Search Results (729)

Background: Presbycusis, also known as age-related hearing loss (ARHL), is the most frequent sensory disability affecting elderly adults worldwide. ARHL is characterized by bilateral, progressive, sensorineural hearing loss that is more pronounced at a high frequency. Conventional factors associated with ARHL include diabetes, hypertension, and a family history of hearing loss. The severity of hearing impairment varies between individuals. The defined causative molecular pathogenesis for ARHL is unknown, thus the identification of underlying pathogenic mechanisms involved in ARHL is imperative for the development of effective therapeutic approaches. Epigenetics is the study of phenotypic changes caused by the modification of gene expression rather than the alteration of a DNA sequence. While it is hypothesized that ARHL could result from undiscovered epigenetic susceptibility, there is a shortage of information on the role that epigenetic modification plays in ARHL. Here we present an investigation on the involvement of DNA methylation in ARHL. Results: Clinical, audiometric and DNA testing, and high-throughput methylation pattern screening were undertaken for ARHL patients and matched control subjects. Our results demonstrate a strong correlation between patients’ hearing measurements and methylation at CpG sites cg1140494 (ESPN) and cg27224823 (TNFRSF25). We identified 136 differentially methylated CpGs that were shared between a high and low audiometric frequency in the patient’s cohort. CpG cites in hearing loss candidate genes, KCNQ1, TMEM43, GSTM1, TCF25, and GSR, were found to be highly methylated in presbycusis patients as compared to the controls. A methylation polymerase chain reaction (PCR) assay was used to confirm methylation levels at a specific gene locus in ARHL patients and controls. Conclusions: Altered DNA methylation and its impact on gene expression has been implicated in many biological processes. By interrogating the methylation status across the genome of both hearing loss patients and those with normal hearing, our study can help to establish an association between the audiometric patterns and methylation status in ARHL, yielding new avenues for the identification of potential candidate genes for hearing loss. Full article

Recurrent vulvovaginal candidiasis (RVVC) is a common condition that affects women of reproductive age. The etiology of RVVC remains largely unknown, but it is believed to be associated with changes in vaginal microbiota composition. This study investigates the vaginal microbiota in 57 women with RVVC and 38 healthy controls. Bacterial DNA was analyzed using high-throughput 16S rRNA gene sequencing, and Candida and Saccharomyces species were determined by PCR. RVVC cases had a higher prevalence of Nakaseomyses glabratus (former Candida glabrata) compared to controls. Alpha diversity metrics were similar between groups, but beta diversity analysis revealed significant differences in vaginal microbiota composition. The Firmicutes abundance was altered in RVVC cases, with genus Bifidobacterium and phylum Actinobacteriota being more abundant than in the controls. At the genus level, Lactobacillus dominated controls using antibiotics, while Bifidobacterium was higher in cases with no antibiotic intake. Our study provides evidence that Nakaseomyses glabratus (former Candida glabrata) is a significant pathogen in RVVC, while Candida albicans was more prevalent in healthy women. The vaginal microbiota composition differs significantly between the two groups, with distinct patterns of bacterial abundance and changes in Firmicutes abundance. Full article

Few studies have addressed the coupling of arsenic (As) and nitrogen (N) geochemistry in natural soil. This research focused on the vertical distribution and coupling behavior of As and N in coastal wetland sediments. Pore water and sediment from barren wetlands and coastal wetlands near three estuaries (Guanhe River, Sheyang River, and Liangduo River) in central Jiangsu Province of China with Spartina alterniflora (S. alterniflora) were sampled, which were analyzed for total As content and speciation and N inorganic fractions. The bacterial community was investigated through 16s rDNA sequencing; diversity indices were calculated. The As change trend in pore water of surface sediment with increasing depth was opposite to that of NO₃⁻, possibly because NO₃⁻ promoted arsenite (As(III)) oxidation to arsenate (As(V)). Increased NO₃⁻ contents seemed to mitigate As toxicity. The vertical distribution of NH₄⁺ indicated anaerobic ammonium oxidation and iron (Fe) ammonium oxidation to reduce Fe oxides, resulting in As release, especially in the deeper sediment. High-throughput sequencing analysis revealed some potential bacteria possibly involved in As-N geochemical coupling, such as Bacillus and Psychrobacter, which can couple denitrification with As oxidation, and Sva1033, which may favor ammonium oxidation-induced As release. Our results suggest that the N-driven oxidation of As(III) and the ammonium oxidation-induced As release can be relevant to As-N coupling processes in the coastal wetland and emphasize the importance of microorganisms in such processes. This research deepens our understanding of As-N coupling in natural coastal wetlands, providing a theoretical basis for controlling As pollution. Full article

