how carbon-to-nitrogen contrast, buffering capacity, hydrolysis recalcitrance, and inhibitor profiles jointly define synergy potential. Key mechanisms, including C/N balancing, hydrolysis complementarity, inhibitor mitigation, and direct interspecies electron transfer (DIET), are discussed together with their applicability limits. Representative evidence shows methane-yield or methane-production increases of about 41–55% for selected food-waste–manure blends, approximately 45% for rice–straw–pig manure systems after cellulolytic pretreatment, and approximately 16–55% for selected additive strategies; these values are illustrative rather than directly comparable because the underlying studies differ in substrates, baselines, reactor configurations, pretreatment conditions, and operating parameters. The review then translates mechanism into practice through pretreatment, reactor-selection templates, operating windows, additive reinforcement, and artificial-intelligence-assisted monitoring. Representative cases and life-cycle evidence indicate that AcoD can improve methane productivity while lowering greenhouse-gas emissions relative to landfill or mono-digestion pathways when energy substitution and nutrient recycling are credibly counted. Remaining bottlenecks include incomplete kinetic integration, limited DIET quantification, insufficient reporting of quantitative operating ranges and additive dosages, and weak coupling of carbon, economics, and regional feedstock dynamics. The revised review therefore treats AcoD as a sludge-centered mechanism-to-engineering framework and highlights two transferability gaps that require stronger standardization: biodegradation/toxicity testing and local co-substrate logistics. Full article

The impact of dietary inert digestibility markers on gut microbiota and intestinal fermentation remains poorly understood. This study investigated the effects of dietary titanium dioxide (TiO₂) supplementation at 4 kg/t feed, representing a typical dose used in animal nutrition studies, on fermentation dynamics and microbial composition in broiler chickens using combined ex vivo and in vivo approaches. Ex vivo fermentations were conducted using ileal and caecal microbiota and substrates collected from 32-day-old broiler chickens. Titanium dioxide (TiO₂) was supplemented directly to the fermentations, and gas production and short-chain fatty acid (SCFA) profiles were used as the main outcome measures. In parallel, 392 broiler chickens were fed diets with or without TiO₂ for 32 days, and ileal and caecal digesta were analysed for fermentation end-products and microbial composition using shotgun metagenomic sequencing. A second ex vivo experiment was performed using microbiota adapted to dietary TiO₂. In the first ex vivo model, TiO₂ reduced gas production and acetic acid concentration in the ileum (p < 0.05), whereas in the caecum it increased gas production, total eubacterial counts, and branched-chain fatty acids (BCFAs) (p < 0.05). In vivo, TiO₂ did not affect growth performance or organ development but significantly increased isobutyric acid and total BCFA concentrations in the caecum (p < 0.05). Metagenomic analysis revealed increased caecal alpha diversity (Shannon index) and enrichment of taxa associated with amino acid metabolism, including Massilicoli timonensis, Blautia merdavium, Rubneribacter badeniensis, and Mediterraneibacter caccavium. The second ex vivo experiment showed similar trends, with increased gas and BCFA production. Collectively, these findings indicate that TiO₂ can modulate intestinal fermentation and microbial composition in a segment-specific manner, suggesting that dietary markers may not be biologically inert. Full article

Several strategies can be employed for the identification of novel microbial lipases. Despite the increasing importance of metagenomics in bioprospecting, significant limitations in the expression of recombinant proteins, and lipases in particular, remain. Culture-based bioprospecting approaches are, therefore, still valuable. In this work, a collection of bacterial isolates, mainly of marine origin, was screened for lipase activity through a culture-based approach. Screening for lipolytic bacteria was performed in solid media containing olive oil emulsions and rhodamine B. Positive isolates were subsequently grown in liquid media, to confirm lipase production. Significant hydrolytic activity towards the triglyceride substrates tributyrin and triolein could be observed with the biomass produced, although no lipase activity could be detected in the culture supernatants. Six isolates presenting high activity were characterized as whole-cell biocatalysts, and all were found to be active at temperatures ranging between 25 and 65 °C, and at pH values between 6 and 10.5. Genomic analyses of two of these Gram-negative lipase-producing isolates revealed the presence of several hypothetical genes encoding for lipolytic enzymes, including outer cell-bound enzymes, predicted through the application of machine-learning tools. These natural isolates, containing cell-associated lipases, may therefore be of special interest for application as whole-cell biocatalysts. Full article

