Search Results (383)

The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet–microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet–microbiome associations in 79 prostate-cancer survivors (ages 62–81) enrolled in a randomized exercise intervention trial, 59.5% of whom still have active metastatic disease. Dietary intake was assessed using the Diet History Questionnaire (201 variables) and analyzed using three validated dietary pattern scores: Mediterranean Diet Adherence Score (MEDAS), Healthy Eating Index-2015 (HEI-2015), and the Mediterranean-Dash Intervention for Neurodegenerative Delay (MIND) diet score. Gut microbiome composition was characterized via 16S rRNA sequencing. Dimensionality reduction strategies, including theory-driven diet scores and data-driven machine learning (Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO)), were used. Statistical analyses included beta regression for alpha diversity, Permutational Multivariate Analysis of Variance (PERMANOVA) for beta diversity (both Bray–Curtis and Sørensen metrics), and Microbiome Multivariable Associations with Linear Models (MaAsLin2) with negative binomial regression for taxa-level associations. All models tested interactions with exercise intervention, APOLIPOPROTEIN E (APOE) genotype, and testosterone levels. There was an interaction between MEDAS and exercise type on gut alpha diversity (Shannon: p = 0.0022), with stronger diet–diversity associations in strength training and Tai Chi groups than flexibility controls. All three diet-quality scores predicted beta diversity (HEI p = 0.002; MIND p = 0.025; MEDAS p = 0.034) but not Bray–Curtis (abundance-weighted) distance, suggesting diet shapes community membership rather than relative abundances. Taxa-level analysis revealed 129 genera with diet associations or diet × host factor interactions. Among 297 dietary variables tested for cognitive outcomes, only caffeine significantly predicted Montreal Cognitive Assessment (MoCA) scores after False Discovery Rate (FDR) correction (p = 0.0009, q = 0.014) through direct pathways beneficial to cognitive performance without notable gut microbiome modulation. In cancer survivors, dietary recommendations should be tailored to exercise habits, genetic background, and hormonal status. Full article

Accurate characterization of seafloor sediment properties is critical for marine engineering design, resource assessment, and environmental management. Sidescan sonar offers efficient wide-area mapping capabilities, yet establishing robust quantitative relationships between acoustic backscatter intensity and sediment texture remains challenging, particularly in heterogeneous coastal environments. This study investigates the correlation between sidescan sonar backscatter intensity and sediment grain size parameters in waters southwest of Hainan Island, China. High-resolution acoustic data (450 kHz) were acquired alongside surface sediment samples from 18 stations spanning diverse sediment types. Backscatter intensity, represented by grayscale values, was systematically compared with grain size distributions and individual size fractions. Results reveal that mean grain size shows no meaningful correlation with backscatter intensity; however, fine sand fraction content (0.075–0.25 mm) exhibits a strong negative linear relationship (R² = 0.87 under optimal conditions). Distribution-level analysis demonstrates that backscatter variability mirrors sediment textural complexity, with coarse sediments producing broad, elevated intensity distributions and fine sediments yielding narrow, suppressed distributions. Inter-survey variability highlights the sensitivity of absolute intensity values to environmental conditions during acquisition. Spatial distribution analysis reveals that sediment grain size follows a systematic NE-SW gradient controlled by hydrodynamic energy, with notable local anomalies controlled by reef structures (producing coarse bioclastic sediment) and topographic sheltering (maintaining fine-grained deposits in shallow areas). These findings provide a quantitative basis for fraction-specific acoustic classification approaches while emphasizing the importance of multi-scale analysis incorporating both regional hydrodynamic trends and local morphological controls. The established relationship between fine sand abundance and acoustic response enables semi-quantitative sediment prediction from remotely sensed data, supporting improved seafloor mapping protocols for offshore infrastructure siting, aggregate resource evaluation, and coastal zone management in morphologically complex environments. Full article