Tomato yellow leaf curl virus (TYLCV), tomato leaf curl New Delhi virus (ToLCNDV), and tomato chlorosis virus (ToCV) are emerging viruses that cause significant damage to tomato (Solanum lycopersicum). TYLCV and ToLCNDV are single-stranded DNA viruses from the genus Begomovirus, family Geminiviridae, while ToCV is an RNA virus from the genus Crinivirus (family Closteroviridae). These viruses share overlapping geographic ranges, vectors (the whitefly Bemisia tabaci), and host plants, making mixed infections common. This study investigated interactions between TYLCV and ToLCNDV and between ToLCNDV and ToCV in mixed infections of susceptible and TYLCV-resistant tomato genotypes. We evaluated infection, disease development, trans-replication of genome components, and genetic exchange. Our results showed no significant synergistic or antagonistic interactions, complementation, or interference between the viruses. TYLCV resistance in tomato genotypes remained stable. The DNA-B component of ToLCNDV exhibited impaired functionality and was not complemented by TYLCV. No evidence was found that the crinivirus tomato chlorosis virus (ToCV) enhances ToLCNDV infection, suggesting limited interactions despite shared vectors. Genetic exchange was detected in defective DNA (def-DNA) molecules using high-throughput sequencing (HTS), indicating potential genetic interactions between these viruses. These findings suggest that mixed infections do not pose immediate concerns for increased pathogenicity but highlight the ecological implications of genetic exchange, warranting further study of the evolutionary consequences of such interactions in mixed-virus environments. Full article

Background: While intratumoral microbiota have been identified in various cancers, their presence and clinical significance in lacrimal gland tumors remain largely unexplored. This study investigates the existence, composition, and potential clinical significance of intratumoral bacteria in lacrimal gland tumors. Methods: High-throughput 16S rDNA sequencing was performed on tumor DNA extracted from 89 paraffin-embedded tissues from patients with lacrimal gland tumors. Diversity analysis and LEfSe differential analysis were conducted to identify tumor-type-specific bacterial taxa. LASSO regression and the Cox proportional hazards models were used to analyze the relationship between intratumoral microbiota and prognosis. Results: Significant differences in the β diversity of intratumoral microbiota were observed across adenoid cystic carcinoma (ACC), carcinoma ex pleomorphic adenoma (CXPA), pleomorphic adenoma (PA), and IgG4-related disease (IgG4-RD) patients. After FDR correction, Garicola, Prevotella, Polaribacter, and Helicobacter were notably enriched in the tumors of ACC, CXPA, PA, and IgG4-RD patients, respectively. Importantly, patients with malignant lacrimal gland tumors who experienced relapse, distant metastasis, or death had significantly higher α diversity within their tumors. Furthermore, specific genera, such as Roseburia and Alloprevotella, were particularly associated with poorer prognosis in patients with malignant lacrimal gland tumors. Conclusions: This study provides a comprehensive analysis of microbial profiles in lacrimal gland tumors, highlighting distinct microbial characteristics across tumor types. Our findings suggest that intratumoral bacterial diversity and specific genera may serve as potential prognostic markers for malignant lacrimal gland tumors. Full article

Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study. Full article

A powerful strategy to accelerate bioprocess development is to complement parallel bioreactor systems with an automated approach, often achieved using liquid handling stations. The benefit of such high-throughput experiments is determined by the employed monitoring procedures. To gain a molecular understanding of the microbial production strains in miniaturized parallel single-use bioreactors, we extended the at-line monitoring procedures to transcriptome analysis in a parallel approach using RNA-Seq. To perform automated RNA-Seq experiments, we developed a sample preparation workflow consisting of at-line cell disruption by enzymatic cell lysis, total RNA extraction, nucleic acid concentration normalization, and Nanopore cDNA Library preparation. The pH-controlled aerobic batch growth of Saccharomyces cerevisiae was studied with six different carbon sources (glucose, pyruvate, fructose, galactose, sucrose, and mannose) on a 11 mL scale using 24 parallel stirred tank bioreactors integrated into a liquid handling station while performing at-line sample preparation for RNA-Seq on the same deck. With four biological replicates per condition, 24 cDNA libraries were prepared over 11.5 h. Off-line Nanopore sequencing yielded 20.97 M classified reads with a Q-score > 9. Differential gene expression analysis revealed significant differences in transcriptomic profiles when comparing growth with glucose (exponential growth) to growth with pyruvate (stress conditions), allowing identification of 674 downregulated and 709 upregulated genes. Insignificant changes in gene expression patterns were measured when comparing growth with glucose and fructose, yielding only 64 differentially expressed genes. The expected differences in cellular responses identified in this study show a promising approach for transcriptomic profiling of bioreactor cultures, providing valuable insights on a molecular level at-line in a high-throughput fashion. Full article

Environmental DNA (eDNA) is DNA isolated from environmental samples. It is distinctly different from genomic DNA, which is extracted directly from biological specimens. eDNA metabarcoding technology is a novel surveillance tool combining eDNA and second-generation high-throughput sequencing technology. Different from conventional approaches and biomonitoring techniques, eDNA metabarcoding technology (eMT) has many advantages, such as promising timeliness and accuracy, lower time consumption, and low cost, and thus is widely used in ecological and environmental monitoring, including that in rivers, lakes, oceans, soils, and sediments. As a tool, eDNA metabarcoding technology supplements the evaluation of environmental qualities by monitoring both the diversity of aquatic biology communities and target species. In addition, it is essential to understand the limitations of eDNA metabarcoding technology in practical applications. As a tool, eDNA metabarcoding technology features high efficiency, providing indicators of environmental health and allowing for the indirect estimation of the impact and extent of water pollution with respect to aquatic ecosystems. It provides new insights for aquatic environment protection. Full article

An accurate assessment of fish stocks is crucial for maintaining the health and stability of aquatic ecosystems. To understand the characteristics of fish diversity in the Qingshui River, this study utilized high-throughput sequencing data obtained through environmental DNA macrobarcoding technology (eDNA). The research explored differences in fish diversity and community characteristics in the Qingshui River by analyzing fish community structure, α diversity, β diversity, and the redundancy of environmental factors. This analysis aims to provide data support for water ecological monitoring and management. The results were as follows: (1) A total of 91 species of fishes from 18 families and seven orders were detected in the eDNA survey, and the dominant species was Cypriniformes, accounting for 72.5%. (2) There were significant differences in α diversity analysis in the Qingshui River (p < 0.05). (3) The fish community structure was similar in β diversity analysis. (4) In the redundancy analysis of environmental factors, pH, DO, TN, TP, ${\mathrm{N}\mathrm{O}}_2^{-}$ and ${\mathrm{M}\mathrm{n}\mathrm{O}}_4^{-}$ have the greatest impact on the Qingshui River Basin. eDNA technology has the advantages of high efficiency and low harm and can be used for water ecological monitoring and management. It provides a scientific basis for fish protection and a valuable reference for fish monitoring in the future. Full article

Sheep (Ovis aries), domesticated from wild Asian mouflon ~10,000 years ago, are an important livestock species adapted to various ecological environments. Recent advancements in high-throughput sequencing and global environmental databases have facilitated the exploration of genetic–environmental associations, uncovering the genetic and epigenetic mechanisms behind sheep’s adaptation to multiple environments. Studies show that HIF-1α and EPAS1 enhance high-altitude adaptation via hypoxic stress regulation; UCP1 contributes to cold adaptation through non-shivering thermogenesis; SLC4A4 and GPX3 increase drought resistance by regulating renal water reabsorption; and SOCS2 likely plays a role in metabolic and stress response regulation. Additionally, sheep adapt to temperature, drought, and environmental stress through DNA methylation, transcriptional regulation (e.g., SOD1, GPX4), heat shock proteins (e.g., HSP70), and metabolic pathways (e.g., UCP1). These findings offer valuable insights for improving sheep breeding and genetic enhancement. This review summarizes the mechanisms of adaptation to high altitude, cold, heat, drought, and comprehensive climate stress. Full article

