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<h4>Introduction</h4>Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.<h4>Methods</h4>In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected …
Read PDF<h4>Background</h4>Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for …
Read PDFBloodstream infections and sepsis necessitate rapid, sensitive, and clinically relevant diagnostics to minimize treatment delays and improve clinical outcomes. Next-generation sequencing enables culture-independent pathogen detection, antimicrobial resistance profiling, and genome-informed epidemiology. This narrative review integrates …
Read PDFHeavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic …
Read PDFPlants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant …
Read PDF<b>Introduction.</b> <i>Pneumocystis jirovecii</i> pneumonia (PJP, formerly known as <i>Pneumocystis carinii</i> pneumonia), an opportunistic fungal infection caused by the fungus <i>P. jirovecii</i>, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung …
Read PDFA field-deployable DNA sequencing approach for quantitative microbial community profiling can enable rapid responses for a range of applications in the water sector-from process control to wastewater surveillance. Current quantitative approaches require complex instrumentation and …
Read PDF<h4>Introduction</h4>Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal …
Read PDFHuman <i>pegivirus</i> (HPgV) genomes were detected in HCV-infected plasma via nanopore metagenomics. Six nearly complete HPgV-2 genomes were identified. Phylogenetic analysis confirmed HPgV-2 genotype. This study reveals co-infection dynamics, highlights viral diversity, and supports improved …
Read PDFShotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, …
Read PDFThe metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of …
Read PDFBACKGROUND: Shotgun metagenomics enables to study microbial communities without biases from culturing and isolation, but taxonomic classification to the species level remains challenging due to high false positive rates. Oxford Nanopore Technologies offers new opportunities …
Read PDFMetagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely defined. For this systematic review, a …
Read PDF<h4>Background</h4>Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can …
Read PDFThe mealworm (<i>Tenebrio molitor</i>) is one of the most commonly mass-reared insects for food and feed. Monitoring the health status of commercially reared mealworm populations is of great importance for the early detection of entomopathogens …
Read PDF<h4>Background</h4>Biological heterogeneity in host inflammatory responses to severe pneumonia predicts clinical outcomes and may influence the effectiveness of immunomodulatory therapy. The upstream drivers of this heterogeneity remain poorly defined. We hypothesized that microbial translocation from …
Read PDFFew human metapneumovirus coding-complete genomes are available from Africa despite significance in optimizing local molecular diagnostics and global phylogeographic analysis. We report eight genomes recovered following nanopore metagenomic sequencing of samples collected in coastal Kenya …
Read PDFMetagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses …
Read PDFHypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), …
Read PDF<h4>Introduction</h4>Very few studies have examined the diagnostic sensitivity and specificity of currently available laboratory tests for detecting respiratory pathogens in cattle, and even fewer have examined test performance on samples from animals before the onset …
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