Search Results (266)

Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study, we conducted comparative metagenomic analyses of rhizosphere and root-adhering soils associated with healthy and diseased Morchella crops from two major production regions in China, aiming to elucidate shifts in microbial community composition, assembly processes, and functional potential. Disease conditions were linked to pronounced microbial dysbiosis, with community assembly shifting from stochastic to deterministic processes, particularly within fungal communities under host selection and pathogen pressure. Co-occurrence network analysis revealed substantial reductions in connectivity, modularity, and clustering coefficients in diseased soils, indicating the loss of ecological stability and keystone taxa. Functional annotations using CAZy, COG, and KEGG databases showed that healthy soils were enriched in genes related to carbohydrate metabolism, aerobic respiration, and ecosystem resilience, whereas diseased soils exhibited higher abundance of genes associated with stress responses, proliferation, and host defense. Furthermore, elemental cycling analysis demonstrated that healthy soils supported pathways involved in aerobic carbon degradation, nitrogen fixation, phosphate transport, and sulfur oxidation, while diseased soils favored fermentation, denitrification, phosphorus limitation responses, and reductive sulfur metabolism. Collectively, these results highlight the importance of microbial functional integrity in maintaining soil health and provide critical insights into microbiome-mediated disease dynamics, offering a foundation for developing microbiome-informed strategies for sustainable fungal crop management. Full article

Aging is a complex biological process influenced by internal and external factors, with diet and gut microbiota emerging as pivotal, interconnected modulators. This review explores their triangular relationship, emphasizing how they dynamically interact to shape health across the lifespan. Aging involves notable shifts in gut microbiota, including reduced diversity, increased pro-inflammatory taxa, and impaired production of key metabolites, like short-chain fatty acids. These changes contribute to systemic inflammation, immune-senescence, and age-related conditions, such as cognitive decline and metabolic disorders. Diet, particularly Mediterranean and plant-based patterns, plays a critical role in modulating gut microbiota by enhancing beneficial microbes and their metabolic functions. In contrast, Western-style diets rich in saturated fats and processed foods promote dysbiosis and accelerate aging. The review synthesizes evidence from human studies, animal models, and interventions to show how microbiota mediates diet-driven effects on aging. It also explores the role of specific nutrients, fiber, omega-3 fatty acids, and polyphenols in influencing microbial and host aging biology. Emerging therapies, including probiotics, prebiotics, and precision nutrition, show promise for promoting healthy aging by restoring microbial balance. However, gaps remain, including the need for long-term, age-specific studies, standardized microbiome protocols, and integrated omics approaches to support targeted longevity strategies. Full article

Technological advancements in computational power and algorithm design have enabled artificial intelligence to become a transformative force in microbiome research. This paper presents a concise overview of recent applications of this computational paradigm in human and animal health, with a particular emphasis on aquaculture. International projects focused on the intestinal microbiome have allowed human research to consistently dominate in terms of application cases, offering insights into various pathological conditions. In contrast, animal research has leveraged artificial intelligence in microbiome analysis to promote sustainable productivity, addressing environmental and public health concerns linked to livestock husbandry. In aquaculture, on the other hand, artificial intelligence has mainly supported management practices, improving rearing conditions and feeding strategies. When considering microbiome manipulation, however, fish farms have often relied on traditional methods, without harnessing the immense potential of artificial intelligence, whose recent applications include biomonitoring and modeling interactions between microbial communities and environmental factors in farming systems. Given the paradigm shift currently underway in both human health and animal husbandry, we advocate for a transition in the aquaculture industry toward smart farming, whose interconnected infrastructure will allow to fully leverage artificial intelligence to seamlessly integrate both biological measurements and rearing parameters. Full article

