Search Results (5,209)

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

Respiratory microbiota and lipids are closely associated with airway inflammation. This study aimed to analyze the correlations among the respiratory microbiome, the airway glycerophospholipid–sphingolipid profiles, and airway inflammation in patients with asthma. We conducted a cross-sectional study involving 61 patients with asthma and 17 healthy controls. Targeted phospholipidomics was performed on exhaled breath condensate (EBC) samples, and microbial composition was analyzed via the 16S rDNA sequencing of induced sputum. Asthma patients exhibited significant alterations in the EBC lipid profiles, with reduced levels of multiple ceramides (Cer) and glycerophospholipids, including phosphatidylethanolamine (PE) and phosphatidylcholine (PC), compared with healthy controls. These lipids were inversely correlated with the sputum interleukin-4 (IL-4) levels. Microbiome analysis revealed an increased abundance of Leptotrichia and Parasutterella in asthma patients, both positively associated with IL-4. Correlation analysis highlighted a potential interaction network involving PA, PE, ceramides, Streptococcus, Corynebacterium, Parasutterella, and Leptotrichia. Specific alterations in airway microbiota and phospholipid metabolism are associated with asthma-related inflammation, supporting the concept of a microbiota–phospholipid–immune axis and providing potential targets for future mechanistic and therapeutic studies. Full article

Background: Myeloproliferative neoplasms (MPN), a group of chronic hematologic neoplasms, are driven by inflammatory mechanisms that influence disease initiation and progression. Emerging evidence highlights the gut microbiome and plasma metabolome as pivotal immunomodulators, yet their causal roles in MPN pathogenesis remain uncharacterized. Methods: We conducted a two-sample Mendelian randomization (MR) analysis to systematically evaluate causal relationships between 196 gut microbial taxa, 526 plasma metabolites, and MPN risk. Instrumental variables were derived from genome-wide association studies (GWASs) of microbial/metabolite traits. Validation utilized 16S rRNA sequencing data from NCBI Bioproject PRJNA376506. Mediation and multivariable MR analyses elucidated metabolite-mediated pathways linking microbial taxa to MPN. Results: Our MR analysis revealed that 7 intestinal taxa and 17 plasma metabolites are causally linked to MPN. External validation confirmed the three taxa’s differential abundance in MPN cohorts. Mediation analysis revealed two mediated relationships, of which succinylcarnitine mediated 14.5% of the effect, and lysine 27.9%, linking the Eubacterium xylanophilum group to MPN. Multivariate MR analysis showed that both succinylcarnitine (p = 0.004) and lysine (p = 0.040) had a significant causal effect on MPN. Conclusions: This study identifies novel gut microbiota–metabolite axes driving MPN pathogenesis through immunometabolic mechanisms. The validated biomarkers provide potential therapeutic targets for modulating inflammation in myeloproliferative disorders. Full article

As the primary biological risk threatening safe dairy production, bovine mastitis control highly relies on environmental disinfection measures. However, the mechanisms by which chemical disinfectants influence host–environment microbial interactions remain unclear. This study systematically investigated the disinfection efficacy and regulatory effects on microbial community composition and diversity of glutaraldehyde-benzalkonium chloride (BAC) and glutaraldehyde-didecyl dimethyl ammonium bromide (DAB) at recommended concentrations (2–5%), using 80 environmental samples from intensive dairy farms in Xinjiang, China. Combining 16S rDNA sequencing with culturomics, the results showed that BAC achieved a disinfection rate of 99.33%, higher than DAB’s 97.87%, and reduced the environment–gut microbiota similarity index by 23.7% via a cationic bacteriostatic film effect. Microbiome analysis revealed that BAC selectively suppressed Fusobacteriota abundance (15.67% reduction) and promoted Bifidobacterium proliferation (7.42% increase), enhancing intestinal mucosal barrier function through butyrate metabolism. In contrast, DAB induced Actinobacteria enrichment in the environment (44.71%), inhibiting pathogen colonization via bioantagonism. BAC’s long-acting bacteriostatic properties significantly reduced disinfection costs and mastitis incidence. This study first elucidated the mechanism by which quaternary ammonium compound (QAC) disinfectants regulate host health through “environment-gut” microbial interactions, providing a critical theoretical basis for developing precision disinfection protocols integrating “cost reduction-efficiency enhancement-risk mitigation.” Full article

