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Metagenomics is the study of the metagenome—the collective genome of microorganisms from an environmental sample—to provide information on the microbial diversity and ecology of a specific environment. Shotgun metagenomics refers to the approach of shearing DNA extracted from the environmental sample and sequencing the small fragments.
Here, by applying evolutionary genomics approaches to metagenomics data of lake microbiomes, the authors reveal that freshwater species with small genomes face extended periods with their niche adaptation capabilities frozen.
The rising incidence of young-onset sporadic colorectal cancer (yCRC) is global concern. Here, leveraging a substantial number of deep sequencing metagenomes, the authors show striking similarities in gut microbial patterns at both the taxonomic and selected gene marker levels between yCRC and old-onset CRC.
Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one profile with high precision and sensitivity. RAT provides a comprehensive view of the microbiome.
Little is known about viral communities in deep-sea seamounts. In this study, the authors performed metagenomic and virome analysis from sediments in the western Pacific Ocean and characterize the diversity, distribution and potential ecological roles of viruses in deep-sea seamount sediments.
Multidisciplinary culture-dependent and -independent techniques elucidate the unique microbial nitrogen cycle in nutrient-poor coastal Antarctica soils and reveal the contribution of novel key microbes to their nitrogen budget.
Metatranscriptomic data from more than 2,000 mosquitoes of 81 species show that the composition of mosquito viral communities is determined more by host phylogeny than by climate and land-use factors, which will help to inform arbovirus surveillance.
This Genome Watch highlights different tools and strategies used to enhance the quality of metagenome-assembled genomes (MAGs) generated in microbiome studies.
An experiment that simulates rainfall events in dry soils reveals that virus members of the soil microbiome maintain the turnover of prokaryotic host communities through a ‘cull-the-winner’ model.
Modern high-throughput metagenomics is producing hundreds of thousands of metagenome-assembled genomes (MAGs), which is overwhelming traditional sequence-similarity search methods. We present a computational method, skani, that efficiently compares MAGs on a terabyte scale while being robust to the inherent noise in MAGs, enabling larger and more accurate analyses.