ArticleNucleic acids research2022
How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 60 citations in OpenAlex.
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- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
- Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.Scientific data · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean.mSystems · 2026Article
- Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.Frontiers in microbiology · 2026Article
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- Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.Scientific data · 2025Article
- Phylogenomic and Pangenomic Assessment of a Mediterranean Strain of Raphidiopsis raciborskii Extends Knowledge of the Global Distribution and Characteristics of a Potentially Toxigenic Cyanobacterium.Environmental microbiology reports · 2025Article
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- Predicting climate-change impacts on the global glacier-fed stream microbiome.Nature communications · 2025Article
- Structure and metabolic function of spatiotemporal pit mud microbiome.Environmental microbiome · 2025Article
- Distinct microbial communities within and on seep carbonates support long-term anaerobic oxidation of methane and divergent pMMO diversity.The ISME journal · 2025Article
- Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.Nature microbiology · 2025Article
- Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.ISME communications · 2025Article
- Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD).ISME communications · 2025Article
- Temporal signals in dairy cattle slurry and fertilized field soil resistomes and bacterial communities.Frontiers in microbiology · 2025Article
- Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.FEMS microbiology reviews · 2024Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As of today, the majority of environmental microorganisms remain uncultured and is therefore referred to as 'microbial dark matter' (MDM). Hence, genomic insights into these organisms are limited to cultivation-independent approaches such as single-cell- and metagenomics. However, without access to cultured representatives for verifying correct taxon-assignments, MDM genomes may cause potentially misleading conclusions based on misclassified or contaminant contigs, thereby obfuscating our view on the uncultured microbial majority. Moreover, gradual database contaminations by past genome submissions can cause error propagations which affect present as well as future comparative genome analyses. Consequently, strict contamination detection and filtering need to be applied, especially in the case of uncultured MDM genomes. Current genome reporting standards, however, emphasize completeness over purity and the de facto gold standard genome assessment tool, checkM, discriminates against uncultured taxa and fragmented genomes. To tackle these issues, we present a novel contig classification, screening, and filtering workflow and corresponding open-source python implementation called MDMcleaner, which was tested and compared to other tools on mock and real datasets. MDMcleaner revealed substantial contaminations overlooked by current screening approaches and sensitively detects misattributed contigs in both novel genomes and the underlying reference databases, thereby greatly improving our view on 'microbial dark matter'.
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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.