Winter wheat (Triticum aestivum L.) silage has high feeding value and has become an important roughage resource in China. To recognize the optimal fermentation time of the silage product, this study systematically evaluated the temporal dynamics of microbial communities and metabolic profiles in whole winter wheat silage at days 7, 14, 30, 50, and 70. The dry matter (DM) content slightly fluctuated with the extension of fermentation time, with 28.14% at 70 days of ensiling. The organic matter and neutral detergent fiber content gradually decreased with the extension of fermentation time. A significant decrease in pH was observed at days 30, 50, and 70 compared to days 7 and 14 (p < 0.05), with the lowest pH value of 4.4 recorded at day 70. The contents of lactic acid, acetic acid, butyric acid, and total volatile fatty acids gradually increased with the extension of fermentation time, reaching a maximum at 70 days of ensiling. The dominant bacteria were Proteobacteria and Firmicutes at the phylum level, and the predominant bacteria were Hafnia-Obesumbacterium, Enterobacter, and Lactobacillus at the genus level. The relative abundance of Hafnia-Obesumbacterium and Lactobacillus fluctuated slightly with the duration of fermentation, reaching a minimum for the former and a maximum for Lactobacillus at 50 days of ensiling. By day 70, Sporolactobacillus emerged as a distinct silage biomarker. The dominant fungi was Ascomycota at the phylum level, and the predominant fungi were Fusarium and an unidentified fungus at the genus level. The correlation analysis revealed significant pH–organic acid–microbe interactions, with pH negatively correlating with organic acids but positively with specific bacteria, while organic acids showed complex microbial associations. Collectively, under natural fermentation conditions, the optimal fermentation period for wheat silage exceeds 70 days, and Sporolactobacillus shows potential as a microbial inoculant for whole winter wheat silage. These findings provide a theoretical foundation for optimizing whole winter wheat silage utilization and enhancing fermentation quality. Full article

This research investigated the impact of corn–soybean meal-based fermented feed on the growth performance, pork quality, and fatty acid profiles of lean-type finishing pigs. A total of 80 lean-type growing DLY (Duroc × Landrace–Yorkshire) pigs were randomly assigned to 2 groups, with 5 replicates of 8 pigs per pen. The pigs in control group (CON group) were fed a basal diet, while the pigs in fermented feed group (FF group) were fed a diet supplemented with 10% fermented feed. The experimental period lasted 70 days. Results exhibited that pigs in FF group had a significant increase in final body weight and average daily gain (ADG) (p < 0.05) and had a significant decrease in the feed-to-gain ratio (F/G) (p < 0.05). The FF group also exhibited significant promotion in muscle intramuscular fat content, marbling score, and meat color and significantly reduced the meat shear force and drip loss (p < 0.05). Serum analysis indicated that fermented feed significantly elevated blood glucose, total cholesterol, triglyceride levels, and serum hormones such as insulin, leptin, and IGF-1 (p < 0.05). Additionally, fermented feed significantly elevated the levels of polyunsaturated fatty acids (PUFAs) and monounsaturated fatty acids (MUFAs), whereas it decreased the saturated fatty acids (SFAs) contents (p < 0.05). The fermented feed also significantly enhanced pork nutritional values (p < 0.05). The fermented feed increased the expression of IGF-1, SREBP1c, PDE3, PPARγ, SCD5, and FAT/CD36 mRNA (p < 0.05). Furthermore, microbial 16S rDNA analysis uncovered that FF supplementation significantly reduced the Campilobacterota phylum abundance, while increasing the genus abundances of Clostridium_sensu_stricto, norank_f_Oscillospiraceae, unclassified_c_Clostridia, and V9D2013 (p < 0.05). In summary, the results indicated that the microbial fermented feed exhibited the regulation effects on pork quality and nutritional values of lean-type pigs through regulating lipid metabolism and gut microbial composition. Full article

