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Recovery and Analysis of Long-Read Metagenome-Assembled Genomes
The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly...
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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 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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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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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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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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Metagenome-derived virus-microbe ratios across ecosystems
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of...
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Structure and Metabolic Potential of the Microbiome of Lake Baikal Upper Sediment Layers Determined by Metagenome Analysis
Abstract —This is the first report on the application of metagenomic analysis of the microbiome of Lake Baikal bottom sediments in order to assess the...
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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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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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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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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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Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease
BackgroundThe gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease...
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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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CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine
Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a...
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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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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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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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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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Preparation of Soil Metagenome Libraries and Screening for Gene-Specific Amplicons
Cosmid libraries constructed from environmental metagenome samples are powerful tools for capturing the genomic diversity of complex microbial...