ArticleNature microbiology2024
Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 62 citations in OpenAlex.
- Phage-ICE tandems facilitate bacterial adaptation and antimicrobial resistance spread.Science advances · 2026Article
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.BMC bioinformatics · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Integrating theory and machine learning to reveal determinants of plasmid copy number.Nature communications · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment.Genome biology · 2026Article
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Sulfonamide resistance geneMicrobiology spectrum · 2026Article
- Large-scale plasmidome and carbapenem mobilome analysis reveals a mechanistic duality: high-power specialists and structural generalists mobile genetic elements.Frontiers in microbiology · 2026Article
- Transfer potential of F-like plasmids inISME communications · 2026Article
- Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits.PloS one · 2026Article
- Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.BMC microbiology · 2025Article
- Intracellular competition shapes plasmid population dynamics.Science (New York, N.Y.) · 2025Article
- Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.Nature communications · 2025Article
- The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.Current opinion in microbiology · 2025Review
- A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes.Nature communications · 2025Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
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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.