The effect of periodical heatwaves and related thermal stratification in freshwater aquatic ecosystems has been a hot research issue. A large dataset of samples was generated from samples exposed to temporary thermal stratification in mesocosms mimicking shallow eutrophic freshwater lakes. Temperature regimes were based on IPCC climate warming scenarios, enabling simulation of future warming conditions. Surface oxygen levels reached 19.37 mg/L, while bottom layers dropped to 0.07 mg/L during stratification. Analysis by FlowCAM revealed dominance of Cyanobacteria under ambient conditions (up to 99.2%), while Cryptophyta (up to 98.9%) and Chlorophyta (up to 99.9%) were predominant in the A2 and A2+50% climate scenarios, respectively. We identified temperature changes and shifts in nutrient concentrations, particularly phosphate, as critical factors in microbial community composition. Furthermore, five distinct Microcystis morphospecies identified by FlowCAM-based analysis were associated with different microbial clusters. The combined use of imaging flow cytometry, which differentiates phytoplankton based on morphological parameters, and nanopore long-read sequencing analysis has shed light into the dynamics of microbial communities associated with different Microcystis morphospecies. In our observations, a peak of algicidal bacteria abundance often coincides with or is followed by a decline in the Cyanobacteria. These findings highlight the importance of species-level classification in the analysis of complex ecosystem interactions and the dynamics of algal blooms in freshwater bodies in response to anthropogenic effects and climate change. Full article

 Stipagrostis pennata is an important plant in desert ecosystems. Its seed-endophytic bacteria may play a critical role in plant growth and environmental adaptation processes. This study systematically analyzed the community composition and potential plant growth-promoting (PGP) functions of seed-endophytic bacteria associated with S. pennata. The results showed that while the overall diversity of bacterial communities from different sampling sites was similar, significant differences were observed in specific functional genes and species abundances. Nine endophytic bacterial strains were isolated from the seeds, among which Bacillus altitudinis strain L7 exhibited phosphorus solubilizing capabilities, nitrogen fixing, IAA production, siderophore generation, and multi-hydrolytic enzyme activities. Additionally, the genomic sequencing of L7 revealed the key genes involved in plant growth promotion and environmental adaptation, including Na⁺ efflux systems, K⁺ transport systems, compatible solute synthesis genes, and the gene clusters associated with nitrogen metabolism, IAA synthesis, phosphate solubilization, and siderophore synthesis. Strain L7 exhibits salt and osmotic stress tolerance while promoting plant growth, providing a promising candidate for desert microbial resource utilization and plant biostimulant development. Full article

Although age-related changes in the gut microbiome of pigs have been extensively studied, the dynamic patterns of fecal microbiota and SCFAs during the gestation-to-weaning period in sows remain poorly characterized. We aim to characterize the changes in fecal microbiota and SCFAs from pregnancy to weaning, and to investigate their associations with maternal weight gain during gestation. We systematically collected 100 fecal samples at four time points (day 30 of pregnancy (T1), 1–2 days before delivery (T2), day 10 after delivery (T3), and day 21 of weaning stage (T3)), and measured the body weight of sows at T1 (132 kg ± 10.8) and T2 (205 kg ± 12.1). The primary nutrient components of the diets during the gestation and lactation periods are summarized. All fecal samples were subjected to 16S rRNA gene sequencing. We found that a high proportion of crude fiber (bran) is a key feature of the gestation diet, which may affect enterotype shifts and gut microbial composition. Sows fed a high-fiber diet showed significant enrichment of gut microbiota, including genera such as Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, and Prevotella_9 during the gestational period (LDA score > 2). Moreover, Eubacterium_coprostanoligenes_group (average relative abundance: 5.5%) and Lachnospiraceae_NK4A136_group (average relative abundance: 2.5%) were the dominant bacteria during the lactation stage. Fecal propionate and butyrate levels were lowest in late gestation, and propionate negatively and acetate positively correlated with body weight change (p < 0.05). Additionally, certain Prevotella taxa were associated with arachidonic acid metabolism and acetate production (p < 0.05). Our study identified key microbial communities across four stages from gestation to weaning and revealed that dietary patterns can shape the sow gut microbiota. Furthermore, we observed significant correlations between SCFAs and body weight change during pregnancy. These findings provide a scientific basis and theoretical support for future strategies aimed at modulating gut microbiota and targeting SCFAs to improve maternal health and productivity throughout the gestation-to-weaning period. Full article

