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   Articles with "metagenome" as a keyword



Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

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recommendations! 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

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recommendations! 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

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recommendations! 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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recommendations! Published in 2020 at "mSystems"

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

Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus

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recommendations! Published in 2025 at "BMC Genomics"

DOI: 10.1186/s12864-025-12149-w

Abstract: Background Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis is established by two distinct fungal groups, with the distinctive ‘fine root endophyte’ morphotype formed by fungi from the sub-phylum Mucoromycotina rather than the sub-phylum Glomeromycotina.… read more here.

Keywords: metagenome; arbuscular mycorrhizal; root endophyte; fine root ... See more keywords

Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance

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recommendations! Published in 2025 at "BMC Microbiology"

DOI: 10.1186/s12866-025-04327-3

Abstract: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut… read more here.

Keywords: metagenome; black soldier; bsfl; gut microbiome ... See more keywords

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies

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recommendations! Published in 2024 at "Genome Biology"

DOI: 10.1186/s13059-024-03234-6

Abstract: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know… read more here.

Keywords: metagenome; representation bacterial; improving representation; evaluating improving ... See more keywords

The chromosomal genome sequence of blue blubber, Catostylus mosaicus (Quoy & Gaimard, 1824) and its associated microbial metagenome sequences

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recommendations! Published in 2025 at "Wellcome Open Research"

DOI: 10.12688/wellcomeopenres.24798.1

Abstract: We present a genome assembly from a specimen of Catostylus mosaicus (blue blubber; Cnidaria; Scyphozoa; Rhizostomeae; Catostylidae). The genome sequence has a total length of 217.98 megabases. Most of the assembly (99.58%) is scaffolded into… read more here.

Keywords: metagenome; catostylus mosaicus; genome sequence; blue blubber ... See more keywords

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning

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recommendations! 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

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recommendations! 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