Search Results (1,982)

Freshwater amphipods of the genus Gammarus are important trophic components of aquatic ecosystems and are increasingly considered a potential bioresource for aquaculture. However, their role in the maintenance and transmission of infectious agents remains poorly understood. This study evaluated the presence of major crustacean and fish pathogens in Gammarus lacustris populations from Kazakhstan and characterized associated viral communities using metagenomic sequencing. Six pooled samples collected from freshwater ecosystems across Kazakhstan were screened using PCR and RT-PCR assays targeting World Organisation for Animal Health (WOAH)-listed pathogens, including White Spot Syndrome Virus, Taura Syndrome Virus, Infectious Myonecrosis Virus, Aphanomyces astaci, and Aphanomyces invadans. In parallel, high-throughput sequencing (Illumina NovaSeq) was performed to assess virome composition and structure. No WOAH-listed pathogens were detected, suggesting a low detectable occurrence of major notifiable agents under the conditions of the present study. Metagenomic analysis revealed a virome dominated by RNA viruses, particularly picorna-like viruses (Picornaviridae), Dicistroviridae, and Marnaviridae. Phylogenetic and genome organization analyses identified potentially novel or highly divergent viral lineages within Picornavirales. Collectively, these findings suggest a favorable epizootiological profile of G. lacustris populations while highlighting freshwater amphipods as hosts of diverse and partially uncharacterized viral communities relevant to aquatic disease surveillance and aquaculture biosecurity. Full article

Dairy cows are economically significant ruminants in China, and the dairy industry is closely linked to food safety and the agricultural economy. However, various factors such as pathogenic microorganisms often lead to frequent diseases in dairy cows. Furthermore, as potential hosts for diverse viruses, dairy cows can harbor zoonotic pathogens, which pose a threat to public health. The Shaanxi–Gansu–Ningxia region boasts abundant natural resources and extensive pastures. It is a major animal husbandry base in Northwest China, and dairy farming plays a significant role in the local economy. However, research on dairy cow virus diversity in this region remains limited; epidemic prevention and control capabilities are constrained, and the risk of disease outbreaks is elevated. In this study, 790 dairy cow samples were collected from 13 large-scale farms and free-range households in the Shaanxi–Gansu–Ningxia region from 2021 to 2023. Sample types consisted of nasal and anal swabs. Six viral metagenomic libraries were constructed and analyzed using high-throughput sequencing and bioinformatics methods, leading to the identification of 51 viral families. These comprised 16 positive-sense single-stranded RNA virus families, one Retroviridae family, four double-stranded RNA virus families, 21 double-stranded DNA virus families, and nine single-stranded DNA virus families. Among these, RNA viruses were represented by families such as Astroviridae, Coronaviridae, Caliciviridae, Picornaviridae, and Picobirnaviridae; DNA viruses were primarily detected in Circoviridae, Papillomaviridae, Genomoviridae, and Smacoviridae. Alpha diversity analysis revealed no significant differences in viral diversity and abundance among the three regions (p > 0.05); however, significant differences were observed in the read counts and proportions of RNA and DNA viruses across the provinces. Phylogenetic analysis further indicated that viruses carried by dairy cows exhibit considerable genetic diversity and pose potential cross-species transmission risks. This study established a reference database for the dairy cow virome in the Shaanxi–Gansu–Ningxia region, elucidated the phylogenetic relationships of key viruses, and provided a scientific basis for future monitoring and prevention of dairy cow viruses. Full article

High-throughput sequencing methods have made it possible to identify numerous novel tick-borne viruses that are potentially pathogenic to humans. Among these, Songling virus (Orthonairovirus songlingense, SGLV) has been associated with febrile illness in patients following tick bites in China, but its geographic distribution outside China remains largely unexplored. In this study, we aimed to detect SGLV circulation in ticks across Asian Russia, focusing on regions bordering China. A total of 3444 adult ticks representing six species were collected from 170 locations across 11 regions during the summer of 2024. SGLV RNA was detected in Haemaphysalis concinna ticks, with 11 positive specimens yielding an SGLV RNA prevalence rate of 2.2%. Positive ticks were found in four regions, with the highest positivity rate (5.8%) recorded in Amur Oblast, which directly borders China. The detection of SGLV in the Republic of Altai represents the westernmost record of this virus to date. Full-length nucleoprotein-coding sequences obtained for all Russian isolates revealed up to 1.2% nucleotide divergence. Phylogenetic analysis confirmed that all Russian SGLV isolates belong to Orthonairovirus songlingense, with the Altai SGLV isolate showing genetic similarity to a human-derived Chinese SGLV isolate. Co-infections with Rickettsia heilongjiangensis were detected in four SGLV-positive ticks, highlighting the potential for simultaneous pathogen transmission. These findings establish the first evidence of SGLV circulation in Russia across a wide geographic range and underscore the need for differential diagnosis of febrile illnesses following tick bites in this region. Full article