Magnetic biochars (MBCs) have been shown to inhibit the horizontal transfer of antibiotic resistance genes (ARGs) in soils, both with and without microplastics (MPs); however, the underlying molecular biological mechanisms remain unclear. This study examined the effects of MBCs and coexisting polybutylene adipate terephthalate microplastics (PBAT MPs) on the physiological characteristics of Serratia marcescens ZY01 (a host strain carrying the tet gene) and further investigated their relationships with the absolute abundance of the tet gene in soil. The results demonstrated that MBCs promoted prodigiosin synthesis in Serratia marcescens ZY01 by mediating the electron transfer process, the effect of which was further enhanced in the presence of PBAT MPs. In treatments without PBAT MPs, MBCs generally suppressed the production of both proteins and polysaccharides in the extracellular polymeric substances. In contrast, in treatments containing PBAT MPs, the protein content gradually decreased with decreasing iron-to-biochar ratios, while the polysaccharide content remained largely unchanged. MBCs also elevated intracellular ROS levels due to the increased oxidative stress, particularly in treatments with PBAT MPs. A positive correlation between intracellular ROS levels and cell membrane permeability indicates that intracellular ROS was the primary driver of the increased cell membrane permeability. The presence of MBCs and PBAT MPs generally provided favorable habitats for Serratia marcescens ZY01, thereby enhancing its cell viability. Mantel test analysis indicated that MBCs influenced Serratia growth in soil by modulating its cell viability. Furthermore, the increased intracellular ROS level was significantly positively correlated with the absolute abundance of the tet gene in soil, implying the horizontal transfer of the tet gene at the intra-genus level. These findings offer helpful insights for developing environmental remediation strategies based on biochar–iron composites. Full article

Reductive soil disinfestation (RSD) is an effective approach for controlling horticultural plant diseases by improving soil properties. However, its effects on microbial communities and their functional characteristics across soil depths remain poorly researched. In this study, we evaluated the impacts of RSD using solid (rice bran, RB) and liquid (molasses, MO) organic amendments in a Fusarium-infested field. Changes in biotic and abiotic properties were examined at two soil depths (0–15 cm and 15–30 cm) and the potential of different amendments to restore microecological functions in deeper soil was assessed. Both RSD treatments alleviated soil acidification and salinization compared with the control. The absolute abundances of Fusarium oxysporum and Fusarium solani were significantly reduced under both treatments, with MO-RSD showing stronger pathogen suppression in the 15–30 cm layer. MO-RSD exerted a greater influence on microbial community structure across soil depths, resulting in bacterial-fungal co-occurrence networks with higher complexity. Metabolic activity and carbon source utilization increased significantly following both RSD treatments, with the greatest enhancement observed in the 0–15 cm layer under MO-RSD. Furthermore, MO-RSD enriched a higher diversity and abundance of beneficial microorganisms such as Bacillus, Paenibacillus, and Tumebacillus in the 0–15 cm layer, and Azotobacter, Penicillium, and Neurospora in the 15–30 cm layer. These microbes were closely associated with enhanced metabolic activity and pathogen suppression. Overall, MO-RSD established a more integrated and functionally diverse microbiota across the 0–30 soil profile, likely due to the greater permeability and mobility of liquid organic amendments in shaping deeper soil microbial communities. Full article

Background: Amoxicillin, clindamycin and azithromycin are the most frequently prescribed antibiotics for odontogenic infections, but their comparative effects on gut microbiota and intestinal homeostasis remain insufficiently understood. Disruption of gut microbiota, short-chain fatty acid (SCFA) production, and mucosal barrier integrity may contribute to gastrointestinal symptoms. We aimed to compare the impacts of these antibiotics on gut microbiota, SCFA levels, and colonic goblet cells. Methods: C57BL/6N mice were treated with oral amoxicillin, clindamycin, or azithromycin at clinically relevant dosages. Cecal index, fecal water content, and diarrhea index were assessed during treatment and recovery. Gut microbiota composition and absolute bacterial abundance were determined using 16S rRNA amplicon absolute quantification sequencing. SCFAs in cecal contents were quantified by gas chromatography–mass spectrometry. Goblet cell abundance and Muc2 mRNA expression in colon tissues were evaluated using Alcian blue staining and RT-PCR. Results: Amoxicillin caused moderate increases in cecal index, reduced Ligilactobacillus abundance, increased Escherichia-Shigella, lowered SCFA levels, and decreased goblet cells and Muc2 expression, with partial recovery after two weeks. Clindamycin induced more severe dysbiosis, including sustained Proteobacteria expansion, persistent loss of beneficial taxa, 86–90% reduction in SCFA production, and lasting decreases in goblet cells and Muc2 expression without recovery during the observation period. Azithromycin caused mild and reversible changes across all parameters. Conclusions: Among the three antibiotics, azithromycin had the least detrimental effects on gut microbiota, SCFA production, and mucosal barrier function, whereas clindamycin caused profound and persistent intestinal disruption. These findings provide comparative evidence to inform antibiotic selection in clinical practices. Full article