An estimated 2.6 billion individuals are currently living with overweight or obesity, and this number is projected to exceed 4 billion by 2035. Consequently, unless this increasing trajectory is effectively addressed, the trend is expected to continue in the coming years. The gut microbiome has emerged as a central regulator of host metabolism and energy homeostasis, making its detailed characterization crucial for the advancement of innovative therapeutic strategies and for elucidating mechanisms underlying metabolic health and disease. This review examines human obesity through the lens of the gut microbiome, providing a comprehensive overview of its role by addressing gut microbiome alterations, microbiome-driven mechanisms, dietary influences, prebiotic effects, microbiome-based therapeutics, and other approaches in the treatment of obesity and related metabolic disorders. The composition of the gut microbiome is altered in obesity and characterized by reduced microbial diversity and inconsistent shifts in dominant bacterial phyla, which collectively contribute to metabolic dysregulation. The gut microbiome influences obesity through multiple mechanisms. These include regulating energy balance and insulin sensitivity via short-chain fatty acids, inducing chronic inflammation, modulating metabolic and appetite genes, altering bile acid signaling, and promoting fat storage by inhibiting fasting-induced adipose factor. Dietary patterns exert a profound influence on gut microbiome composition and function, with plant-based diets conferring protective effects against obesity and its comorbidities. Microbiome-based therapeutics, including probiotics, synbiotics, and fecal microbiota transplantation, have demonstrated potential in modulating key metabolic and inflammatory pathways associated with obesity. As the scientific understanding of the human gut microbiome continues to advance, the integration of microbiome-based therapies into standard clinical practice is poised to become increasingly feasible and therapeutically transformative, particularly for obesity, a complex condition that demands innovative and customized interventions. Full article

This randomized, double-blind, controlled trial evaluated the effects of 4-week dietary fiber supplementation on gut microbiota, bowel-related quality of life, and secondary outcomes, including sleep and skin condition. A total of 105 healthy adults received either low-fiber foods (2.2 g/day total fiber, 1.2 g/day fermentable fiber) or high-fiber foods (8.2 g/day total fiber, including 6.4 g/day fermentable fiber). Gut microbiota was analyzed by 16S rRNA sequencing. Outcomes included stool diary, JPAC-QOL (Japanese version of the Patient Assessment of Constipation Quality of Life), OSA-MA (Oguri-Shirakawa-Azumi sleep inventory MA version), skin questionnaires, and fecal organic acids. The high-fiber group showed significant improvements in JPAC-QOL and increases in SCFA-associated genera such as Anaerostipes, Bifidobacterium, and Fusicatenibacter. These taxa positively correlated with other beneficial bacteria, including Faecalibacterium, suggesting ecological cooperation. The effects on sleep and skin were limited but correlated with beneficial bacteria, implying possible gut–brain and gut–skin axes involvement. This study demonstrated that short-term fiber supplementation meaningfully improved the bowel-related quality of life and beneficially modulated the gut microbiota in healthy adults. Although the systemic effects were modest, microbial shifts suggest that higher fiber intake may provide broader health benefits with longer interventions. This study was registered in the UMIN Clinical Trial Registry (UMIN000054712). Full article

Even with significant advances in therapeutic interventions and monitoring protocols, cystic fibrosis (CF) remains a critical pediatric health challenge affecting respiratory function and long-term patient outcomes. CF, caused by mutations in the CFTR gene, disrupts normal mucociliary clearance and creates conditions for chronic respiratory infections. The disorder affects individuals globally, with pediatric patients facing particularly complex microbial challenges that evolve throughout childhood growth. CF poses significant risks with progressive lung function decline and increased mortality, leading to potential short- and long-term respiratory complications. There is a growing concern among clinicians about the dynamic nature of airway microbial communities, with classical pathogens like Pseudomonas aeruginosa and Staphylococcus aureus showing sequential emergence patterns that complicate treatment strategies, highlighting an urgent need for microbiome-informed therapeutic approaches. Our review aims to provide a comprehensive overview of airway microbiome evolution in pediatric CF patients. We outline the molecular and ecological mechanisms involved in microbial community progression, as well as the age-related trajectories leading to pathogen-dominated ecosystems and the subsequent complications associated with microbial dysbiosis. Given the widespread implications of disrupted microbial balance on disease progression, our review also presents the temporal landscape of airway microbiome changes, including age-related microbial succession patterns, and explores the underlying mechanisms driving these ecological shifts. The progressive nature of microbial simplification frequently leads to treatment challenges, emphasizing the importance of investigating microbiome-targeted therapeutic interventions. Therefore, in this review, we also explore established therapeutic strategies, including CFTR modulators and probiotics, which could offer promising approaches to maintaining microbial balance and improving outcomes in pediatric CF patients. Full article