Venous thromboembolism (VTE) significantly impacts lung adenocarcinoma outcomes, yet current predictive tools lack precision. We investigated plasma extracellular vesicle (EV) mRNA as a liquid biopsy source to identify a pro-thrombotic molecular profile in VTE patients. Within a prospective cohort of 260 patients, we performed a retrospective nested case–control study, matching 10 VTE cases with 11 thrombosis-free controls. Plasma EV-RNA was analyzed via high-throughput sequencing. Differentially expressed genes (DEGs) were integrated with functional enrichment and explored across public non-cancer VTE datasets, buffy coat samples, and cell lines. RNA-seq identified 483 DEGs within the VTE patient EV compartment, predominantly linked to neutrophil degranulation (NETosis), inflammation, and coagulation. We identified a set of EV-associated candidate genes (SELP, ELANE, MYL9, DNASE1L3) distinguishing cancer-associated thrombosis from non-malignant VTE, along with transcripts (TFPI, FCGR2A) selectively enriched within the EV compartment relative to circulating blood cells. P-selectin (SELP) was the only significantly increased marker, providing the strongest complementary support at the protein level. This molecular state was detectable prior to the occurrence of VTE. Plasma EVs capture a multicellular mRNA profile, reflecting the systemic immunothrombotic activation in lung adenocarcinoma. Despite sample size limitations, these findings should be considered exploratory and hypothesis-generating, but they suggest the EV-derived mRNA in combination with circulating markers such as SELP may provide a framework for future studies aimed at improving risk stratification. Full article

As important silkworm varieties reared on artificial diet, Youshi No. 1 (YS) and Guangshi No. 1 (GS) showed remarkable differences in physiological characteristics. GS had significantly better performance than YS in body weight, cocooning ability, food intake, feed utilization efficiency, and digestive enzyme activities. We further performed metabolomics and 16S rRNA high-throughput sequencing to analyze their metabolic profiles and midgut microbiota. More than 40 differential metabolites were screened out, and four metabolic pathways related to feeding divergence were determined via KEGG enrichment, among which L-valine was enriched in multiple pathways. Significant structural differences were also observed in midgut microbiota, and Bacillus was positively correlated with pantothenic acid and valine metabolism. These correlational results disclosed that differential metabolites and gut microbiota might underlie the phenotypic variations between the two varieties. Integrated analysis combined with functional verification experiments demonstrated that supplementation of 1% L-valine or specific Bacillus strains in an artificial diet was associated with the improvement of the growth performance, cocoon quality, and feed utilization efficiency of the YS silkworm variety. Full article

Suspended particulate matter (SPM) is a key environmental driver in aquatic ecosystems and plays a significant role in shaping microbial communities, particularly in sediment-rich rivers. Dam construction alters hydrological regimes and creates distinct SPM gradients; however, the response mechanisms of microeukaryotic plankton communities remain poorly understood. In this study, we used 18S rRNA gene high-throughput sequencing to characterize microeukaryotic plankton communities across riverine, lacustrine, and transitional zones of the Xiaolangdi Reservoir on the Yellow River (China). Our results revealed distinct community compositions in the lacustrine zone, with SPM identified as the primary factor driving community differentiation. Alpha diversity was highest in the riverine zone, while beta diversity differences among zones were dominated by species turnover. Dominant taxa included Cryptophyta (44.71% ± 30.79%), Metazoa (18.98% ± 17.71%), Perkinsea (7.97% ± 9.78%), Chlorophyta (7.06% ± 5.80%), and Dinophyta (6.06% ± 6.73%). Metazoa, Dinophyta, and Phaeophyta were enriched in high-SPM riverine waters, whereas Alveolata dominated low-SPM lacustrine zones. Community assembly was primarily deterministic, governed mainly by homogeneous selection, with stochastic processes exerting stronger influence in riverine zones. Network analysis indicated that riverine zones exhibited more complex and stable networks, lacustrine zones showed higher local but lower global connectivity, and transitional zones displayed stronger interactions but lower stability. These findings advance our understanding of microeukaryotic plankton responses to dam-induced environmental changes and provide a basis for assessing biodiversity impacts in regulated river systems. Full article

