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Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses
Viral metagenomics is one of the most widely used approaches to study viral population genomics. With the recent development of bioinformatic tools,...
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House dust metagenome and pulmonary function in a US farming population
BackgroundChronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine...
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Characterization of metagenome-assembled genomes from the International Space Station
BackgroundSeveral investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were...
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Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
BackgroundPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although...
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A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach
Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune...
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Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse
BackgroundAs a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food...
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Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining
BackgroundMicrobial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites,...
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HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data
BackgroundA major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome...
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Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction
BackgroundThe viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process....
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Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster
BackgroundThe RCA ( Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in...
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Giant virus-related sequences in the 5300-year-old Ötzi mummy metagenome
Giant viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic...
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The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany
Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of...
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A comprehensive investigation of metagenome assembly by linked-read sequencing
BackgroundThe human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial...
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Reduced metagenome sequencing for strain-resolution taxonomic profiles
BackgroundStudies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon...
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CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in...
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An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
BackgroundGastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an...
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MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
BackgroundMicrobes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene...
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Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing
BackgroundDairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This...
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Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties
BackgroundChickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is...
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Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories
BackgroundDespite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon...