Organic farming is widely recognized as a promising practice for sustainable agriculture, yet its long-term ecological impacts remain insufficiently investigated. In this study, we evaluated these impacts by comparing heavy metal concentrations, soil invertebrate communities, and microbial profiles between long-term organic and conventional farming systems. A comparative analysis was conducted on 24 plot soils from two paired organic and conventional farm systems in Beijing, each managed continuously for over 20 years. Our results revealed that soils under organic management consistently contained 10.8% to 73.7% lower heavy metals, along with reduced geo-accumulation indices (I_geo, a standardized metric for soil contamination assessment), indicating decreased contamination risks. In terms of soil fauna, while conventional soils showed higher Collembola abundance, organic farming significantly enhanced Collembola richness and diversity by 20.6% to 55.0%. Microbial sequencing likewise revealed enhanced richness and diversity of bacteria and fungi in organic soils. These microbial communities also displayed shifts in dominant taxa and more stable co-occurrence networks under organic management. Principal component analysis and Mantel tests identified soil pH and nutrients as key drivers of soil biodiversity, while heavy metals also imposed negative influences. Collectively, these findings demonstrate that long-term organic farming not only mitigates environmental risks associated with soil contaminants but also promotes belowground ecological integrity by supporting biodiversity of soil fauna and microbiota. This study highlights the ecological significance of sustained organic practices and provides critical insights for advancing sustainable agricultural developments. Full article

To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation. Full article

Mast cell tumours (MCT) are the most common cutaneous neoplasms in dogs, with variable behaviours and patient survival time. Both indolent and aggressive forms have been described, but much remains to be explored regarding prognosis and therapy. Evidence has highlighted the influence of microbiota on multiple health and disease processes, including certain types of cancer in humans. However, knowledge remains scarce regarding microbiota biology and its interactions in both humans and canine cancer patients. This study aimed to characterise the faecal microbiota of dogs with MCT and compare it with that of healthy individuals. Twenty-eight dogs diagnosed with MCT and twenty-eight healthy dogs were enrolled in the study. Faecal samples were collected and analysed by Illumina sequencing of 16S rRNA genes. Alpha diversity was significantly lower in dogs with cancer, and the species diversity InvSimpson Indexwas reduced (p = 0.019). Principal coordinate analysis showed significant differences in the bacterial profile of the two groups: there was a significant lower abundance of the genera Alloprevotella, Holdemanella, Erysipelotrichaceae_UCG-003, and Anaerobiospirillum and, conversely, a significant increase in the genera Escherichia-Shigella and Clostridium sensu stricto 1 in diseased dogs. At the phylum level, Bacteroidota was significantly reduced in diseased dogs (25% in controls vs. 19% in MCT dogs). In conclusion, sequencing analysis provided an overview of the bacterial profile and showed statistical differences in the microbial communities of dogs with MCT compared with healthy dogs, suggesting a link between the gut microbiota and MCT in this species. Full article