Common bean (Phaseolus vulgaris L.) is a strategic crop whose sustainable production depends on symbiosis with nitrogen-fixing bacteria. However, the composition and functional potential of the nodule microbiome in varieties adapted to semi-arid regions, such as northern Mexico, remain poorly documented. Therefore, this study evaluated the influence of host genotype on nodule-associated bacterial communities in three improved varieties (Pinto Bravo, NOD1, and Jamapa) under conventional management, using high-throughput sequencing of the V3–V4 regions of the 16S rRNA gene. Alpha and beta diversity analyses showed no significant differences among varieties, indicating a similar nodular microbiome regardless of genotype. At the phylum level, Proteobacteria and Bacteroidota predominated, suggesting a conserved microbial core. At the genus level, Rhizobium was the most abundant taxon, while non-rhizobial genera such as Acinetobacter and the JC017 lineage were also detected. Functional prediction using PICRUSt2 revealed conserved metabolic profiles, with dominant pathways associated with amino acid biosynthesis, carbon metabolism, aerobic respiration, and fatty acid biosynthesis, indicating metabolic redundancy linked to tolerance to osmotic, thermal, and oxidative stress. The results suggest that under semi-arid conditions, the symbiotic interaction is governed by mechanisms at the host species level (P. vulgaris), which ensure the recruitment of a functional core microbiome, whereas intraspecific variation among improved varieties may influence the recruitment of specific accessory taxa. Full article

High-throughput sequencing (HTS) was applied to investigate the virome of European beech (Fagus sylvatica) from asymptomatic leaves and symptomatic leaves exhibiting chlorosis, line patterns and malformation. Total RNA extracted from six samples, including herbarium material collected in 1967 and 1968 and contemporary samples from France, Germany, and The Netherlands, was subjected to Illumina sequencing followed by de novo assembly, sequence similarity searches and phylogenetic analyses. In each sample, contigs belonging to a previously undescribed virus within the genus Carlavirus were obtained. The virus was tentatively named beech carlavirus. No additional virus contigs were detected in the samples. The detection of the virus over more than five decades and in three European countries indicates its long-term and a probable wider occurrence and circulation. Moreover, its prolonged unnoticed presence suggests that it does not induce noticeable and acute disease outbreaks. These findings underscore the value of integrating historical and recent field samples through collaborative data sharing to improve insight into virus diversity and ecology in forest trees. Full article

Tailings remediation alleviates ecosystem degradation and protects species. To conserve terrestrial biodiversity and address sustainability challenges while achieving economic growth, numerous researchers have devoted efforts to monitoring ecological functions and optimizing community structures. This study investigates the microbial characteristics and functional diversity across ecological succession stages of tailings. Selecting three typical restoration stages, including biological crust, moss, and grassland stages, we adopt 16S rRNA and ITS gene amplification, Illumina high-throughput sequencing, spectroscopy, and network correlation analysis to explore the responses of soil multifunctionality index, microbial communities, and carbon metabolism during tailings restoration. The experimental results indicate that the functional diversity index increases with ecological succession and is significantly correlated with the bacterial genera Rubrobacter and Arenimicrobium, whereas no significant correlation is observed with dominant fungi. The network interactions among bacterial communities are gradually strengthened along the succession process. In terms of carbon metabolic functions, the relative abundances of galactose, starch, and sucrose metabolism pathways increase obviously with restoration progression, while inositol phosphate metabolism, peroxisome metabolism, retinol metabolism, glyoxylate and dicarboxylate metabolism, and xenobiotics metabolism exhibit no significant variations. These findings provide novel empirical evidence for explaining microbe-mediated ecological succession in tailing ecosystems and highlight the necessity of multi-perspective analysis for ecological restoration. Policy and practical implications emphasize that the application of specific microorganisms and their interspecific interactions to promote iron tailings ecological restoration should fully consider the spatiotemporal heterogeneity of tailings areas. This study deepens the understanding of differential microbial responses at different tailings restoration stages and provides actionable insights for balancing mining economic development and terrestrial ecosystem conservation. Full article