Background: As an innovative approach to deep-sea aquaculture, fish farm vessels offer a dual benefit by alleviating the pressure on offshore fishing resources while providing an additional high-quality protein source. However, the potential impacts of vessel coatings on farmed fish remain poorly understood. Methods: In this study, to investigate the effects of vessel coatings on the large yellow croaker (Larimichthys crocea), we established four experimental groups with coating concentrations at 1-fold, 10-fold, 20-fold, and 80-fold levels. Antioxidant enzyme activities in kidney tissues were measured across all groups, while histological and transcriptome analyses were specifically conducted for the 1-fold and 80-fold concentration groups. Results: Firstly, significant alterations in antioxidant enzyme activity were observed in the 80-fold concentration group. Moreover, histological analysis demonstrated more severe pathological changes in kidney tissue at the higher concentration, including interstitial hemorrhage and tubular epithelial cell fatty degeneration. In addition, we identified 11,902 differentially expressed genes (DEGs) by high-throughput sequencing. KEGG pathway enrichment analysis revealed that the DEGs were predominantly involved in critical biological processes, including endoplasmic reticulum protein processing, oxidative phosphorylation, cytokine–cytokine receptor interactions, cell cycle regulation, DNA replication, and PPAR signaling pathways. Finally, the validation of nine selected DEGs through quantitative real-time PCR (qRT-PCR) showed significant correlation with RNA-Seq data, confirming the reliability of our transcriptome analysis. Conclusions: This study provides preliminary insights into the antioxidant stress response mechanisms of L. crocea to coating exposure and establishes a theoretical foundation for optimizing healthy fish farming practices in aquaculture vessels. Full article

Qinghai Lake, the largest inland saline lake in China, plays a vital role in wetland carbon cycling. However, the structure and function of soil bacterial communities in its estuarine and nearshore estuarine wetlands remain unclear. This study examined the effects of wetland type and soil depth on bacterial diversity, community composition, and functional potential in the Shaliu, Heima, and Daotang River wetlands using high-throughput sequencing. The results showed that wetland type and soil depth significantly influenced bacterial communities. Nearshore wetlands exhibited lower bacterial diversity in the 0–10 cm layer, while deeper soils (10–20 cm) showed greater regional differentiation. Estuarine wetlands were enriched with Proteobacteria, Actinobacteriota, and Chloroflexi, whereas nearshore wetlands were dominated by Actinobacteriota and Cyanobacteria. Functionally, estuarine wetlands had higher sulfate reduction and anaerobic decomposition potential, with Desulfovibrio, Desulfobacter, and Desulfotomaculum regulating sulfur cycling and carbon decomposition. In contrast, nearshore wetlands showed greater nitrogen fixation and organic matter degradation, facilitated by Rhizobium, Azotobacter, Clostridium, and nitrogen-fixing Cyanobacteria (e.g., Anabaena, Nostoc). Microbial metabolic functions varied by depth: surface soils (0–10 cm) favored environmental adaptation and organic degradation, whereas deeper soils (10–20 cm) exhibited lipid metabolism and DNA repair strategies for low-oxygen adaptation. These findings highlight the spatial heterogeneity of bacterial communities and their role in biogeochemical cycles, providing insights into wetland carbon dynamics and informing conservation strategies. Full article

