ArticleNucleic acids research2020
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Metalog: curated and harmonised contextual data for global metagenomics samples.Nucleic acids research · 2026Article
- Contrasting associations between microbiota respiratory strategies and seafloor macrofauna.ISME communications · 2026Article
- The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.Genome biology · 2025Article
- The BeeBiome data portal provides easy access to bee microbiome information.BMC bioinformatics · 2025Article
- Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.Cell genomics · 2025Review
- Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.Microbiome · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.PLoS computational biology · 2024Article
- Towards predicting the geographical origin of ancient samples with metagenomic data.Scientific reports · 2024Article
- Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.Microbiology spectrum · 2024Article
- The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.Database : the journal of biological databases and curation · 2024Article
- A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand.Nature communications · 2024Article
- Article
- The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.Animal microbiome · 2023Article
- Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.Foods (Basel, Switzerland) · 2023Review
- ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.PLoS computational biology · 2023Article
- The media composition as a crucial element in high-throughput metabolic network reconstruction.Interface focus · 2023Article
- A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data.Microbiome · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.
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