The application of nitrogen (N) fertilizer is one of the most important measures to affect crop yield and soil bacterial communities. In this study, the four rates of N (namely N0F 0 kg N ha⁻¹, N1F 90 kg N ha⁻¹, N2F 180 kg N ha⁻¹, and N3F 270 kg N ha⁻¹) along with a control (no fertilization, CK) were evaluated for their influence on sorghum yield, soil chemical properties, bacterial community, and diversity. The results showed that the yield-increasing effect was reduced by the higher dose of N input. Compared with N0F, sorghum yield increased by 58.8% in N1F and 68.2% in N2F but decreased by 8.1% in N3F relative to N2F. The soil pH decreased significantly with increasing N application. Compared with CK or N0F, N3F treatment increased the available P content by up to 18.6% or 32.2% but decreased the alkaline hydrolysis N, available K, organic matter, and total N contents by 8.4% or 23.8%, 5.5% or 10.6%, 8.4% or 28.8%, and 11.1% or 39.6%, respectively. In addition, different fertilization treatments altered the soil bacterial communities. Excess N fertilizer led to a decrease in bacterial abundance, and compared with N0F, the absolute abundance of bacteria increased by 18.7% in N1F, while it decreased by 31.8% in N3F. The predominant phyla, including Acidobacteria, Proteobacteria, and Chloroflexi, in the microbiome shift under different N application levels. The redundancy analysis (RDA) and Pearson’s correlation analyses indicated that the soil properties, especially soil pH, available P, total P, total N, and organic matter, were the key environmental factors that defined the bacterial community in the ecosystem. Within the scope of the present experiment, N application at 90 kg N ha⁻¹ (N1F) optimized soil bacterial community abundance in sorghum-cultivated soil, while N2F (180 kg N ha⁻¹) achieved the highest sorghum yield, suggesting a trade-off between optimizing the soil microbiome and maximizing crop yield under long-term fertilization. Full article

Microbial succession serves as a promising tool for estimating the postmortem interval (PMI). However, the patterns of microbial succession in burial scenarios require further exploration. This study established a pig carcass model, including buried and surface (control) groups, to investigate this. Using 16S ribosomal RNA (16S rRNA) gene sequencing, we analyzed microbial community changes and their differences across various decomposition stages. Results indicated that the decomposition rate of buried carcasses was slower than that of surface carcasses. Following the early decomposition stages, the alpha diversity of skin and underlying soil samples from buried carcasses decreased, a trend similar to that observed in the surface group. A significant shift in bacterial communities occurred in the buried group during abdominal rupture, mirroring the pattern in the surface group. At the phylum level, the relative abundance of Proteobacteria in the skin and soil of the buried group increased during later stages, consistent with the surface group. Furthermore, the buried and surface groups each possessed unique microbial taxa that responded to PMI changes. Using genus-level data, we identified feature taxa and constructed Random Forest models for PMI estimation. In the buried group, the mean absolute error (MAE) was 5.47 days for skin and 4.91 days for soil, while in the surface group, it was 5.59 days for skin and 5.30 days for soil. Although the model’s generalizability is currently limited by the sample size, the results demonstrate the predictability of microbial succession across different environmental contexts, underscoring its potential as a tool for PMI estimation in buried remains. Full article

To tackle grape branch and leaf waste and alleviate global feed shortages, this study tested silage made from Xinjiang ‘Seedless White’ grape foliage. Three treatments were established: CK (control, only grape branches and leaves), PL (inoculated with 5 × 10⁶ CFU·g⁻¹ fresh weight Lactiplantibacillus plantarum), and PLC (inoculated with 5 × 10⁶ CFU·g⁻¹ L. plantarum and 0.3% cellulase). Silages were fermented at 18–23 °C and analyzed on days 7, 15, 30, and 60. PLC reduced dry matter loss in the late fermentation stage, while lowering Neutral detergent fiber (NDF) and Acid detergent fiber (ADF) contents to solve the high-fiber issue of grape foliage silage. It also maintained a lower pH in the mid-to-late stage and higher Lactic acid (LA) content to ensure anti-spoilage. Microbiologically, PLC had the highest Lactiplantibacillus abundance on day 7; on day 60, its Simpson index was higher, meaning stronger microbial community stability. Firmicutes replaced Cyanobacteria as the new dominant phylum, with Lactiplantibacillus remaining the absolute dominant genus, and the growth of molds and yeasts was effectively inhibited. In conclusion, the combined application of L. plantarum and cellulase enhances the quality of grape branch and leaf silage. This study turns low-value grape branches and leaves into high-quality feed, providing support for grape branch and leaf resource utilization and helping alleviate global feed shortages. Full article

