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The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description …
Read PDF<h4>Importance</h4>The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders. The stability of the microbiome in the oral cavity makes it a potentially ideal sample that …
Read PDF<h4>Motivation</h4>Metagenomic binning methods to reconstruct metagenome-assembled genomes (MAGs) from environmental samples have been widely used in large-scale metagenomic studies. The recently proposed semi-supervised binning method, SemiBin, achieved state-of-the-art binning results in several environments. However, this …
Read PDFMetagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained …
Read PDFThe gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding …
Read PDFThis study investigated age-related changes in the gut microbiota and metabolome of Sapsaree dogs through metagenomic and metabolomic analyses. Using Illumina (short-read) and Nanopore (long-read) sequencing technologies, we identified both common and unique bacterial genera …
Read PDFGenetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing …
Read PDF<h4>Background</h4>Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, mapping-based tools and two general-purpose long reads mappers. …
Read PDFCurrent metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. …
Read PDFThe study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read …
Read PDFHydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput …
Read PDFThe COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, …
Read PDFMetagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short-read sequencing remains the primary approach for metagenomic research; however, long-read sequencing may offer advantages of improved metagenomic assembly and resolved …
Read PDF<h4>Background</h4>Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing …
Read PDFMost microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on …
Read PDFPhylogenetic marker gene sequencing is often used as a quick and cost-effective way of evaluating microbial composition within a community. While 16S rRNA gene sequencing (16S) is commonly used for bacteria and archaea, other marker …
Read PDFWe investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection …
Read PDFThe emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these …
Read PDFAt present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in a field or clinical sample, particularly when followed by long-read sequencing. Our work …
Read PDFMost of the knowledge available on the composition and functionality of microbial communities in different ecosystems comes from short-read sequencing methods. It implies limitations regarding taxonomic resolution, variant detection, and genome assembly contiguity. Long-read sequencing …
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