Search Results (477)

Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76–83 years) enrolled from the randomized controlled trial entitled the “Generation 100 Study”, all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states. Full article

The gut microbiota plays a vital role in regulating the host’s physiological functions, including metabolism and immunity. The microbial composition and metabolism are modulated by multiple factors; host sex is an important yet under-explored determinant. To investigate the sex-dependent differences in the gut microbiota within the small and large intestine, sixteen somatic mature Jiangshan black pigs (eight males and eight females) were analyzed. The ileal and colonic microbial community and metabolites were profiled using 16S rRNA gene high-throughput sequencing and gas chromatography. Distinct sex-related discrepancies were observed in both the microbial composition and metabolism of the ileum and colon. In the ileum, compared with the male group, the female group exhibited higher abundances of Unclassified Chloroplast and Pseudomonas but a lower abundance of Romboutsia (adjusted p < 0.05). Functional prediction indicated enrichment in amino acid metabolism pathway in females, with more copy numbers of genes encoding key enzymes for propionate (mmdA) generation and elevated valerate levels (p < 0.05). In the colon, compared with the male group, the female group showed higher abundances of Streptococcus, Phascolarctobacterium, and Prevotella spp. and lower abundances of Eubacterium coprostano-ligenes group, Blautia, Christensenellaceae R-7 group, and Ruminococcus (adjusted p < 0.05). Additionally, the female group had more copies of genes mmdA and LcdA (associated with lactate production), along with higher concentrations of propionate and lactate (p < 0.05). Correlation analysis between microbial metabolites and sex-biased bacteria further revealed that the SCFA concentration positively correlated with Prevotella spp. and negatively correlated with Romboutsia, Christensenellaceae R-7 group, and Blautia. Collectively, these findings highlight the pronounced sex-dependent discrepancies in the microbial composition and metabolism within the small and large intestines of Jiangshan black pigs, providing new insights for precisely modulating the microbiota community and metabolism in pigs according to sex. Full article

Peat mosses of the genus Sphagnum are keystone species in peatland ecosystems and play critical roles in carbon sequestration, nitrogen fixation, and hydrological regulation. Indeed, these ecological functions are largely mediated by endophytic bacteria associated with Sphagnum. Here, five populations of the endemic Chinese moss species, S. multifibrosum, were sampled across southern China in peatland (PH) and rock habitats (RH). High-throughput sequencing of 16S rRNA and nitrogenase (nifH) genes was applied to characterize overall endophytic bacterial diversity and diazotroph diversity associated with S. multifibrosum, respectively, alongside host microsatellite genotyping. Proteobacteria was the dominant endophytic bacterial phylum. The bacterial communities exhibited significant spatial separation between eastern and western communities and community dissimilarities significantly increased with increasing geographic distances. Environmental heterogeneity and host genetics jointly shaped endophytic bacterial community assemblage. Climate was the most important determinant influencing bacterial composition, followed by host genotype and habitat type. Temperature, precipitation, and nitrogen deposition were the primary environmental factors that influenced composition. Bacterial diversity and composition exhibited no statistically significant differences between the two habitats. Further, the richness and abundances of diazotrophs and methanotrophs from PH communities were higher than in RH communities. Co-occurrence network analysis suggested that RH bacterial networks had lower connectance but were more modularized and exhibited higher complexity than PH networks. These results highlight the ecological functions of peat mosses in carbon and nitrogen cycling and suggest a need to prioritize the conservation of S. multifibrosum in peatland environments under global climate change. The results also provide a framework to help future wetland management and biodiversity conservation efforts in China. Full article

Osorno volcano (41.1° S, 72° W) is located in the Andean Southern Volcanic Zone. The volcano lies within a national park as part of the protected areas system. This setting provides an opportunity to compare soil microbial communities between sectors with (H) and without (NI) anthropogenic activities within a volcanic territory. To do so, we selected one of the most visited volcanoes in Chilean Patagonia to examine composition, diversity (taxonomic and phylogenetic), and co-presence and mutual exclusion interaction networks between members of volcanic soil bacterial communities. Soil DNA was extracted, and the 16S rRNA gene was analyzed by high-throughput DNA sequencing, followed by taxonomic identification. The most prevalent phylum across all sites (H and NI) was Pseudomonadota, followed by Acidobacteriota, Actinobacteriota, and Chloroflexota. Based on taxonomic and phylogenetic indices, we found that the diversity of bacteria was significantly less in the humanized area than in the non-intervened areas. Beta diversity analysis also revealed a clear separation between humanized and non-intervened soils. Additionally, a decrease in network connectivity was observed at NI sites. Our results provide clear evidence that anthropogenic factors, such as tourism, vehicle parking, and combustion processes, are key drivers shaping bacterial community structure in volcanic soils, with potential consequences for ecosystem health and the capacity to provide ecosystem services. Full article

