Search Results (361)

Ultrafine bubbles (UFBs) represent an emerging technology with unique physicochemical properties. This study investigated the effects of air-filled UFBs infused in drinking water on gut microbiota composition and the associated health markers in Sprague Dawley rats over a 12-week period. Using a two-phase design, UFB concentration was increased from 1.7 × 10⁶ to 6.5 × 10⁹ UFBs/mL at week 7 to assess dose-dependent effects. Administration of UFBs in drinking water induced significant shifts in gut microbiome populations, characterized by increased Bacteroidetes (+122% weeks 8–12) and decreased Firmicutes (−43% weeks 8–12) compared to controls. These microbial shifts coincided with enhanced short-chain fatty acid production (butyrate +56.0%, p ≤ 0.001; valerate +63.1%, p ≤ 0.01) and reduced inflammatory markers (TNF-α −84.0%, p ≤ 0.05; IL-1β −41.0%, p ≤ 0.05; IL-10 −69.8%, p ≤ 0.05). UFB effects demonstrated systematic concentration-dependent threshold responses, with 85.7% of parameters exhibiting directional reversals between low (1.7 × 10⁶ UFBs/mL) and high (6.5 × 10⁹ UFBs/mL) concentration phases rather than linear dose–response relationships. The systematic nature of these threshold effects, with 71.4% of parameters achieving statistical significance (p ≤ 0.05), indicates concentration-dependent biological mechanisms rather than random effects on gut biology. Despite current metagenomic techniques identifying only 25% of the total gut microbiome, the observed changes in characterized species and metabolites demonstrate UFB technology’s therapeutic potential for conditions requiring microbiome modulation, providing new insights into UFB influence on complex biological systems. Full article

Low-dose carrot rhamnogalacturonan-I (cRG-I) has shown consistent modulatory effects on the gut microbiota and immune function in humans. In this study we investigated its effects on the microbial composition and metabolite production of the gut microbiota of small (5–10 kg), medium-sized (10–27 kg), and large (27–45 kg) dogs, using inulin and xanthan as comparators. Fecal samples from six dogs of each size group were evaluated. Overall microbiome composition, assessed using metagenomic sequencing, was shown to be driven mostly by dog size and not treatment. There was a clear segregation in the metabolic profile of the gut microbiota of small dogs versus medium-sized and large dogs. The fermentation of cRG-I specifically increased the levels of acetate/propionate-producing Phocaeicola vulgatus. cRG-I and inulin were fermented by all donors, while xanthan fermentation was donor-dependent. cRG-I and inulin increased acetate and propionate levels. The responses of the gut microbiota of different sized dogs to cRG-I were generally consistent across donors, and interindividual differences were reduced. This, together with the significant increase in P. vulgatus during fermentation in both this study and an earlier human ex vivo study, suggests that this abundant and prevalent commensal species has a core capacity to selectively utilize cRG-I. Full article

Background/Objectives: Celiac disease (CD) is an autoimmune disorder characterized by small intestinal enteropathy triggered by gluten ingestion, often associated with gut dysbiosis. The most effective treatment is strict adherence to a gluten-free diet (GFD), which alleviates symptoms. This study uniquely integrates taxonomic, functional, and resistance profiling to evaluate the gut microbiota of women with CD on a GFD. Methods: To evaluate the long-term impact of a GFD, this study analyzed the gut microbiota of 10 women with CD on a GFD for over a year compared to 10 healthy controls with unrestricted diets. Taxonomic diversity (16S rRNA gene sequencing and the analysis of α and β-diversity), metabolic functionality (Biolog EcoPlates^®), and antibiotic resistance profiles (Cenoantibiogram) were assessed. Results: Metagenomic analysis revealed no significant differences in taxonomic diversity but highlighted variations in the abundance of specific bacterial genera. Women with CD showed increased proportions of Bacteroides, Streptococcus, and Clostridium, associated with inflammation, but also elevated levels of beneficial genera such as Roseburia, Oxalobacter, and Paraprevotella. Despite no significant differences in metabolic diversity, higher minimum inhibitory concentrations (MICs) in women in the healthy control group suggest that dietary substrates in unrestricted diets may promote the proliferation of fast-growing bacteria capable of rapidly developing and disseminating antibiotic resistance mechanisms. Conclusions: These findings indicate that prolonged adherence to a GFD in CD supports remission of gut dysbiosis, enhances microbiota functionality, and may reduce the risk of antibiotic resistance, emphasizing the importance of dietary management in CD. Full article

Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness—28% lower than expected for similar ecosystems—likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments. Full article

Antibiotic resistance genes (ARGs) in suburban freshwater ecosystems pose a growing public health concern by potentially reducing the effectiveness of medical treatments. This study investigated how rainfall influences ARG dynamics in Lake Katherine, a 62-hectare suburban lake in Columbia, South Carolina, over one year. Surface water was collected under both dry and post-rain conditions from three locations, and ARGs were identified using metagenomic sequencing. Statistical models revealed that six of nine ARG classes with sufficient data showed significant responses to rainfall. Three classes, Bacitracin, Aminoglycoside, and Unclassified, were more abundant after rainfall, while Tetracycline, Multidrug, and Peptide resistance genes declined. Taxonomic analysis showed that members of the Pseudomonadota phylum, especially Betaproteobacteria, were prevalent among ARG-carrying microbes. These findings suggest that rainfall can alter the distribution of ARGs in suburban lakes, highlighting the importance of routine monitoring and water management strategies to limit the environmental spread of antibiotic resistance. Full article

Potassium fertilizer management is critical for achieving high yields of Korla fragrant pear, yet current practices often overlook or misuse potassium inputs. In this study, a two-year field experiment (2023–2024) was conducted with 7- to 8-year-old pear trees using four potassium levels (0, 75, 150, and 225 kg/hm²). Metagenomic sequencing was employed to assess the effects on soil microbial communities, sulfur cycle functional genes, and fruit yield. Potassium treatments significantly altered soil physicochemical properties, the abundance of sulfur cycle functional genes, and fruit yield (p < 0.05). Increasing application rates significantly elevated soil-available potassium and organic matter while reducing pH (p < 0.05). Although alpha diversity was unaffected, NMDS analysis revealed differences in microbial community composition under different treatments. Functional gene analysis showed a significant decreasing trend in betB abundance, a peak in hpsO under K150, and variable patterns for soxX and metX across treatments (p < 0.05). All potassium applications significantly increased yield relative to CK, with K150 achieving the highest yield (p < 0.05). PLS-PM analysis indicated significant positive associations between potassium rate, nutrient availability, microbial abundance, sulfur cycling, and yield, and a significant negative association with pH (p < 0.05). These results provide a foundation for optimizing potassium fertilizer strategies in Korla fragrant pear orchards. It is recommended that future studies combine metagenomic and metatranscriptomic approaches to further elucidate the mechanisms linking potassium-driven microbial functional changes to improvements in fruit quality. Full article

Urine-derived and plant-derived benzoic acid can accumulate within soil, and it likely changes the soil microbial community as well as N₂O emissions; however, its mechanism is not clear. This study conducted an incubation experiment to monitor N₂O emissions under low moisture (40% water-filled pore space (WFPS)) and high moisture (85% WFPS) conditions. Metagenomic sequencing and q-PCR methods were used to determine the link between N₂O emissions and the composition and functions of soil microbiota. Benzoic acid (BA) was found to significantly, yet dose-dependently, impact N₂O emissions; that is, low BA concentrations increased N₂O, whereas high BA decreased N₂O. However, this was only found under high moisture conditions. In contrast, BA had little impact on N₂O emissions under low moisture conditions. Under high moisture conditions, BA increased the gene copy number of bacteria and fungi, and decreased the ratio of bacteria to fungi. Similarly, BA significantly increased the abundance of denitrification functional genes, but reduced the (NirS + NirK)-to-NosZ ratio at the peak of emission. This is in agreement with the observation of the increased relative abundance of genes encoding N₂O reductase (EC 1.7.2.4) and NO₃⁻ heterotrophic reductase (EC 1.7.1.15, EC 1.7.2.2) in the metagenomic analysis. In summary, high concentrations of benzoic acid reduce N₂O emissions by promoting the reduction of N₂O. This study revealed the impact of BA on soil microbiota and highlighted the favorable conditions and underlying mechanism behind BA’s significant impact on soil N₂O emissions. This study’s novelty lies in the fact that it deepens our understanding of the complicated role of root exudates and metabolites of animals and plants in soil. Full article

