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A 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 PDFAn essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical …
Read PDF<b>Background and Aims:</b> Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the …
Read PDF<h4>Background</h4>Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.<h4>Methods</h4>This was a prospective cohort study of patients …
Read PDFWater kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile …
Read PDFThe anabolic pathways of key volatile flavor compounds (VFCs) in <i>Hongqujiu</i> (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an …
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 PDF<h4>Background</h4>The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet …
Read PDF<h4>Background</h4>Metabolite production, consumption, and exchange are intimately involved with host health and disease, as well as being key drivers of host-microbiome interactions. Despite the increasing prevalence of datasets that jointly measure microbiome composition and metabolites, …
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 PDFFood is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as …
Read PDF<h4>Background</h4>Metagenomics offers a culture-independent framework for comprehensively characterizing microbial communities by directly extracting and sequencing DNA from environmental samples. In this study, we employed high-throughput metagenomic sequencing to explore microbial communities inhabiting fungal-rich environments, emphasizing …
Read PDF<h4>Motivation</h4>Analysis of genomic variation in microbial genomes is crucial for understanding how microbes adapt, interact with their hosts, and influence health and disease. In metagenomic studies, where genetic material from entire microbial communities is sequenced, …
Read PDFNext-generation sequencing (NGS) has become an essential tool for antimicrobial resistance (AMR) surveillance, enabling comprehensive detection of AMR determinants in both bacterial isolates and complex microbial communities. Metagenomic sequencing enables culture-independent profiling of antimicrobial resistance …
Read PDFCoastal ecosystems are increasingly threatened by microbiological risk due to urban wastewater discharges, which might affect public health and have important economic consequences on the blue tourism. Here, we examine the changes in water and …
Read PDFGut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis …
Read PDFThis review aims to bring together current research on the importance, recent applications, and possible impacts of metagenomic analysis and emphasize that metagenomic analyses, which provide direct analysis of the genomes of the food itself …
Read PDFssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary …
Read PDF<h4>Background</h4>Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.<h4>Aims</h4>To identify gut microbial alterations in MDD and to …
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