ArticleScientific data2023
Trait biases in microbial reference genomes.
Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Low-pH sulfate reduction in acid mine drainage treatment systems: implications for acidophilic and acid-tolerant sulfate-reducing bacteria - a systematic review.Biodegradation · 2026Pooled it
- Large-Scale Comparative Genomics of 1,374 Lactiplantibacillus plantarum Genomes Reveals an Open Pan-genome and Strain-Level Variation in Probiotic-Associated and Safety-Related Genomic Features.Current microbiology · 2026Article
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Translating biosynthetic gene cluster architecture into biosensor design for microbial natural product discovery.Essays in biochemistry · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.Scientific data · 2026Article
- Carbon regime structures functional trait trajectories during primary succession in microorganisms.The ISME journal · 2026Article
- Host life-history strategy is a critical determinant of virulent phage infection propensity.The ISME journal · 2026Article
- From humans to the wild: revisiting assumptions in gut microbiome analysis.ISME communications · 2026Article
- Uncovering the Hidden Diversity and Antimicrobial Resistance of Uropathogens in a Tertiary-Care Hospital in Bangladesh.International journal of microbiology · 2026Article
- Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.Environmental microbiology reports · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Article
- Machine learning models for delineating marine microbial taxa.NAR genomics and bioinformatics · 2025Article
- Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.bioRxiv : the preprint server for biology · 2024Article
- Leveraging genomic information to predict environmental preferences of bacteria.The ISME journal · 2024Review
- Ecological relevance of flagellar motility in soil bacterial communities.The ISME journal · 2024Article
- Taxonomic and genomic attributes of oligotrophic soil bacteria.ISME communications · 2024Article
- Taxonomic and environmental distribution of bacterial amino acid auxotrophies.Nature communications · 2023Article
- Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioHScientific reports · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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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.