Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Sign Up to like & getrecommendations! Published in 2017 at "Nature Methods"
DOI: 10.1038/nmeth.4458
Abstract: Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global… read more here.
Keywords: metagenome; assessment metagenome; critical assessment; assessment ... See more keywords
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
Sign Up to like & getrecommendations! Published in 2022 at "Nature Biotechnology"
DOI: 10.1038/s41587-021-01130-z
Abstract: Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with… read more here.
Keywords: closely related; metagenome assembled; complete metagenome; microbial communities ... See more keywords
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-14576-6
Abstract: The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for… read more here.
Keywords: metagenome; metagenome skimming; lichenized fungi; skimming approach ... See more keywords
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity
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DOI: 10.1128/msystems.01045-20
Abstract: Microbiome studies on a select few mammalian species (e.g., humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in… read more here.
Keywords: genomic diversity; gene; metagenome; microbial genomes ... See more keywords
ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning
Sign Up to like & getrecommendations! Published in 2022 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1011001
Abstract: The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging to detect for… read more here.
Keywords: quality; resmico; metagenome assembled; deep learning ... See more keywords
Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.1000634
Abstract: Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and… read more here.
Keywords: metagenome; bifunctional phosphomannomutase; phosphomannomutase phosphoglucomutase; laminaria digitata ... See more keywords