Bare soil expansion in urban forests, driven by persistent high-intensity trampling, degrades both macro-scale natural resources and micro ecological conditions. Targeted interventions are therefore essential. In this study, trampled bare ground in forest parks and artificially cultivated Ophiopogon japonicus were used as experimental models We employed trampled bare ground in forest parks as well as artificially cultivated O. japonicus as experimental models. Five treatments were implemented: enclosure control (CK), ploughing (F), Bacillus thuringiensis NL-11 application (J), biochar addition (C), and co-application of B. thuringiensis NL-11 with biochar (JC). Our results indicate that, compared with CK, biochar treatments reduced soil bulk density by 30%, increased soil porosity by 89%, and improved water-holding capacity. The soil nitrate nitrogen content in the NL-11 treatment was increased by 113.8% compared with CK, while the co-application of NL-11 with biochar exhibited the highest sucrase and urease activities. Notably, the co-application of B. thuringiensis NL-11 with biochar exhibited the most pronounced effects on aboveground biomass, plant height, and root development, followed by the B. thuringiensis NL-11 treatment. Microbial β-diversity shifts under co-application of B. thuringiensis NL-11 with biochar treatment strongly correlated with soil enzyme activation and plant growth enhancement (Mantel test, p < 0.05). Correlation analysis confirmed that exogenous nutrient inputs significantly influenced enzyme activities, thereby promoting plant development. These results highlight the effectiveness of integrating microbial inoculation with biochar to restore trampled urban forest soils. Full article

Fermentation is a crucial stage in the production of washed mild coffees, as it enables the generation of compounds that influence overall quality. The conditions to optimize this process are still unknown. This study evaluated the effects of fermenting coffee fruits and depulped coffee under two conditions: an open tank (semi-anaerobic-SA) and a closed tank (self-induced anaerobic fermentation, SIAF) over 192 h. Samples were taken every 24 h using a sacrificial bioreactor. A randomized complete block design with a factorial arrangement (2 × 2 + 1), plus a standard control, was employed, incorporating two factors: coffee type and fermentation condition. High-throughput sequencing of 16S and ITS amplicons identified an average of 260 ± 71 and 101 ± 24 OTUs, respectively. Weisella was the dominant lactic acid bacteria, followed by Leuconostoc and Lactiplantibacillus. Acetic acid bacteria, mainly Acetobacter, were more abundant under semi-anaerobic conditions. The yeast genera most affected by the fermentation condition were Pichia, Issatchenkia, and Wickerhamomyces. Repeated measures analysis revealed significant differences in pH, glucose consumption, lactic acid production, dry matter content, embryo viability, and the percentage of healthy beans. Principal component analysis was used to develop an index that integrates physical, physiological, and sensory quality variables, thereby clarifying the impact of each treatment. Samples from shorter fermentation times and SIAF conditions scored closest to 1.0, reflecting the most favorable outcomes. Otherwise, samples from longer fermentation times in both depulped and coffee fruits scored 0.497 and 0.369, respectively, on the SA condition. These findings support technically and economically beneficial fermentation strategies. Full article

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by social communication deficits, repetitive behaviors, and frequent gastrointestinal comorbidities. Emerging research suggests gut microbiota alterations contribute to ASD symptoms and gastrointestinal dysfunction, but detailed microbial profiles and clinical correlations remain underexplored. Methods: This study analyzed gut microbiota in 45 children aged 2–18 years diagnosed with ASD. Stool samples underwent 16S rRNA gene sequencing. Clinical assessments included ASD diagnostic subtype, adaptive functioning using the Vineland Adaptive Behavior Scale, gastrointestinal symptoms as per the Rome IV criteria, dietary patterns, and demographic variables. Statistical analyses correlated microbiota profiles with clinical features. Results: Gut microbiota composition was significantly influenced by delivery mode, age, sex, and diet. Vaginally delivered children had higher beneficial SCFA-producing bacteria, whereas Cesarean section was linked to increased pathogenic Clostridiales. High-calorie and protein-rich diets correlated with shifts toward pro-inflammatory taxa. Microbial diversity and specific genera correlated with adaptive behavior domains (communication, socialization, motor skills) and severity of gastrointestinal symptoms. Both pro-inflammatory and anti-inflammatory bacteria variably impacted neurodevelopmental outcomes. Conclusions: Gut microbiota composition in children with ASD is shaped by multifactorial influences and connected to neurobehavioral and gastrointestinal phenotypes. The findings of this study support the potential of microbiota-targeted interventions to ameliorate ASD-associated symptoms and improve quality of life. Full article