The overuse of antibiotics has led to the dissemination of antibiotic resistance genes (ARGs) in agricultural ecosystems, posing a threat to food safety. While current research on ARG transfer in soil–crop systems mainly concerns raw-consumed vegetables like lettuce, its impact on staple crops remains insufficiently studied. This study investigates how organic fertilizer affects ARG dissemination in the soil–millet system. Four fertilization treatments were established: no fertilization (CK), chemical fertilizer only (F), chemical fertilizer combined with manure (FM1), and chemical fertilizer combined with double amount of manure (FM2). Samples were collected from millet rhizosphere soil, roots, stems, leaves, and grains. High-throughput quantitative PCR was employed to investigate the transfer and dissemination of ARGs across the soil–millet system. Results showed that a total of 130 ARGs and 13 mobile genetic elements (MGEs), belonging to 17 gene families, were detected across all samples. The number of unique ARGs was higher in treatments FM1 and FM2 with manure. The accumulated absolute abundances of ARGs, MGEs and gene families all showed an order of FM1 > CK > FM2 > F. Pearson correlation analysis showed a close correlation among ARGs and MGEs. Although organic fertilizer application increased the absolute abundance of ARG-related genes in the rhizosphere soil and millet tissues, posing a potential threat to food safety, the rational strategy employed in the FM1 treatment effectively reduced ARG accumulation in millet leaves and grains. Therefore, this optimized application rate is recommended for millet production. Full article

Deep-sea cold seep ecosystems, known for their unique geochemical niches and chemosynthetic communities, harbor numerous “dark matter fungi (DMF)” that remain understudied compared to their bacterial and archaeal counterparts. Integrating 105 metagenomic datasets from 12 global cold seep sites, this study systematically elucidated the diversity, biogeography, and assembly mechanisms of cold seep fungal communities. Our analysis revealed highly diverse and abundant fungi, spanning 21 phyla and 928 genera, characterized by the absolute dominance of Ascomycota and a pervasive presence of unclassified DMF. Crucially, the fungal communities exhibited significant geographical and seep-type heterogeneity, with peak abundance notably in methane seep environments. Further analyses revealed that fungal community diversity and structure are influenced by both spatial and biological factors. Moreover, assembly exhibits multi-scale characteristics: dispersal limitation is the primary determinant globally, while local-scale structure is jointly driven by environmental variables and biological interactions with key chemosynthetic genes. These findings establish the macro-biogeographical pattern of deep-sea cold seep fungi, underscoring their tight coupling with core energy metabolism and providing essential data for future research and potential utilization. Full article

Cellulose nanocrystals (CNCs) have emerged as highly efficient adsorbents for heavy metal removal owing to their biodegradability, wide availability, and rich surface chemistry. Their abundant hydroxyl and other reactive functional groups provide a high density of active sites, significantly enhancing their affinity and adsorption capacity for toxic metal ions such as chromium (VI). The green adsorbent was characterised using FTIR to identify the functional groups. The optimum conditions were pH 6, concentration 140 mg/L, time 120 min, and adsorbent dosage 6 g/L, with a percentage removal of 95%. Deep machine learning was employed to predict the removal capacity of green and biodegradable adsorbents for chromium (VI) removal from wastewater. The findings show that adaptive neuro-fuzzy inference systems effectively model the prediction of Chromium (VI) adsorption. The Levenberg–Marquardt algorithm (LM) was used to train the network through feedforward propagation. In the training dataset, R² was 0.966, Mean Square Error (MSE) 0.042, Absolute average relative error (AARE) 0.053, Root means square error (RMSE) 0.077, and average relative error (ARE) 0.053 for the artificial neural network. The RMSE of 0.021, AARE of 0.015, ARE of 0.01, MSE of 0.017, and R² of 0.998 for the adaptive neuro-fuzzy inference system. These findings confirm the strong adsorption potential of CNCs and the suitability of advanced machine learning models for forecasting heavy metal removal efficiency. Full article

Background/Objectives: Metabolic enzymes are crucial for the detoxification of exogenously administered drugs, especially enzymes expressed in the intestine and the liver. Recent advancements in analytical methodologies enable sensitive and specific quantitative measurements of proteins, facilitating a more accurate evaluation of their expression and relative contribution to drug metabolism. Methods: The aim of the study was to characterize the protein expression levels of 16 Cytochrome P450s (CYP450s) and 2 carboxylesterases (CESs) in human liver and intestinal tissues using absolute quantification by HPLC-MS/MS. Human hepatocytes (HHEP) and human liver microsomes (HLM) were utilized, along with a novel intestinal preparation from cryopreserved human intestinal mucosa (CHIM), to perform proteomic analyses. Results: A comprehensive evaluation of 16 CYP450s and 2 CES enzyme expression in human liver and intestinal tissues is provided to reflect their relative abundance. Among the various in vitro systems evaluated, 14 of 16, 15/16, and 7/16 CYP450 of the isoforms analyzed were detected in HHEP, HLM, and CHIM, respectively. In hepatic systems, CYP2C9 exhibited the highest expression among CYP450 isoforms, a trend consistently observed in both HHEP and HLM. CYP3A4 was the most abundantly expressed isoform in CHIM preparations. Across all systems tested, CES1 and CES2 showed the highest overall protein expression levels, surpassing those of the CYP450s. Conclusions: Our findings demonstrate that the absolute quantification method employed is reliable, producing consistent results across two different in vitro hepatic systems (HHEP and HLM). This study supports the utility of absolute quantification approaches for accurately profiling drug-metabolizing enzymes and provides new, valuable insights to improve in vitro/in vivo extrapolation and more informed predictive pharmacokinetic modeling strategies. Full article