Background: Thrushes (family Turdidae) are ecologically important passerine birds widely distributed across the Northern Hemisphere. However, the phylogenetic placement of several East Asian congeners, including Turdus pallidus, remains insufficiently resolved due to the limited resolution of partial mitochondrial or nuclear markers used in previous studies. Methods: In this work, we sequenced and annotated the complete mitochondrial genome of T. pallidus (16,739 bp) using high-throughput Illumina sequencing. The mitogenome exhibited the typical circular architecture and contained 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), with an overall GC content of 47.32%. Results: Most protein-coding genes initiated with the standard ATG codon, although lineage-specific deviations such as GTG in COX1 and ND2 were identified, and incomplete stop codons (T– or TA–) were observed, consistent with post-transcriptional polyadenylation. The 22 tRNA genes displayed typical cloverleaf secondary structures, except for trnS(AGN), which lacked a DHU arm, while rRNA genes were 977 bp (12S, 48.52% GC) and 1590 bp (16S, 44.65% GC), showing conserved stem regions but variable loop regions. Codon usage analysis revealed a strong bias toward A/T-ending codons, with a total of 3798 codons and an effective number of codons (ENC) of ~40, indicating moderate codon bias shaped by both mutational pressure and translational selection. Comparative analysis of evolutionary rates demonstrated that conserved genes such as COX1 and CYTB are suitable for resolving deeper relationships, whereas rapidly evolving genes like ATP8 provide resolution among closely related taxa. Conclusions: Phylogenetic reconstructions based on 13 mitochondrial protein-coding genes robustly supported the monophyly of Turdidae and recovered T. pallidus as most closely related to T. obscurus. Overall, this study provides a novel mitogenomic resource for T. pallidus, enhances phylogenetic resolution within Turdus, and underscores the value of complete mitochondrial genomes for molecular identification, conservation management, and avian evolutionary studies. Full article

Salinity is a key determinant governing microalgal growth, biochemical composition, and the structure of associated epiphytic bacterial communities. To investigate the effects of salinity on the structure and function of the epiphytic bacterial community in Desmodesmus intermedius, this study utilized 16S rRNA gene high-throughput sequencing to analyze the communities across the control (S0) and experimental groups (S5, S10, S15). The results demonstrated that salinity is a key environmental driver governing the structural and functional succession of the bacterial community. Alpha diversity analysis revealed that the control group exhibited the highest bacterial diversity and greater evenness. In contrast, the experimental groups showed a significant increase in the relative abundance of Thauera and a concurrent decrease in Roseococcus with increasing salinity. Beta diversity analysis revealed clear segregation of the epiphytic bacterial communities across the salinity groups. FAPROTAX functional prediction revealed that increasing salinity led to a reduction in chemoheterotrophy, photoheterotrophy, and aerobic chemoheterotrophy, while enhancing nitrogen respiration, nitrate reduction, and other denitrification processes. This shift indicates a substantial reconfiguration of carbon and nitrogen metabolic pathways. BugBase phenotype analysis further revealed that the experimental groups exhibited a higher proportion of Gram-positive bacteria and enhanced biofilm-forming capacity. Canonical correspondence analysis identified salinity as the predominant factor shaping bacterial community structure. This study comprehensively investigates the response mechanisms of the D. intermedius epiphytic bacterial community to salt stress, laying a foundation for understanding microbial functions within the phycosphere. Full article