Morels (Morchella spp.) are medicinal and edible mushrooms, renowned for their distinctive taste and appearance. Due to the low yields and difficulty of foraging wild morels, artificial cultivation has significant economic value. Outdoor cultivation yields are influenced by factors such as weather and diseases, which can result in crop instability or failure, thereby causing losses to farmers. Previous studies have typically concentrated on either the fungal or bacterial communities. In this study, we investigated the ecological relationships between morel growth and both the fungi and bacteria in soil, analyzed over multiple trophic levels. We investigated three soil types: soil in which morel death was observed (DM), soil in which no morels emerged (UM), and soil that is suitable for normal fruiting (NM). We used high-throughput ITS and 16S rDNA amplicon sequencing, alongside assessment of soil physicochemical properties, to investigate factors contributing to morel emergence and death. The results indicated that the richness and diversity of both fungal and bacterial communities in the normal fruiting soil (NM) were significantly higher than those in the non-fruiting soils (DM and UM). The bacterial community was primarily composed of Proteobacteria and Bacteroidota, while the fungal community was dominated by Ascomycota and Mucoromycota. Furthermore, Morchella was significantly enriched in NM, indicating that it had successfully colonized and could develop into fruiting bodies. The morel mycelium in NM effectively utilized external nutrient bags, enhancing the soil nitrogen and organic matter content while reducing the consumption of available phosphorus and potassium. LEfSe and random forest analyses identified Pedobacter and Massilia as biomarkers of NM, potentially associated with the symbiosis of Morchella, which may promote its growth. Furthermore, the construction of the fungal-bacterial co-occurrence network revealed that the NM soil exhibited a higher number of nodes and greater network stability, suggesting that its complex microbial community structure may play a crucial role in the successful cultivation of Morchella. Our results indicate that the failures in morel production were due to inadequate management practices. Elevated greenhouse temperatures may have promoted pathogen proliferation, hindering the effective utilization of external nutrient bags by morel mycelium. Consequently, the mycelium was unable to accumulate nutrients efficiently, leading to the inability of Morchella to fruit or resulting in developmental failures. This study offers valuable insights into the interactions between morel mycelium and soil microorganisms, elucidating the reasons for morel cultivation failure and suggesting strategies for optimizing morel cultivation. Full article

The microbiome remains a top area of research, and it is now common to examine any organic and inorganic samples for bacterial colonization. However, due to the ubiquity of bacteria in the environment, separating the low-burden colonization of bacteria from the possible contamination of laboratory reagents remains problematic. When examining samples of expected low bacterial burden, it is common to first amplify any bacterial DNA present through PCR before sequencing. In this work, we examined nine different commercial PCR enzymes and their reaction components as possible sources of bacterial DNA contamination. We found contaminating bacterial DNA in seven of the nine reactions, and this DNA was shown to come from a variety of species. Importantly, we were able to perform these studies solely with endpoint PCR and Sanger sequencing, which are more accessible and affordable than high-throughput, short-read sequencing and real-time PCR. This work confirms that there needs to be an increased emphasis on including control reactions in microbiome studies so that contaminating DNA sequences can be identified and addressed, and that this can be achieved with minimal resources. Full article

This experiment investigated the role of the gut microbiota in the growth and development of Antheraea pernyi, isolated gut bacteria related to lignin degradation in oak trees, and preliminarily verified their lignin degradation ability, providing a new tool for the field of biodegradation. The changes in the structure of the gut microbial community of the oak silkworm Antheraea pernyi at different developmental stages were analyzed via high-throughput sequencing of the 16SrDNA genes of the gut microbiota of fifth-instar larvae. A series of biological analyses were conducted, including amplicon sequence variant (ASV), microbial community diversity, microbial community composition, species difference, and evolutionary analyses. Ralstonia, Achromobacter, Pseudomonas, Cupriavidus, Bacteroidetes, Enterococcus, and Bacillus were the dominant bacterial groups in the gut microbiota of the larvae, with Ralstonia comprising the highest proportion, thereby providing a reference basis for a deeper understanding of the functions of the gut microbiota in insect growth and development. In this study, we activated and identified the MYZ028 strain isolated from the fifth-instar larvae of Antheraea pernyi through molecular biology, and we determined that the strain belonged to Bacillus subtilis. In terms of performance, the strain exhibited a high lignin-degrading ability and could effectively degrade lignin in a short time and simple environment. Due to the complex and difficult nature of degrading the lignin structure, research on the degradation of lignin by composite strains can be explored in the field of biodegradation. Full article