Denitrification and nitrification are two pivotal microbial processes relating to N₂O emissions. However, the difference in N₂O emission fluxes and N₂O-producing bacteria between a karst (KA) and non-karst area (NKA) remains unclear. The objective of this study is to compare the differences in soil N₂O emissions, nitrifying bacteria, and denitrifying bacteria during the growth period of rice in KA and NKA, and to explore the mechanisms by which microorganisms and environmental factors drive N₂O emissions. Here, N₂O emission fluxes of paddy fields were collected using the static dark chamber and measured using gas chromatography at KA and NKA in the Maocun Karst Experimental Site in Guilin, China. The nitrifying bacteria (ammonia-oxidizing bacteria, AOB) and denitrifying bacteria (nirK-denitrifier) were determined using real-time PCR and high-throughput sequencing, respectively. Results showed that during the rice growth period, the N₂O emission fluxes in KA was generally lower than that in NKA, with cumulative N₂O emissions of −0.054 and 0.229 kg·hm⁻² in KA and NKA, respectively. The absolute abundance of AOB in KA (8.91 × 10⁶–2.68 × 10⁷ copies·g⁻¹) was significantly higher than that in NKA (1.57 × 10⁶–6.48 × 10⁶ copies·g⁻¹), while the absolute abundance of nirK-denitrifier had no significant difference between the two areas. The composition and diversity of AOB and nirK-denitrifier differed significantly between KA and NKA. Results from partial least squares structural equation modeling (PLS-SEM) indicated that soil properties, carbon sources, and nitrogen sources had positive effects on AOB and nirK-denitrifier, while nirK-denitrifier had a negative effect on N₂O emissions. Partial least squares regression (PLSR) predictions revealed that NO₃⁻-N, SOC, TN, Mg²⁺, Ca²⁺, and pH were the most important factors influencing N₂O emission fluxes. This study highlights the critical role of the typical characteristics of KA soils in reducing N₂O emissions from paddy fields by driving the evolution of AOB and nirK-denitrifier. Full article

Accurate bacterial quantification is critical in many biological fields, from clinical diagnostics to environmental microbiology. Here, we establish a robust workflow for absolute quantification of bacterial species within mixed communities using Crystal Digital PCR^TM. Using a synthetic consortium of Clostridium acetobutylicum and Nitratidesulfovibrio vulgaris, we optimized primer design for species-specific detection and demonstrated that Crystal Digital PCR^TM enables reliable quantification of low-abundance species, down to a 1:10,000 ratio. We further show that the presence of one species does not interfere with the quantification of another. Finally, we demonstrate that Crystal Digital PCR^TM can also be used to determine plasmid-to-chromosome copy number ratios in bacteria carrying megaplasmids. Full article

The coastal restricted fishing area of Guangdong contains key spawning and nursery habitats with high biodiversity but growing ecological pressure, yet the influence of survey design and sampling frequency on biodiversity detection and abundance estimates remains unclear. We conducted four seasonal bottom-trawl surveys in 2023–2024 at 186 stations and compared fixed-site sampling (FS), simple random sampling (SRS), stratified random sampling by depth (StRS), and systematic sampling (SS). We recorded 563 species (446 fishes, 101 crustaceans, 16 cephalopods), observed seasonal shifts in dominant taxa, and found catch rates varied seasonally and spatially, peaking in summer. Species detection rose with station number and sampling frequency. For species richness, SS produced the highest detection and the lowest error and bias but showed volatility; StRS and SRS were more stable. For abundance, StRS had the lowest error, whereas SRS had the smallest absolute bias. Across all four seasons, 88 stations achieved an 80% richness detection rate; among reduced-frequency designs, autumn-only, spring–autumn, and autumn–spring–summer minimized errors. These results guide cost–precision trade-offs: SS (with random starts and interval rotation) for richness-oriented aims, and depth-based StRS for abundance, supporting optimized long-term monitoring and management in the northern South China Sea. Full article