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46 results for “Metagenome-assembled genomes”
Metagenome-assembled genomes obtained from fecal and salivary microbiomes of pancreatic cancer patients and controls
<p>7,546 MAGs obtained from fecal and salivary metagenomes of pancreatic cancer patients and controls</p>
Early-life human gut metagenome-assembled genomes and proteins catalogs
<p>The description of the files:</p> <p>(1) The 32,277 genomes include six parts: ELGG_part_1.zip, ELGG_part_2.zip, ELGG_part_3.zip, ELGG_part_4.zip, ELGG_part_5.zip, ELGG_part_6.zip.</p> <p>(2) The 2,172 representative species: ELGG_representatives_2172.zip.</p> <p>(3) The ELGP catalog clustered at 95% amino acid identity: ELGP_95.faa.gz.</p> <p> </p>
Metagenome-assembled genomes (MAGs), colorectal cancer (CRC)
<p>This archive contains (i) Metagenome assemblies of short-term enrichment cultures of CRC mucosal tissue microbiota, and (ii) Reconstructed metagenome-assembled genomes (MAGs) generated through binning of metagenome contigs.</p>
Fathi Camel Microbiome Project (FCMP) Fecal Metagenome-assembled Genomes (MAGs)
<p>The Fathi Camel Microbiome Project (FCMP) aims to characterize the diversity and phenotypic associations of the dromedary camel microbiome. The gut microbiome of N = 55 camels was deeply sequenced via dropped stool. The raw reads, after QC, were assembled and binned into metagenome-assembled genomes (MAGs). We include here a collection of 3165 medium-quality or higher prokaryotic MAGs by MiMAG-like criteria (completeness >= 50%, contamination <= 5%). </p>
Metagenome-Assembled Genomes and Annotations for McGivern et al
<h3>Files:</h3> <ul> <li><code>reactorEMERGE_annotations.txt</code>: DRAM annotations for MAGs</li> <li><code>gene_lengths.txt</code>: gene length file used to calculate geTMM</li> <li><code>genes.gff.tar.gz</code>: gff file needed for metaT processing</li> <li><code>genes.faa.tar.gz</code>: amino acid sequences for MAG genes</li> <li><code>genes.fna.tar.gz</code>: nucleotide sequences for MAG genes, used as database for metaT mapping</li> </ul>
Novel canine high-quality metagenome-assembled genomes by long-read metagenomics together with Hi-C proximity ligation
<p>We characterized a canine fecal sample of a healthy dog by combining a long-read metagenomics assembly (Nanopore sequencing) with Hi-C cross-linking data, and further correction of the frameshift errors. We retrieved and characterized 27 HQ MAGs and seven MQ MAGs considering MIMAG criteria.</p> <p>Find in this repository the final Hi-C genomics bins (CanMAG_XX-HiCbin.fa), including both the genome and the extra-chromosomal elements within the bin. </p> <p> </p>
Metagenome-assembled genomes(MAGs) generated from CRC human gut (PRJEB27928).
<p>MAGs generated from CRC human gut (PRJEB27928) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from dog gut (PRJEB20308).
<p>MAGs generated from dog gut (PRJEB20308) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Metagenome-assembled genomes(MAGs) generated from ocean (PRJEB1787).
<p>MAGs generated from ocean (PRJEB1787) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
Oceanic Prokaryotes Metagenome-Assembled Genomes reconstructed using metagenomic distances
<p>Sets of reconstructed Metagenome-Assembled Genomes (MAGs) from Tara Oceans dataset. The reconstructed MAGs belong to Magneto paper: https://doi.org/10.1128/msystems.00432-22</p> <p>The dataset is composed of 93 oceanic metagenomes sampled from non-polar oceanic regions.</p> <p>The Metagenomic Distance MAGs were reconstructed following a co-assembly protocol driven by nucleotidic composition similarity, as detailed in the publication.</p> <p>The Oceanic Region MAGs were reconstructed by co-assembly of samples belonging to the same Oceanic Regions.</p> <p>The file clusters.tsv sum up the metagenomic distance cluster and the oceanic region each sample belongs to.</p>
179 high quality metagenome-assembled genomes sequences and annotations
<p>We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations. </p>
Metagenomes and metagenome-assembled genomes from Onthophagus taurus
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Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Metagenome-assembled genomes generated from dog dental plaque microbiome
<p>Metagenome-assembled genomes generated from dog dental plaque microbiome from the study "Newly identified species from the dog dental plaque microbiome highlight little overlap with humans"</p>
Metagenome-Assembled Genomes of 2_1_SS_W3_F1
<p>This dataset is featured in the data report <em>"Exploring the Taxonomical and Functional Profiles of Marine Microorganisms in Submarine Groundwater Discharge Vent Water from Mabini, Batangas, Philippines through Metagenome-Assembled Genomes."</em> The assembled genomes were taxonomically identified and analyzed for nutrient metabolism genes involved in biogeochemical cycles, as well as potential biosynthetic gene clusters of medical relevance. The dataset includes generated bins with corresponding RAST annotations.</p>
Metagenome-assembled genomes for "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed"
<p>This dataset includes all of the metagenome-assembled genomes (MAGs) used in Roth et al.: "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed" (in prep.). The metagenomic sequencing was completed on a suite of sediment samples collected from the sediment-water interface of beaver ponds within wildfire burn scars.</p>
Expanded catalog of metagenome-assembled genomes reveals resistome characteristics athletic performance- associated microbes in horse
<p><strong>Background</strong><br> As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.<br> <strong>Results</strong><br> Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing wide use of antibiotic in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in elite racehorses than that in normal horses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fiber fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.<br> <strong>Conclusions</strong><br> Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalog for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.</p>
Prokaryotic gene catalog, prokaryotic Metagenome-Assembled Genomes (MAGs) and taxonomic profiling of metagenomic data of NEREA Augmented Observatory
<p>The NEREA_metaG directory is dedicated to the in-depth analysis of NEREA microbial communities using metagenomic sequencing data. </p> <p><strong>Gene catalog:</strong> This directory contains the gene catalog compiled from metagenomic data, which includes: Protein and nucleotide sequence files for genes; Cluster files grouping similar genes; Annotation files mapping genes to KEGG pathways; Normalized gene abundance profiles.</p> <div><strong>MAGs:</strong> Directory for Metagenome-Assembled Genomes (MAGs). It contains comprehensive annotation files for the MAGs, providing insights into gene functions, metabolic pathways, and other genomic features. It also contains the individual MAGs categorized by sample origin. Each MAG is stored in a compressed FASTA format.</div> <p><strong>mOTUs</strong>: Contains files related to microbial taxonomic units identified and quantified using the mOTUs profiler. </p>
Dataset for "Metagenome-Assembled Bacterial Genomes from Long Accurate Reads Associated with Capilliphycus salinus ALCB114379"
<p>We present the raw genomic dataset of the marine cyanobacterium Capilliphycus salinus ALCB114379, sequenced using PacBio HiFi long-read technology.</p> <p><strong>ABSTRACT</strong></p> <p><span>We report the complete genome sequences of five bacteria linked to the marine cyanobacterium <em>Capilliphycus salinus</em> ALCB114379 from the phylum Pseudomonadota. This genetic diversity offers new insights into the genetic landscape and potential symbiotic relationships of cyanobacteria-associated microbiota.</span></p>
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
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