Metagenome-assembled genomes: concepts, analogies, and challenges.
Sign Up to like & getrecommendations! Published in 2021 at "Biophysical reviews"
DOI: 10.1007/s12551-021-00865-y
Abstract: Metagenome-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.… read more here.
Keywords: analogies challenges; assembled genomes; genomes concepts; metagenome assembled ... See more keywords
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-21295-0
Abstract: Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine… read more here.
Keywords: metagenome assembled; assembled genomes; catalog; pig gut ... See more keywords
MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac398
Abstract: MOTIVATION Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG,… read more here.
Keywords: rrna genes; mags 16s; 16s rrna; metagenome assembled ... See more keywords
AGC: compact representation of assembled genomes with fast queries and updates
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad097
Abstract: Abstract Motivation High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Each project has already generated assemblies… read more here.
Keywords: agc compact; assembled genomes; compact representation; representation assembled ... See more keywords
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac420
Abstract: Abstract Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’… read more here.
Keywords: tara oceans; biogeography; assembled genomes; ocean gene ... See more keywords
Deep‐sea hydrothermal vent metagenome‐assembled genomes provide insight into the phylum Nanoarchaeota
Sign Up to like & getrecommendations! Published in 2019 at "Environmental Microbiology Reports"
DOI: 10.1111/1758-2229.12740
Abstract: Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or… read more here.
Keywords: metagenome assembled; deep sea; sea hydrothermal; assembled genomes ... See more keywords
Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories
Sign Up to like & getrecommendations! Published in 2019 at "mBio"
DOI: 10.1128/mbio.00725-19
Abstract: In their recent study, Espinoza et al. employ genome-resolved metagenomics to investigate supragingival plaque metagenomes of 88 individuals (1). The 34 metagenome-assembled genomes (MAGs) that the authors report include those that resolve to clades that… read more here.
Keywords: metagenome assembled; genome; quality; assembled genomes ... See more keywords
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
Sign Up to like & getrecommendations! Published in 2017 at "BMC Genomics"
DOI: 10.1186/s12864-017-4294-1
Abstract: BackgroundMicrobiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called… read more here.
Keywords: reconstruction; metagenome assembled; binning tools; assembled genomes ... See more keywords
Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?
Sign Up to like & getrecommendations! Published in 2020 at "BMC Genomics"
DOI: 10.1186/s12864-020-07087-8
Abstract: Background Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic… read more here.
Keywords: core functionalities; human gut; assembled genomes; metagenomic species ... See more keywords
Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan
Sign Up to like & getrecommendations! Published in 2022 at "Microbes and Environments"
DOI: 10.1264/jsme2.me22039
Abstract: The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and read more here.
Keywords: cattle japan; assembled genomes; metagenome assembled; 146 metagenome ... See more keywords
Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.857901
Abstract: Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can… read more here.
Keywords: haitanensis microbiome; haitanensis; pyropia; assembled genomes ... See more keywords