High-altitude wetland holds unique peatland ponds subjected to extreme diel environmental condition changes. Herein, we evaluate the response of photoautotrophic and nitrification activities and compare it with bacteria and archaea composition shifts in sediment and water changes during key hours of the day. Results indicate the presence of photo-inhibition, including ammonia oxidizers, but a high recovery of photosynthetic activities in the microbial mat and of potential specific functional groups towards the afternoon. The microbial community was composed of 45 phyla, mainly proteobacteria from Alpha-, Delta-, and Gammaproteobacteria and Bacteroidota in the water and sediments, and these later groups were notoriously enriched during the afternoon. The microbial community composition changes were associated with chlorophyll a, nutrients, and greenhouse gases reservoir variability, including methane potential release towards the atmosphere at hours of high radiation. Peatland pond microbial communities and their biogeochemical contribution change in a complex interplay coupled by time to environmental conditions predominantly driven by the extreme solar radiation. Full article

The biotechnological conversion of CO₂ to biomethane represents an energy-efficient, environmentally friendly, and sustainable approach within the waste-to-energy cycle. This process, in which CO₂ and H₂ are converted to biomethane in anaerobic bioreactors, is referred to as hydrogenotrophic biomethane production. While several studies have investigated hydrogenotrophic biomethane production, there is a lack of research comparing flocculent and granular sludge inoculum in continuously operated systems fed with a gas substrate. Both granular and flocculent sludge possess distinct advantages: granular sludge offers higher density, stronger microbial cohesion, and superior settling performance, whereas flocculent sludge provides faster substrate accessibility and more rapid initial microbial activity. In this study, two UASB (Upflow Anaerobic Sludge Blanket) reactors operated under mesophilic conditions were continuously fed with synthetic off-gas composed of pure H₂ and CO₂ in a 4:1 ratio and were compared in terms of microbial community shifts and their effects on hydrogenotrophic biomethane production. Biomethane production reached 75 ± 2% in the granular sludge reactor, significantly higher than the 64 ± 1.3% obtained with flocculent sludge. Although hydrogen consumption did not differ significantly, the granular sludge reactor exhibited higher CO₂ removal efficiency. Microbial analyses further revealed that granular sludge was more effective in supporting methanogenic archaea under conditions of gas substrate feeding. These findings offer advantageous suggestions for improving biogas production, enhancing waste gas management, and advancing sustainable energy generation. Full article

In the case of a notifiable animal disease like salmonellosis, manure is contaminated and must be disinfected. This can be performed using heat measures, chemical disinfectants, or long-term storage. All these measures bring along severe economic, ecological, and logistical problems. The aim of this study was to evaluate lactic acid fermentation (LAF) as an alternative disinfection method. Fermentation was started by adding a carbohydrate source to the manure and creating anaerobic conditions. For testing, cattle manure was enriched with different carbohydrate (CHO) sources and spiked with Salmonella Typhimurium (S. Ty.). The samples were incubated at 10 °C and 21 °C for 111 days (Exp1) and at 21 °C for 50 days (Exp2). The microbial shift was determined using cultural methods and MALDI-TOF. Both the change in pH and Enterococcus spp. were tested as suitable indicators. The results showed the different suitability of the selected CHO for hygienization by LAF. Using squeezed oat as an additive, S. Ty was reduced to below the detection limit under both temperature conditions within 21 days and 14 days. Additional saccharose decreased the reduction time. This study showed that LAF is a valuable alternative for disinfecting cattle manure in the case of bovine salmonellosis. Using this method, both manure and feed residues can be treated in one approach and afterwards be used as fertilizer. Full article