Rammed earth walls in traditional villages in the humid and hot climate of Lingnan are susceptible to microbial damage and disease. Paishan Village in Zhuhai, which is the largest extant rammed earth building complex in the Pearl River Delta with rammed earth walls dating from the Ming (1368–1644) and Qing (1644–1912) Dynasties to the Republic of China (1912–1949) period, faces weathering and hollowing issues, yet targeted microbial research is lacking. This study, with a focus on the village’s rammed earth walls, aimed to reveal microbial diversity and its relationship to the environment, providing a basis for heritage conservation. We used SEM (scanning electron microscopy) to analyze the microstructure of walls facing different orientations. High-throughput sequencing (based on the 16S rRNA gene V3–V4 region) was combined with microbial community analysis. Species annotation and differential analysis were performed using QIIME2 and R. The results indicated that the west wall had the highest microbial diversity (45 at the phylum level and 2969 at the genus level), while the south wall exhibited the lowest. Different orientations shaped distinct community structures, with the north wall harboring a higher concentration of hygrophilous microorganisms, while the south wall was dominated by thermotolerant bacteria. All four walls shared only 0.29% of the core microorganisms. This study elucidates the distribution patterns of microorganisms in rammed earth walls in humid and hot areas, offering scientific support for their ecological restoration. Full article

As a typical heavy metal pollutant, cadmium (Cd) poses significant threats to ecosystems and human health. Giant duckweed (Spirodela polyrhiza), a small aquatic plant characterized by rapid growth and efficient heavy metal accumulation, holds great promise for phytoremediation. However, the mechanisms by which S. polyrhiza enriches Cd—particularly the contributions of its surface-associated microbiota—remain poorly understood. In this study, S. polyrhiza fronds were exposed to 0, 1, and 10 μM Cd, and we observed a concentration-dependent increase in the abundance of epiphytic microorganisms on the frond surfaces. High-throughput 16S rRNA gene sequencing revealed that Cd stress significantly altered the diversity of the frond-epiphytic bacterial community. Notably, the relative abundances of the genera Herbaspirillum, Enterobacter, and Pantoea increased significantly with rising Cd concentrations. Functional prediction using PICRUSt2 indicated enrichment under Cd stress of specific traits—such as the nitrate/nitrite transporter NarK, signal transduction mechanisms, and ion channel proteins—suggesting these taxa may actively participate in Cd uptake and tolerance. Together, our results reveal a synergistic S. polyrhiza–microbiome response to Cd and identify taxa/functions as targets and biomarkers for microbe-augmented remediation. Full article

Drought stress severely limits peanut productivity, highlighting the urgent need to understand the molecular mechanisms that underlie drought adaptation. While microRNAs (miRNAs) are known to play essential roles in plant stress responses, their functional contributions in polyploid crops like peanut remain insufficiently explored. This study provides the first integrated transcriptomic analysis of drought-responsive miRNAs in tetraploid peanut (Arachis hypogaea). We performed high-throughput sRNA sequencing on a drought-tolerant cultivar Fenhua 8 under PEG6000-simulated drought stress, identifying 10 conserved drought-responsive miRNAs. Among these, ahy-miR398 and ahy-miR408 were significantly downregulated under drought conditions. Degradome sequencing revealed that ahy-miR398 targets copper chaperones for superoxide dismutase (CCSs), potentially reducing SOD activation and amplifying oxidative stress. In contrast, ahy-miR408 targets laccase 12 (LAC12), P-type ATPase copper transporters (COPAs), and a blue copper protein-like (PCL) gene. These targets are involved in copper homeostasis and the regulation of reactive oxygen species (ROS), suggesting that ahy-miR408 plays a role in oxidative stress management. Functional validation in transgenic Arabidopsis lines overexpressing ahy-miR398 or ahy-miR408 showed significantly reduced drought tolerance, with impaired seed germination, shorter primary roots, and exacerbated growth suppression during water deprivation. Taken together, these findings highlight a novel miRNA-mediated regulatory network in peanut drought adaptation, centered on copper-associated oxidative stress management. This study provides new insights into miRNA-based regulation in polyploid crops and offers potential molecular targets for breeding climate-resilient peanut varieties, especially in arid regions where yield stability is crucial. Full article

Monitoring freshwater resources is crucial to drinking water quality. The Ismailia Canal supplies most freshwater to the Suez Canal area in Egypt. However, information on the freshwater microbiome is limited in this region. A total of 59 freshwater samples were collected. Along with determining the physicochemical properties of the samples, we used conventional methods to identify indicator bacteria. To overcome limitations of conventional culture, we employed high-throughput 16S rRNA gene sequencing, taxonomy profiling, and functional prediction to study uncultivated microbial communities. Total and fecal coliforms prevailed in 100% and 80% of samples, respectively. Predominant contaminants included E. coli, fecal streptococci, Pseudomonas aeruginosa, and Staphylococcus aureus. Taxonomic profiling revealed dominance of Proteobacteria and Actinobacteriota. Proteobacteria showed a positive correlation with Bacteroidetes and a negative correlation with Actinobacteria. Most samples had similar bacterial community structures, despite location-driven variability. Elevated bacterial loads were notable at the Qassasin district, which exhibited the highest relative abundance of genes associated with bacterial infections. This study provides key insights into the impact of freshwater microbiome on public health. Full article