Probiotics are widely studied as antibiotic alternatives in commercial aquaculture, yet their effects on fish maintained under long-term aquarium conditions remain poorly understood. This study addressed this gap by evaluating dietary Escherichia coli Nissle 1917 (EcN) supplementation on gut microbiota and inflammatory cytokine expression in hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) from a recirculating aquarium system. In this study, hybrid grouper were maintained in triplicate tanks under long-term aquarium environments, and fed a basal diet with 1 × 10⁸ CFU/g EcN (SS group) or a control diet (CS group) for 28 consecutive days. Based on 16S rRNA high-throughput sequencing and qPCR, the intestinal microbiota and expression levels of IL-4, TNF-α, and IL-1β were measured. At the phylum level, the relative abundance of Firmicutes increased from 15.63% (CS) to 66.70% (SS), while Proteobacteria decreased from 76.77% to 30.61%. At the genus level, Exiguobacterium became the dominant taxon in the SS group. Furthermore, EcN supplementation significantly upregulated IL-4 expression and downregulated TNF-α and IL-1β expression. EcN supplementation significantly altered gut microbiota composition, with marked changes in community structure and notable shifts in dominant taxa. Thus, this study provides one of the investigations into EcN-mediated restructuring of intestinal bacterial communities and modulation of host immune transcriptional responses in hybrid grouper maintained under controlled aquarium settings. These findings offer a foundation for designing microbiome-targeted interventions in captive marine fish systems. Full article

A 700 m pilot-scale cast iron pipeline reactor was operated for 120 days to investigate corrosion-stage evolution under reclaimed-water conveyance conditions. Sampling points were arranged at 50, 250, 450, and 650 m, and water-quality monitoring, coupon weight-loss tests, scanning electron microscopy (SEM), and high-throughput 16S rRNA sequencing were combined to characterize corrosion-rate variation, corrosion-product morphology, and microbial community succession. During transport, NH₄⁺ generally decreased while NO₃⁻ increased, indicating nitrification-related nitrogen transformation under aerobic conditions; meanwhile, PO₄³⁻ declined and DOC fluctuated, reflecting coupled physicochemical and biological processes. SEM observations showed a transition from loose porous deposits to relatively compact layered corrosion products, followed by local deterioration and renewed porous structures in the later period. The corrosion rate followed an increase–decrease–re-increase pattern rather than a monotonic trend. Therefore, corrosion acceleration (CA = dc/dt) was introduced as an auxiliary diagnostic indicator to identify whether corrosion activity was increasing, decreasing, or temporarily stabilizing. Microbial community analysis showed stage-associated variation in biofilm and nitrogen-transformation-related taxa, supporting the interpretation that corrosion evolution was jointly affected by water-quality change, corrosion-product development, and microbial succession. Overall, the combined interpretation of corrosion rate, CA, water quality, SEM morphology, and microbial succession provides a more informative basis for diagnosing corrosion-stage transitions in reclaimed-water cast iron pipelines. From a sustainability perspective, this diagnostic framework can support long-term operation, maintenance planning, and risk monitoring of urban reclaimed-water distribution infrastructure, thereby improving pipeline durability, reducing leakage and maintenance risks, and enhancing the reliability of reclaimed-water reuse systems. Full article

High-throughput sequencing is becoming the method of choice for plant diagnostics. It allows the detection of known and novel viruses and viroids, even in co-infection, without preliminary knowledge of the target. However, this method has its own limitations when compared to real-time PCR or ELISA. Laboratories that implement this type of technologies in-house must ensure that the performance criteria meet the requirements associated with their diagnostic activity. In this study, we present a workflow for in-house plant viruses and viroid detection, based on total RNA extraction, ribodepletion, Illumina sequencing and bioinformatics analyses. Performance criteria such as analytical sensitivity, analytical specificity, selectivity, repeatability, reproducibility and robustness were evaluated on the tomato brown rugose fruit virus (RNA genome), the tomato leaf curl New Delhi virus (DNA genome), and the pepper chat fruit viroid (RNA genome). The performance levels obtained meet the requirements for virus and viroid detection in symptomatic plant samples. Full article

