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StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution
<h4>Summary</h4>Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. …
Read PDFmicrontology: a lightweight, data-driven controlled vocabulary to describe earth's microbial habitats
<h4>Motivation</h4>Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.<h4>Results</h4>We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and …
Read PDFnf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction
<h4>Motivation</h4>Reconstructing eukaryotic viral genomes from metagenomic data is challenging due to their extensive diversity and potential genome segmentation. Current approaches often rely on labor-intensive manual curation for reference selection and scaffolding, limiting scalability for large …
Read PDFDevelopment and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever
<h4>Introduction</h4>Blood culture is the cornerstone of microbiological diagnostics for patients with acute undifferentiated fever and no obvious localization of infection; however, up to 50% of cases remain undiagnosed. Infections caused by arboviruses, fastidious or even …
Read PDFComputational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio
In recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have …
Read PDFRecovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample
Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike …
Read PDFAssessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany
Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation …
Read PDFComplete genome sequence of <i>Staphylococcus haemolyticus</i> UMB6531B, isolated from a perineal swab
<i>Staphylococcus haemolyticus</i> UMB6531B was isolated from a perineal swab of a female with overactive bladder symptoms and sequenced to better characterize opportunistic pathogens of the female urogenital tract. Here, we present the complete genome sequence, …
Read PDFClinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance
BACKGROUND: Infective endocarditis (IE) poses significant diagnostic challenges, particularly in blood culture-negative cases where fastidious bacteria evade detection. Metagenomic-based nanopore sequencing enables rapid pathogen detection and provides a new approach for the diagnosis of IE. …
Read PDFComparative analysis of full-length 16s ribosomal RNA gene sequencing in human oropharyngeal swabs using primer sets with different degrees of degeneracy
<h4>Background</h4>Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet …
Read PDFAI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery
Emerging viral outbreaks continue to pose a persistent global health threat, underscoring the urgent need for a shift from reactive to proactive health security strategies. Viral metagenomic next-generation sequencing (mNGS) offers an unbiased, powerful approach …
Read PDFImpact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy
<h4>Background</h4>Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA …
Read PDFMetabarcoding data: Full-length 16S rRNA sequence of endophytic bacteria in the root of asymptomatic and blast-symptomatic rice plants (<i>Oryza sativa</i>, L.)
There is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents …
Read PDFMMonitor for real-time monitoring of microbial communities using long reads
Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source …
Read PDFRapid detection of human and animal respiratory viruses using Microbe Finder (MiFi<sup>®</sup>)
Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi<sup>®</sup>) software for detection of nine RNA …
Read PDFEditorial: Molecular informatics in personalized medicine, volume II
No abstract available.
Read PDFExploratory Metaviromic Analysis of the Sea-Rock Pool Mosquito <i>Aedes mariae</i> and the Water of Its Breeding Habitat
The mosquito-associated virome may modulate host biology and influence vector competence, highlighting the importance of understanding its composition. Here, a metagenomic analysis was conducted to characterize the virome of the sea-rock pool mosquito <i>Aedes mariae</i> …
Read PDFSequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond
This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: <i>filter_ONT</i> for filtering raw reads and creating a FASTQ file with a subset …
Read PDFChoosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence
Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the …
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