Integrated rice–crayfish (Oryza sativa–Procambarus clarkii) co-culture (RC) systems have gained prominence due to their economic benefits and ecological sustainability; however, the interactions between soil properties and microbial communities in such systems remain poorly understood. This study evaluated the effects of the RC systems on soil physicochemical characteristics and microbial dynamics in paddy fields of southern Henan Province, China, over the 2023 growing season and subsequent fallow period. Using a randomized complete design, rice monoculture (RM, as the control) and RC treatments were compared across replicated plots. Soil and water samples were collected post-harvest and pre-transplanting to assess soil properties, extracellular enzyme activity, and microbial community structure. Results showed that RC significantly enhanced soil moisture by up to 30.2%, increased soil porosity by 9.6%, and nearly tripled soil organic carbon compared to RM. The RC system consistently elevated nitrogen (N), phosphorus (P), and potassium (K) throughout both the rice growth and fallow stages, indicating improved nutrient availability and retention. Elevated extracellular enzyme activities linked to carbon, N, and P cycling were observed under RC, with enzymatic stoichiometry revealing increased microbial nutrient limitation intensity and a shift toward P limitation. Microbial community composition was significantly altered under RC, showing increased biomass, a higher fungi-to-bacteria ratio, and greater relative abundance of Gram-positive bacteria, reflecting enhanced soil biodiversity and ecosystem resilience. Further analyses using the Mantel test and Random Forest identified extracellular enzyme activities, PLFAs, soil moisture, and bulk density as major factors shaping microbial communities. Redundancy analysis (RDA) confirmed that total potassium (TK), vector length (VL), soil pH, and total nitrogen (TN) were the strongest environmental predictors of microbial variation, jointly explaining 74.57% of the total variation. Our findings indicated that RC improves soil physicochemical conditions and microbial function, thereby supporting sustainable nutrient cycling and offering a promising, environmentally sound strategy for enhancing productivity and soil health in rice-based agro-ecosystems. Full article

Straw-returning is an effective way to improve straw utilization efficiency and reduce environmental pollution. Various straw-returning methods exist; however, their effects on soil microbial diversity and community composition in cool regions have been little studied. This study investigated the changes of soil microbial diversity and community composition under three straw-returning methods, i.e., straw mulching, straw mulching and overturning, straw crushed and mixed, as compared to straw removal as control. The results showed that straw-returning could alter the soil microbial community composition and abundance compared with straw removal. Alpha diversity analysis showed that straw mulching treatment, and straw crushed and mixed treatment significantly increased the diversity of both soil bacteria and fungi compared with straw mulching and overturning treatment. Moreover, this study preliminarily screened Trichoderma, Chaetomium and Streptomyces as potential straw-degrading microorganisms. This study provides basis for further enhancement of straw degradation by using soil microorganisms and sheds light on future work for improving straw degradation efficiency. Full article

Untreated sewage sludge (SS) and misused stabilization technologies have contributed to great contamination and the accumulation of various pollutants in agricultural soils. Regarding micro-pollutants’ degradation, scalable and effective technologies are still scarce. Although many attempts at composting adaptations have been discussed, only a few have been tested individually under outdoor conditions. To investigate different composting methods (bioaugmentation and semipermeable cover) for the removal of micro-pollutants frequently found in SS, we performed a set of on-site experiments. Windrows of SS and olive pruning were used as the compostable material and were subjected to (i) bioaugmentation with the fungus Penicillium oxalicum, (ii) covered composting, (iii) covered and bioaugmented composting, and (iv) a conventional composting pile, which was included as a control. The entire experiment lasted 99 days. Bioaugmentation without cover increased the phosphorus content, favored a reduction in heavy metal content, and was the only treatment that reduced carbamazepine at the end of the process. Moreover, the inoculation of P. oxalicum under semipermeable cover increased the richness, diversity, and dominance of specific microbial taxa and total bacterial abundance. The four mature composts obtained met the standards required to be classified in the B fertilizer category, showing that we reduced most of the micro-pollutants, and passed the germination test. Full article