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<i>Streptococcus pneumoniae</i> (pneumococcus) is a leading cause of community-acquired pneumonia and invasive diseases, particularly among children and the elderly. The introduction of pneumococcal conjugate vaccines has significantly reduced invasive pneumococcal disease, but the prevalence of …
Read PDFThis dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates …
Read PDFMortality in very-low birth-weight (VLBW) infants accounts for up to 50%-70% of the neonatal mortality and up to 25%-30% of infant mortality. Despite the global increase in survival rates, this population remains at heightened risk …
Read PDFRibosomal RNAs (rRNAs), essential components of the ribosome, are coded by the multi-copy ribosomal DNA (rDNA). Interestingly, rDNA displays substantial variation in all species, both as inter-individual differences in copy number (CN) and inter- and …
Read PDF<i>Pseudomonas</i> sp. CBR-F is a bacterial species isolated from a water treatment plant targeting for per- and poly-fluoroalkyl substances, a difficult-to-degrade family of anthropogenic compounds. Here, we report a complete genome for <i>Pseudomonas</i> sp. CBR-F, …
Read PDFRespiratory syncytial virus (RSV) is a globally circulating virus, causing severe respiratory infections in infants and the elderly. Two RSV vaccines were recently approved, and passive immunization is now recommended in several countries for all …
Read PDFThe genus Ormosia is in the Fabaceae family. China is one of its centers of origin, with almost all species being endemic, suggesting the need for genomic studies to understand its evolution, conservation, and use. …
Read PDFAccurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related <i>Staphylococcus …
Read PDF<h4>Background</h4>Species-level resolution is essential to understand gastric microbiome recovery after Helicobacter pylori eradication, yet short-read 16 S rRNA approaches often obscure clinically relevant changes.<h4>Methods</h4>Gastric biopsies from 121 adults in Bayan-Ölgii, Mongolia (71 H. pylori-positive, 50 …
Read PDFIn this protocol, we detect pseudouridine using nanopore direct RNA sequencing (DRS 002/004) and analyze dynamic changes to mRNA modifications in response to perturbation. We cover RNA extraction, poly(A) selection, DRS, unmodified transcriptome (in vitro …
Read PDFIncreasing the precision of outbreak containment for emerging virus strains requires real-time virus identification that can be integrated with specific public health actions. During the SARS-CoV-2 pandemic, we established a multisector partnership to support rapid …
Read PDFTelomeres cap the extremities of linear chromosomes and prevent their detection as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, …
Read PDF<i>Christensenella minuta</i> is one of the representative bacterial species of the human gut microbiome. We report the complete genome sequence of two strains, <i>Christensenella minuta</i> CIP 112228 and CIP 112229, isolated from two healthy volunteers.
Read PDFProtein-DNA interactions can be manipulated in vitro by changing buffer conditions. Here, we develop a methodology to map the cleavage preferences of chimeric gene editors that are fusions of the I-TevI nuclease domain to CRIPSR …
Read PDFChromosomal inversions and copy-number variants (CNVs) drive genomic and phenotypic diversification in birds by reshaping recombination, gene expression, and genome architecture. Here, we report a complex structural polymorphism on great tit (<i>Parus major</i>) chromosome 1A …
Read PDFSanger sequencing of the first ~500 bp of the 16S rRNA gene is frequently used to identify bacterial pathogens that have ambiguous biochemical profiles or proteomic mass spectra. When diversity does not occur within that …
Read PDFThis study investigates the optimisation of poly(3-hydroxybutyrate) (PHB) production by Mycolicibacterium smegmatis using sugarcane bagasse (SCB) hydrolysate as a low-cost, renewable carbon source. Key fermentation parameters including temperature, pH, agitation, inoculum size and nitrogen supplementation …
Read PDFLong-read metagenomic sequencing allows for the rapid, culture-independent, and accurate identification of causative pathogens and antimicrobial resistance (AMR) profiles, supporting precise antibiotic use and reducing the spread of resistance. However, its application to mastitis milk …
Read PDFWe report the complete mitochondrial genome of the halotolerant green alga <i>Dunaliella salina</i> CS-265, isolated from a hypersaline lake in central Australia. The genome is a circular DNA molecule of 30,073 bp, encoding seven protein-coding …
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