Microbial α-L-rhamnosidases are increasingly recognised as selective biocatalysts in food biotechnology, nutraceutical production, and health-related applications. These glycoside hydrolases catalyse the hydrolysis of terminal alpha-L-rhamnose residues from flavonoids, terpenoids, saponins, and other glycosylated natural products, thereby modulating sensory properties, solubility, intestinal absorption, and biological activity. While their traditional uses include debittering citrus juice and enhancing wine aroma, recent evidence demonstrates their wider value in selective flavonoid biotransformation, production of rare mono-glycosylated derivatives, probiotic fermentations, and microbiome-associated metabolism. This review summarises microbial sources, catalytic mechanisms, CAZy classification, substrate specificity, structure–function relationships, analytical methods, industrial process engineering, and emerging applications in functional foods and targeted nutraceutical applications. Particular attention is given to the distinction between alpha-(1→2)- and alpha-(1→6)-linked substrates, the production of isoquercitrin and prunin, recombinant enzyme platforms, immobilised biocatalysts, and potential future opportunities arising from metagenomics, synthetic biology, and AI-assisted protein engineering. Full article

Mediterranean agricultural systems are highly vulnerable to increased climatic variability, which threatens soil water availability and the functionality of the soil carbon (C) cycle. Soil management practices strongly influence water dynamics and C-substrate quality, thus potentially affecting the temperature sensitivity of soil respiration. We evaluated the combined effects of tillage (traditional tillage, TT; reduced tillage, RT), fertilization (mineral, MF; addition of biosolid compost, BC), and rainfall inputs (ambient conditions, C; reduction of 30% rainfall inputs, EX) on soil water content (SWC) and storage (SWS), and in situ soil respiration (Resp) dynamics over three agricultural seasons in a Mediterranean legume–wheat rotation, using a factorial field experiment. We also evaluated how the sensitivity of soil respiration to temperature could be affected by tillage and fertilization types in a complementary laboratory experiment under controlled moisture and temperature conditions. RT was effective in improving SWS and mitigating surface desiccation, although this advantage was attenuated in wet years due to homogenization of moisture along the soil profile. Soil Resp was primarily controlled by SWC. BC stimulated soil respiration mainly during the first crop season, with a residual non-significant trend in the third season. This effect appeared constrained under dry periods, although no significant fertilization × rainfall exclusion interaction was detected. The diurnal cycle of Resp showed a clear decoupling from diurnal soil temperature. Crucially, the intrinsic thermal sensitivity of respiration (Q₁₀) remained stable across all tillage and fertilization treatments, suggesting that field variability is driven by water dynamics and crop phenology and not by microbial responses to changes in substrate availability. Our results confirmed the hierarchical role of climate on C-cycling processes. Full article

Long-term intensive farming has degraded the structural stability of black soil in Northeast China. This study evaluated the effects of fermentation-derived materials and fungal-derived chitin on water-stable aggregates and microbial functional potential in this soil. Four treatments were established: sterile water control (CK), uninoculated fermentation broth substrate (W), live Trichoderma asperellum fermentation broth (P), and cell-free fermentation filtrate (F). Aggregate stability was monitored during a 60-day incubation, and metagenomic sequencing was performed on the most responsive 0.5–0.25 mm dry-sieved fraction. An exogenous chitin addition experiment was also conducted to evaluate the potential contribution of fungal cell-wall-derived chitin to aggregate stabilisation. The W, P, and F treatments increased the proportion of water-stable aggregates >0.25 mm, mean weight diameter, and geometric mean diameter, while decreasing fractal dimension. Among the treatments, the uninoculated fermentation broth substrate showed the strongest effect, particularly in the 0.5–0.25 mm dry-sieved fraction. Metagenomic analysis showed that the uninoculated fermentation broth substrate altered microbial community composition, changed the relative abundances of taxa such as Sphingomonas sediminicola, Priestia megaterium, and Trichoderma asperellum, and increased the relative abundance of carbohydrate-active enzyme-related genes, including those encoding glycosyltransferases, carbohydrate esterases, and glycoside hydrolases. Chitin addition also improved aggregate stability and altered microbial community structure. These findings suggest that the uninoculated fermentation broth substrate and fungal-derived chitin improved black soil aggregate stability, potentially through shifts in microbial community composition and carbohydrate-related functional potential. This study provides a scientific basis for using fermentation-derived materials to improve the structure of degraded black soil. Full article