Partial substitution of mineral N fertilizer with manure (organic substitution) is considered as an effective way to reduce N input in intensive agroecosystems. Here, based on a 3-year field experiment, we assessed the influence of different organic substitution ratios (15%, 30%, 45%, and 60%, composted chicken manure applied) on vegetable productivity and soil physicochemical and biochemical properties as well as microbiome (metagenomic sequencing) in an intensive greenhouse production system (cucumber-tomato rotation). Organic substitution ratio in 30% got a balance between stable vegetable productivity and maximum N reduction. However, higher substitution ratios decreased annual vegetable yield by 23.29–32.81%. Organic substitution (15–45%) improved soil fertility (12.18–19.94% increase in soil total organic carbon content) and such improvement was not obtained by higher substitution ratio. Soil mean enzyme activity was stable to organic substitution despite the activities of some selected enzymes changed (catalase, urease, sucrase, and alkaline phosphatase). Organic substitution changed the species and functional structures rather than diversity of soil microbiome, and enriched the genes related to soil denitrification (including nirK, nirS, and nosZ). Besides, the 30% of organic substitution obviously enhanced soil microbial network complexity and this enhancement was mainly associated with altered soil pH. At the level tested herein, organic substitution ratio in 30% was suitable for greenhouse vegetable production locally. Long-term influence of different organic substitution ratios on vegetable productivity and soil properties in intensive greenhouse system needs to be monitored. Full article

Background/Objectives: The gut microbiota (GM) is pivotal for immune regulation, metabolism, and neurodevelopment. Infants undergoing surgery for congenital gastrointestinal anomalies are especially prone to microbial imbalances, with a paucity of beneficial bacteria (e.g., Bifidobacteria and Bacteroides) and diminished short-chain fatty acid production. Dysbiosis has been associated with severe complications, including necrotizing enterocolitis, sepsis, and feeding intolerance. This narrative review aims to critically examine strategies for microbiota modulation in this high-risk cohort. Methods: An extensive literature analysis was performed to compare the evolution of GM in healthy neonates versus those requiring gastrointestinal surgery, synthetizing strategies to maintain eubiosis, such as early nutritional interventions—particularly the use of human milk—along with antibiotic management and supplementary treatments including probiotics, prebiotics, postbiotics, and lactoferrin. Emerging techniques in metagenomic and metabolomic analysis were also evaluated for their potential to elucidate microbial dynamics in these patients. Results: Neonates undergoing gastrointestinal surgery exhibit significant alterations in microbial communities, characterized by reduced levels of eubiotic bacteria and an overrepresentation of opportunistic pathogens. Early initiation of enteral feeding with human milk and careful antibiotic stewardship are linked to improved microbial balance. Adjunctive therapies, such as the administration of probiotics and lactoferrin, show potential in enhancing gut barrier function and immune modulation, although confirmation through larger-scale studies remains necessary. Conclusions: Modulating the GM emerges as a promising strategy to ameliorate outcome in neonates with congenital gastrointestinal surgical conditions. Future research should focus on the development of standardized therapeutic protocols and the execution of rigorous multicenter trials to validate the efficacy and safety of these interventions. Full article

Background/Objectives: The main objective of the study is to assess the clinical utility of microbial cell-free DNA (mcfDNA) in neutropenic patients diagnosed with acute myeloid leukemia (AML) undergoing chemotherapy in the outpatient setting. Neutropenia is a common complication in this patient cohort and enhances the risk of fatal opportunistic bacterial and fungal infections. Accurate and timely diagnosis of these infections in outpatient asymptomatic individuals is critical. Methods: Fourteen patients were studied in this prospective observational case series. Traditional blood cultures (BCs) were obtained when clinically indicated and blood samples were collected for plasma mcfDNA metagenomic sequencing up to two times a week at outpatient oncology appointments. Results were compared in identifying potential infectious agents. Results: BCs identified pathogens in only two patients, despite several cases where infection was suspected. In contrast, mcfDNA testing detected pathogens in 11 of the 14 patients, including bacteria, such as Staphylococcus aureus, and invasive fungi, such as Candida and Aspergillus species, and Pneumocystis jirovecii. Conclusions: In the outpatient setting, mcfDNA surveillance offers a more reliable method for detecting pathogens. This approach identified actionable microbiologic results in immunocompromised individuals who did not meet standard clinical criteria for suspicion of infection. Further research is required to confirm the potential of mcfDNA surveillance in an outpatient setting to guide more accurate treatment decisions, reduce extensive clinical investigations, and improve neutropenic patient outcomes. Full article

