ArticleNature microbiology2020
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation.
Article in Nature microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
93 citing papers in PubMed, 173 citations in OpenAlex.
- Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.Nature medicine · 2025Trial
- Insights Gained by High-throughput Chromosome Conformation Capture (Hi-C) into the Viral Modulation of Methane Production in Anaerobic Digestion.Environmental science & technology · 2026Article
- Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Context dependency is essential for predicting intrahost evolution.Nature ecology & evolution · 2026Article
- Information storage across a microbial community using universal RNA barcoding.Nature biotechnology · 2026Article
- Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- A Review of Doxycycline Post-Exposure Prophylaxis and Its Implications for Antimicrobial Resistance and the Human Microbiome.Infectious diseases and therapy · 2026Review
- Microbial Modulation of the Gut-Liver Axis in Autoimmune Liver Diseases.Seminars in liver disease · 2025Review
- The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.Current opinion in microbiology · 2025Review
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- Targeted protein evolution in the gut microbiome by diversity-generating retroelements.Science (New York, N.Y.) · 2025Article
- The Gut Microbiome and Colistin Resistance: A Hidden Driver of Antimicrobial Failure.International journal of molecular sciences · 2025Review
- Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Article
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
- Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.Animal microbiome · 2025Article
- Re-Emergence of Bacteriophages and Their Products as Antibacterial Agents: An Overview.International journal of molecular sciences · 2025Review
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.
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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.