Microbial communities that develop within biofilms on electrodes are necessary for the proper functioning of the microbial electrochemical system. However, the mechanism through which an exogenous exoelectrogen influences the population dynamics and electrochemical performance of biofilms remains unclear. In this study, we explored the community structure dynamics and electrochemical characteristics of iron mine soil biofilm co-cultured with Shewanella oneidensis MR-1, with the anode as the electron acceptor, and compared the results with those of iron mine soil biofilms alone on the anode. Shewanella oneidensis MR-1 improved the electrochemical activity of microbial biofilms, resulting in a higher maximum power density of 195 ± 8 mW/m² compared with that of iron mine soil (175 ± 7 mW/m²) and Shewanella (88 ± 8 mW/m²) biofilms individually. The co-cultured biofilms could perform near the highest power density for a longer duration than the iron mine soil biofilms could. High-throughput 16S rRNA gene sequencing of the biofilms on the anode indicated that the relative abundance of Pelobacteraceae in the co-culture system was significantly (p = 0.02) increased, while that of Rhodocyclaceae was significantly (p = 0.008) decreased, compared with that in iron mine soil biofilms. After continuing the experiment for two months, the presence of Shewanella oneidensis MR-1 changed the predominant bacteria of the microbial community in the biofilms, and the relative abundance of Shewanella was significantly (p = 0.02) decreased to a level similar to that in iron mine soil. These results demonstrate that Shewanella oneidensis MR-1 could improve the performance of iron mine soil biofilms in electrochemical systems by altering the composition of the functional microbial communities. Full article

As one of the key vectors for the transmission of Dengue fever, Aedes albopictus is highly ecologically adaptable. The development of environmentally compatible biological defence and control technologies has therefore become an urgent need for vector biological control worldwide. This study constructed and used double-stranded RNA (dsRNA) expression vectors targeting the cyp314a1 and cyp315a1 genes of Ae. albopictus to transform Chlamydomonas reinhardtii and Chlorella vulgaris, achieving RNA interference (RNAi)-mediated gene silencing. The efficacy of the RNAi recombinant algal strain biocide against Ae. albopictus was evaluated by administering it to Ae. albopictus larvae. The results showed that the oral administration of the cyp314a1 and cyp315a1 RNAi recombinant C. reinhardtii/C. vulgaris strains was lethal to Ae. albopictus larvae and severely affected their pupation and emergence. The recombinant algal strains triggered a burst of ROS (Reactive Oxygen Species) in the mosquitoes’ bodies, resulting in significant increases in the activities of the superoxide dismutase (SOD), peroxiredoxin (POD) and catalase (CAT), as well as significant upregulation of the mRNA levels of the CME pathway genes in larvae. In the simulated field experiment, the number of Ae. albopictus was reduced from 1000 to 0 in 16 weeks by the RNAi recombinant Chlorella, which effectively controlled the population of mosquitoes. Meanwhile, the levels of nitrogen (N), phosphorus (P), nitrate, nitrite, ammonia and COD (Chemical Oxygen Demand) in the test water decreased significantly. High-throughput sequencing analyses of 18S rDNA and 16S rDNA showed that, with the release of RNAi recombinant Chlorella into the test water, the biotic community restructuring dominated by resource competition caused by algal bloom, as well as the proliferation of anaerobic bacteria and the decline of aerobic bacteria triggered by anaerobic conditions, are the main trends in the changes in the test water. This study is an important addition to the use of RNAi recombinant microalgae as a biocide. Full article

