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Critical assessment of pan-genomic analysis of metagenome-assembled genomes
Briefings in Bioinformatics, 2022 Abstract Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs.
Yanbin Yin
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Computational and Structural Biotechnology Journal, 2023 De novo assembly of next generation metagenomic reads is widely used to provide taxonomic and functional information of genomes in a microbial community. As strains are functionally specific, recovery of strain-resolved genomes is important but still a challenge.
Liping Zhao, Menghui Zhang
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Metagenomic Assembly: Reconstructing Genomes from Metagenomes
2021Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the functional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from
Wang Z. +4 more
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Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes
MSystems, 2022 Kelp (brown algae in the order Laminariales ) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions ...
Khashiff Miranda +2 more
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Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation
Applied and Environmental Microbiology, 2021 The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate ...
Elaine Cristina Pereira de Martinis +1 more
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Metagenome-assembled genomes: concepts, analogies, and challenges
Biophysical Reviews, 2021Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenome data. In the last few years, many thousands of MAGs have been reported in the literature, for a variety of environments and host-associated microbiota, including humans.
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Recovery and Analysis of Long-Read Metagenome-Assembled Genomes
2023The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities.
Krithika, Arumugam +3 more
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266 cultured genomes and 482 metagenome-assembled genomes
2021We performed a study of bacteria cultivation and genome sequencing along with deeply metagenome sequencing of 14 fecal samples from weanling piglet. 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) were collected and clustered to 428 species across 10 phylum in this work. Genomic DNA of the 226 represent strains were extracted.
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ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool
Briefings in Bioinformatics, 2023Abstract Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery.
Hoon Je Seong, Jin Ju Kim, Woo Jun Sul
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CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine
Functional & Integrative Genomics, 2023Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a small portion of the viral DNA is inserted into the bacterial DNA in a specific pattern to produce segments known as CRISPR arrays.
Arunmozhi Bharathi, Achudhan +2 more
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