ArticleGenome research2021
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 1 of them a synthesis that pooled it.
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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
66 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.mSystems · 2023Pooled it
- Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition.Gut microbes · 2026Review
- Community-wide adaptive evolution of gut bacteria during dietary transitions.bioRxiv : the preprint server for biology · 2026Article
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Emergent frequency-dependent selection predicts mutation outcomes in complex ecological communities.bioRxiv : the preprint server for biology · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut.Gut microbes · 2025Review
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- Ecological diversification in rapidly evolving populations.bioRxiv : the preprint server for biology · 2025Article
- Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.Cell genomics · 2025Article
- Frequency-dependent fitness effects are ubiquitous.bioRxiv : the preprint server for biology · 2025Article
- Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.mSystems · 2025Article
- Clonal interference and genomic repair during strain coexistence in the gut.PLoS genetics · 2025Article
- Gut microbiome evolution from infancy to 8 years of age.Nature medicine · 2025Article
- Article
- Wine Fermentation as a Model System for Microbial Ecology and Evolution.Environmental microbiology · 2025Review
- Quantifying compositional variability in microbial communities with FAVA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Antibiotic-perturbed microbiota and the role of probiotics.Nature reviews. Gastroenterology & hepatology · 2025Review
6 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
12 authors.
Funding
Abstract
Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.
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