Artificial (technical) snow production is an increasingly common practice in alpine regions, yet little is known about its role in shaping microbial communities at the molecular level. In this study, we combined culture-based methods with high-throughput 16S rRNA gene sequencing and functional trait prediction (FAPROTAX) to investigate bacterial communities across the full technical snowmaking cycle in one of Polish ski resorts. The molecular profiling revealed that technical snow harbors dominant taxa with known cold-adaptation mechanisms, biofilm-forming abilities, and stress tolerance traits (e.g., Brevundimonas, Lapillicoccus, Massilia, with a relative abundance of 2.95, 2.14, 3.38 and 5.61%, respectively). Functional inference revealed a consistent dominance of chemoheterotrophy (up to 38% in relative abundance) and aerobic chemoheterotrophy (up to 36%), with localized enrichment of fermentation (6.9% in cannon filter and 6.5% in sediment) and aromatic compound degradation (3.7% in source waters, 3.8% in cannon filter and 4.6% in sediment). Opportunistic and potentially pathogenic genera (e.g., Acinetobacter, Flavobacterium, Nocardia) persisted in sediments (7.4%, 21.4% and 3.5%) and meltwater (34.9% and 2.31% for the latter two), raising concerns about their environmental reintroduction. Our findings indicate that technical snowmaking systems act as selective environments not only for microbial survival but also for the persistence of molecular traits relevant to environmental resilience and potential pathogenicity. Our study provides a molecular ecological framework for assessing the impacts of snowmaking on alpine ecosystems and underscores the importance of monitoring microbial functions in addition to taxonomic composition. Full article

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) nucleases enable precise genome editing, but off-target cleavage remains a critical challenge. Here, we report the development of MAD7_HF, a high-fidelity variant of the MAD7 nuclease engineered through a bacterial screening system leveraging the DNA gyrase-targeting toxic gene ccdB. This system couples survival to efficient on-target cleavage and minimal off-target activity, mimicking the transient action required for high-precision editing. Through iterative selection and sequencing validation, we identified MAD7_HF, harboring three substitutions (R187C, S350T, K1019N) that enhanced discrimination between on- and off-target sites. In Escherichia coli assays, MAD7_HF exhibited a >20-fold reduction in off-target cleavage across multiple mismatch contexts while maintaining on-target efficiency comparable to wild-type MAD7. Structural modeling revealed that these mutations stabilize the guide RNA-DNA hybrid at on-target sites and weaken interactions with mismatched sequences. This work establishes a high-throughput bacterial screening strategy that allows the identification of Cas12a variants with improved specificity at a given target site, providing a useful framework for future efforts to develop precision genome-editing tools. Full article

Endophytic bacteria play an important role in the growth, stress tolerance, and metabolic function of salt-tolerant peanuts, yet their community assembly across different saline–alkali soils and plant organs remains poorly characterized. In this study, the V3–V4 variable region of the endophytic bacteria 16S rRNA gene in three organs (roots, leaves, and pods) of high-oleic-acid peanut variety Huayu9118 from three saline–alkali locations (Xinjiang, Jilin, and Shandong, China) was analyzed by high-throughput sequencing. A total of 1,360,313 effective sequences yielded 19,449 amplicon sequence variants (ASVs), with Proteobacteria (45.86–84.62%), Bacteroidota (6.52–13.90%), and Actinobacteriota (3.97–10.87%) dominating all samples. Niche strongly influenced microbial diversity: the roots exhibited the highest level of richness (Chao 1/ACE indices), while the leaves showed the greatest diversity (Shannon/Simpson indices) in XJ samples. Significant compositional differences were observed between aerial (leaves) and underground (roots/pods) organs. Geographic location also markedly shaped endophytic communities, with stronger effects in roots and pods than in leaves—a pattern supported by PCoA combined with ANOSIM (R (roots) = 1, R (pods) = 0.874, R (leaves) = 0.336, respectively, p < 0.001). Saline–alkali adaptation led to a marked enrichment of Novosphingobium in roots and pods and of Halomonas in leaves compared to non-saline–alkali-grown peanuts. Furthermore, the endophytic communities within the same organ type varied significantly across the three saline–alkali sites. Redundancy analysis (RDA) identified the key environmental factors shaping bacterial community composition in the root samples from each location: available phosphorus (AP) and sulfate (SO₄²⁻) were the strongest predictors in XJ; available potassium (AK) and chloride (Cl⁻) in DY; and hydrolyzed nitrogen (HN), pH, soil organic matter (SOM), and bicarbonate (HCO₃⁻) in JL. These findings demonstrate that niches and geographical conditions determined the composition and relative abundance of endophytic bacteria in salt-tolerant peanuts, providing new insights into microbial ecological adaptation in saline–alkali ecosystems. Full article