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How to Obtain and Compare Metagenome-Assembled Genomes
Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from...
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Metagenome assembly of high-fidelity long reads with hifiasm-meta
De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short...
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Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies
BackgroundIn the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing...
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Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking
BackgroundSo far, a lot of binning approaches have been intensively developed for untangling metagenome-assembled genomes (MAGs) and evaluated by two...
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Persistent memory as an effective alternative to random access memory in metagenome assembly
BackgroundThe assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without...
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Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life
Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of...
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Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity
The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku...
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Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
BackgroundRumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of...
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Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining
AbstractEnzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes....
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Reconstruction of the personal information from human genome reads in gut metagenome sequencing data
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently...
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using...
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Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
BackgroundThe application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and...
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Critical Assessment of Metagenome Interpretation: the second round of challenges
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome...
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Wochenende — modular and flexible alignment-based shotgun metagenome analysis
BackgroundShotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and...
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Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
BackgroundProducing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane...
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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of...
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Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from...
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Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study
BackgroundGastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in...
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Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide....
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Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome
Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This...