Anaplastic thyroid carcinoma (ATC) is a rare but highly aggressive malignancy characterized by rapid progression, early metastasis, and extremely poor survival outcomes. Effective therapeutic options remain limited, highlighting the need for efficient and biologically relevant preclinical drug-discovery platforms. In this study, high-throughput compound screening using human ATC cell lines identified ANC-3 as a potential anticancer candidate. Its antitumor activity was evaluated through cytotoxicity and functional assays, zebrafish xenograft validation with live fluorescence imaging, colony-formation assays, and bulk RNA sequencing with pathway enrichment analyses. ANC-3 demonstrated consistent antitumor effects by significantly inhibiting cell viability, migration, invasion, and clonogenic survival, while also suppressing tumor growth in zebrafish xenograft models. Transcriptomic analyses revealed modulation of multiple oncogenic pathways, including MAPK, Ras, and NF-κB signaling. Collectively, these findings support zebrafish xenograft-based screening as a rapid and scalable platform for ATC drug discovery and suggest ANC-3 as a promising multi-pathway inhibitor warranting further preclinical development. Full article

The yerba mate psyllid, Gyropsylla spegazziniana, represents a major pest affecting yerba mate production, leading to considerable economic losses. Although several aspects of its ecology and management have been investigated, little is known about the viruses associated with this insect pest. In this study, we conducted the first RNA high-throughput sequencing (HTS) analysis of G. spegazziniana to examine its virome, uncovering a diverse array of previously undescribed RNA viruses. Our analysis led to the identification of five novel viruses spanning different viral lineages. These include representatives with evolutionary affinities to beny-like, picorna-like, and sobemo-like viruses, provisionally designated as Gyropsylla spegazziniana beny-like virus 1 (GSBlV1), Gyropsylla spegazziniana picorna-like virus 1 (GSPlV1), and Gyropsylla spegazziniana sobemo-like virus 1-3 (GSSlV1-3), respectively. Phylogenetic analysis of the bi-segmented, highly divergent sobemo-like viruses revealed that these viruses are grouped with other insect-associated sobemo-like viruses. The beny-like virus clustered together with other insect-associated beny-like viruses, whereas the picorna-like virus clustered together with psyllid-associated picorna-like viruses. Overall, these findings demonstrate that G. spegazziniana harbors a complex and previously uncharacterized virome. This work provides a foundation for further research into the ecological significance, evolutionary patterns, and possible use of these viruses in biological control strategies of this major pest within yerba mate agroecosystems. Full article

Understanding biological communities is essential for elucidating ecosystem structure and function. Metabarcoding based on ribosomal RNA (rRNA) genes, particularly 16S and 23S, is widely used to characterise bacterial and microalgal communities. However, analysing high-throughput sequencing data generated by platforms such as the Illumina MiSeq remains challenging due to fragmented bioinformatics tools, complex parameterisation, and limited accessibility for non-specialist users. In this study, a comprehensive and user-friendly bioinformatics pipeline is proposed for the analysis of 16S and 23S paired-end metabarcoding data. The workflow integrates all critical processing steps, including read merging, primer and adapter trimming, quality filtering, dereplication, chimaera removal, and clustering into Operational Taxonomic Units (OTUs). Taxonomic assignment is performed using curated reference databases, namely EZBioCloud for bacterial communities and µgreen for microalgae. The pipeline was developed in Python 3.11 and incorporates validated tools such as VSEARCH and Cutadapt, ensuring robustness and computational efficiency. Additionally, modules for alpha and beta diversity analysis are included to support comprehensive ecological interpretation. The main novelty of this work lies in providing a unified, GUI-based framework that enables the standardised processing of dual-marker (16S/23S) metabarcoding data within a single environment. In its current implementation, SOMBA supports the analysis of each marker through separate but harmonised workflows, ensuring consistency in parameterisation, processing steps, and output structure. This approach provides an accessible and standardised solution that bridges the gap between raw sequencing data and reliable biological insights, supporting applications in environmental microbiology and biotechnology. Full article