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses to N. scintillans bloom events is crucial for elucidating their underlying mechanisms and ecological impacts. This study investigated the microbial community dynamics, metabolic shifts, and the environmental drivers associated with a N. scintillans bloom in the coastal waters of Qinhuangdao, China, using high-throughput sequencing of 16S and 18S rRNA genes, co-occurrence network analysis, and metabolic pathway prediction. The results revealed that the proliferation of autotrophic phytoplankton, such as Minutocellus spp., likely provided a nutritional foundation and favorable conditions for the N. scintillans bloom. The bloom significantly altered the community structures of prokaryotes and microeukaryotes, resulting in significantly lower α-diversity indices in the blooming region (BR) compared to the non-blooming region (NR). Co-occurrence network analyses demonstrated reduced network complexity and stability in the BR, with keystone taxa primarily belonging to Flavobacteriaceae and Rhodobacteraceae. Furthermore, the community structures of both prokaryotes and microeukaryotes correlated with multiple environmental factors, particularly elevated levels of NH₄⁺-N and PO₄³⁻-P. Metabolic predictions indicated enhanced anaerobic respiration, fatty acid degradation, and nitrogen assimilation pathways, suggesting microbial adaptation to bloom-induced localized hypoxia and high organic matter. Notably, ammonia assimilation was upregulated, likely as a detoxification strategy. Additionally, carbon flux was redirected through the methylmalonyl-CoA pathway and pyruvate-malate shuttle to compensate for partial TCA cycle downregulation, maintaining energy balance under oxygen-limited conditions. This study elucidates the interplay between N. scintillans blooms, microbial interactions, and functional adaptations, providing insights for HAB prediction and management in coastal ecosystems. Full article

To address the problems of eutrophication exacerbation in water bodies caused by low carbon-to-nitrogen ratio (C/N) wastewater and the limited nitrogen removal efficiency of conventional constructed wetlands, this study proposes the use of biochar (Corncob biochar YBC, Walnut shell biochar HBC, and Manure biochar FBC) coupled with intermittent aeration technology to enhance nitrogen removal in constructed wetlands. Through the construction of vertical flow wetland systems, hydraulic retention time (HRT = 1–3 d) and influent C/N ratios (1, 3, 5) were regulated, before being combined with material characterization (FTIR/XPS) and microbial analysis (16S rRNA) to reveal the synergistic nitrogen removal mechanisms. HBC achieved efficient NH₄⁺-N adsorption (32.44 mg/L, Langmuir R² = 0.990) through its high porosity (containing Si-O bonds) and acidic functional groups. Under optimal operating conditions (HRT = 3 d, C/N = 5), the CW-HBC system achieved removal efficiencies of 97.8%, 98.8%, and 79.6% for NH₄⁺-N, TN, and COD, respectively. The addition of biochar shifted the dominant bacterial phylum toward Actinobacteriota (29.79%), with its slow-release carbon source (TOC = 18.5 mg/g) alleviating carbon limitation. Mechanistically, HBC synergistically optimized nitrogen removal pathways through “adsorption-biofilm (bacterial enrichment)-microzone oxygen regulation (pore oxygen gradient).” Based on technical validation, a dual-track institutionalization pathway of “standards-legislation” is proposed: incorporating biochar physicochemical parameters and aeration strategies into multi-level water environment technical standards; converting common mechanisms (such as Si-O adsorption) into legal requirements through legislative amendments; and innovating legislative techniques to balance precision and universality. This study provides an efficient technical solution for low C/N wastewater treatment while constructing an innovative framework for the synergy between technical specifications and legislation, supporting the improvement of watershed ecological restoration systems. Full article

Plant-to-plant interactions are essential for structuring plant communities and supporting adaptation in nutrient-poor, seasonally dry environments. This study examined the interactions between moss Leucobryum aduncum Dozy & Molk and Oreocharis hainanensis by analyzing microbial communities and physicochemical parameters across various sample types. These included soil [bare (B), O. hainanensis (O), moss (M), and moss + O. hainanensis (MO)], rhizosphere soil [O. hainanensis (ORS), moss (MRS), and moss + O. hainanensis (MORS)], and root [O. hainanensis (OHR), moss (MR), and moss + O. hainanensis (MOR)] using metagenomics sequencing across dry and wet seasons in limestone habitats on Hainan Island. During the dry season, combined plant samples MOR, MO, and MORS showed higher nutrients, supported by microbes that enhance nutrient turnover, which may indicate facilitation. Conversely, during the wet season, increased moisture leads to decreased nutrient levels and microbial communities shift, associated with slower nutrient turnover in combined plant samples, which may reflect competition. According to KEGG analysis, an increase in oxidative phosphorylation and ABC transporters in the dry season supported the facilitative interaction, while quorum sensing and two-component systems supported the competitive interaction in the wet season. These findings show how shifts between facilitation and competition arise from seasonal conditions and microbes in the limestone ecosystem. Full article