ArticleEnvironmental microbiome2024
From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.
Article in Environmental microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Functional metatranscriptomics of the rhizosphere: towards an understanding of metabolic processes of the microbial carbon pump.FEMS microbiology ecology · 2026Article
- Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano.FEMS microbiology ecology · 2026Article
- Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.BMC plant biology · 2026Article
- Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient-Degrading Enzyme-Encoding Genes Across Continental US Ecoregions.Ecology and evolution · 2026Article
- Genome sequences of bacteria isolated fromMicrobiology resource announcements · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.Frontiers in plant science · 2026Review
- A conserved bacterial signature characterizes plant microbiome responses to drought.Frontiers in microbiology · 2026Article
- Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.International journal of genomics · 2026Review
- Coastal gradients and human disturbance shape bacterial and fungal rhizosphere microbiomes ofFrontiers in microbiology · 2026Article
- Plant-soil-microbiome interactions: mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems.Frontiers in microbiology · 2026Review
- Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.Microbiome · 2025Article
- Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Analyses of 37 composts revealed microbial taxa associated with disease suppressiveness.Applied and environmental microbiology · 2025Article
- Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.iMeta · 2025Article
- A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.Scientific reports · 2025Article
- Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.Nature microbiology · 2025Article
- Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.Scientific data · 2025Article
- Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.Environmental microbiome · 2025Article
- Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil.Microorganisms · 2025Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.