Nitrate is a promising enhanced natural attenuation (ENA) material that enhances the microbial degradation of petroleum hydrocarbons by acting as an electron acceptor and nitrogen source. This study evaluated nitrate-containing materials (yeast extract, compound nitrogen fertilizer, and nitrate solutions) in microcosm experiments using gasoline-contaminated aquifer soils. Chemical analysis revealed that yeast extract achieved the highest degradation rate (34.33 mg/(kg·d)), reducing 600 mg/kg of petroleum hydrocarbons to undetectable levels within 18 days. Nitrate materials significantly increased nitrate-reducing activity and upregulated both aerobic/anaerobic hydrocarbon degradation genes, expanding microbial degradation potential. Metagenomic analysis identified Pseudomonas and Achromobacter as dominant genera across treatments, suggesting their critical roles in biodegradation. These findings demonstrate that nitrate-enhanced strategies effectively accelerate hydrocarbon attenuation under facultative anaerobic conditions, offering practical ENA solutions for petroleum-polluted sites. Full article

The objective of this study was to assess the effects of gallic acid (GA) on nutrient degradability, gas production, rumen fermentation, and the microbial community and its functions using in vitro fermentation methods. An in vitro experiment was conducted to test GA dose levels (0, 5, 10, 20, and 40 mg/g DM) in the cow’s diet. Based on the results of nutrient degradability, gas production, and rumen fermentation, the control group (0 mg/g DM, CON) and the GA group (10 mg/g DM, GA) were selected for metagenomic analysis to further explore the microbial community and its functions. The degradability of dry matter and crude protein, as well as total gas production, CH₄ production, CH₄/total gas, CO₂ production, and CO₂/total gas, decreased quadratically (p < 0.05) with increasing GA doses, reaching their lowest levels at the 10 mg/g DM dose. Total volatile fatty acid (VFA) (p = 0.004), acetate (p = 0.03), and valerate (p = 0.03) exhibited quadratic decreases, while butyrate (p = 0.0006) showed a quadratic increase with increasing GA doses. The 10 mg/g DM dose group had the lowest levels of total VFA, acetate, and valerate, and the highest butyrate level compared to the other groups. The propionate (p = 0.03) and acetate-to-propionate ratio (p = 0.03) linearly decreased with increasing gallic acid inclusion. At the bacterial species level, GA supplementation significantly affected (p < 0.05) a total of 38 bacterial species. Among these, 29 species, such as Prevotellasp.E15-22, bacteriumP3, and Alistipessp.CAG:435, were less abundant in the GA group, while 9 species, including Aristaeella_lactis and Aristaeella_hokkaidonensis, were significantly more abundant in the GA group. At the archaeal species level, the relative abundances of Methanobrevibacter_thaueri, Methanobrevibacter_boviskoreani, and Methanobrevibactersp.AbM4 were significantly reduced (p < 0.05) by GA supplementation. Amino sugar and nucleotide sugar metabolism, Starch and sucrose metabolism, Glycolysis/Gluconeogenesis, and Pyruvate metabolismwere significantly enriched in the GA group (p < 0.05). Additionally, Alanine, aspartate and glutamate metabolism was also significantly enriched in the GA group (p < 0.05). GA use could potentially be an effective strategy for methane mitigation; however, further research is needed to assess its in vivo effects in dairy cows over a longer period. Full article

Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and functional capacities in sheep. Eighteen ewes (Yunnan semi-fine wool breed, uniparous, 2 years old, and averaging 50 ± 2 kg body weight) were randomly assigned to diets containing an 8.5 (low; H_1), 10.3 (medium; H_m), or 13.9% (high; H_h) crude protein level from the 35th day of pregnancy to the 90th day postpartum. The total duration of the experiment was approximately 202 days. A total of nine fecal samples (three from each group) were analyzed via 16S rRNA and metagenomics sequencing. Higher archaeal alpha diversity and richness were observed in the H_m and H_h groups compared to the H_l group (p < 0.05). A Beta diversity analysis revealed the archaeal community’s distinct clustering mode based on protein levels. The methanogenic genera Methanobrevibacter and Methanocorpusculum were dominant across the three groups, and their abundance was influenced by protein intake. A functional prediction analysis indicated moderate changes in amino acid and carbohydrate metabolism, which are particularly associated with methane production, an important source of greenhouse gases. AMR genes (e.g., tetA (60), patA, vat, and Erm methyltransferase) and virulence factors (Bacillibactin, LPS) were significantly enriched when animals were fed high-protein diets. Our results demonstrated that dietary protein levels significantly influence gut archaeal composition, AMR gene enrichment, and related functional pathways. Medium-protein diets promoted greater archaeal diversity, whereas high-protein diets favored resistance gene proliferation and enhanced methanogenic activity. Optimizing dietary protein intake may enhance gut health, mitigate antimicrobial resistance risk, and reduce methane emissions, thereby supporting livestock sustainability and environmental protection. Full article

The COVID-19 pandemic prompted widespread adoption of intensified hand hygiene practices, raising concerns about their medium-term impact on the skin microbiome. This study investigates alterations in the hand microbiome of healthy adults during the pandemic compared to pre-pandemic periods in Majorca, Spain. A total of 30 volunteers (16 women, 14 men; mean age 44.1 ± 8.8 years) were sampled between 2014 and 2021. Palm swabs were collected following WHO guidelines, alongside measurements of skin pH, temperature, and handwashing frequency. Bacterial DNA was extracted and analyzed via 16S rRNA (V3-V4) metagenomic sequencing to assess microbial diversity and composition. Results revealed a significant decline in microbial diversity during the COVID-19 period, accompanied by a marked shift in the community structure. The Firmicutes phylum dominated, with Bacillales increasing from 30.7% to 84.1%, primarily driven by a surge in Staphylococcus species (e.g., S. pasteuri). Conversely, S. hominis and Actinomycetales nearly disappeared. No significant associations were observed with gender or handwashing frequency. The skin temperature increased during the pandemic, while the pH remained stable. The Staphylococcus/Bacillus ratio shifted significantly, favoring Staphylococcus dominance. These findings, derived from a geographically limited population in Majorca, Spain, demonstrate that stringent hygiene measures during COVID-19 reduced microbial diversity and restructured hand microbiome composition. The study underscores the necessity for balanced hygiene strategies that mitigate pathogen transmission while preserving beneficial microbial communities critical to skin health. Full article

Copiapoa solaris is an endemic cactus species from the Antofagasta region, Chile, thriving in arid coastal ecosystems known as “fog oases,” where the rising marine moisture is the primary water source. This study investigates the role of microbial communities associated with the rhizosphere of C. solaris in adapting to extreme environmental conditions, particularly focusing on the acdS gene, which encodes ACC deaminase—an enzyme that reduces ethylene production under stress. This research aims to elucidate the gene’s contribution to the adaptation of C. solaris in these challenging environments. Samples were collected from three sites (El Cobre, Quebrada Botija, and Quebrada Izcuña) that differ in relative humidity, temperature, and topography. Environmental DNA was extracted, phylogenetic diversity was analyzed, and metagenomic annotation of the acdS gene was conducted. The acdS gene was detected in all samples, with the highest relative abundance at Quebrada Izcuña (0.05%), characterized by low relative humidity (<70%) and severe water stress. Phylogenetic analysis revealed conserved sequences across sites, while taxonomic and alpha diversity were similar among them. However, beta diversity indicated that Quebrada Izcuña was the least homogeneous, hosting distinct taxa potentially associated with stress mitigation. The acdS gene was detected on plasmids at El Cobre and Quebrada Izcuña, suggesting its potential mobility within the metagenome. The results of this study highlight the intricate relationships between microbial communities and the resilient cactus species C. solaris in extreme environments. The conservation and abundance of the acdS gene, particularly in low-humidity conditions, suggest its vital role in facilitating stress tolerance through microbial interactions. Understanding these dynamics is crucial for developing strategies to enhance plant resilience in arid ecosystems, with potential applications in sustainable agriculture and ecosystem management under changing climatic conditions. Full article