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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.
The impact of other pathogens on disease outcome was studied in European infants with RSV infection. Additional viruses were commonly co-detected during infection but were weakly linked to severity. However, presence of Haemophilus bacteria strongly associated with severe cases.
Binning is an essential step in genome-resolved metagenomic analysis in which assembled contigs originating from the same source population are clustered. However it is challenging, especially for low abundance microbial species. Here the authors introduce a toolkit that integrates multiple prominent binning tools and AI for efficient and high-resolution recovery of non-redundant bins from short- and long-read metagenomic sequencing datasets.
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.
In this Journal Club, Anja Spang discusses the discovery of nanosized archaea, transforming our knowledge of archaeal phylogeny and shedding light on their roles in ecology and evolution.
This month’s Genome Watch highlights the use of high-depth genome-centric approaches to further our understanding of the human gut microbiome within the context of industrialized and non-industrialized lifestyles.