ArticleProceedings of the National Academy of Sciences of the United States of America2024
Bacterial lifestyle shapes pangenomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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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
36 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.PLoS genetics · 2026Article
- Unveiling the terra cognita of sequence spaces using Cartesian projection of asymmetric distances.NAR genomics and bioinformatics · 2026Article
- Pangenome ofEcology and evolution · 2026Article
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- Genome Evolution in Plant Pathogenic Bacteria.Genome biology and evolution · 2026Review
- Disruption of bacteriophage integration site promotes rapid diversification of multicellular traits inMicrobiology spectrum · 2026Article
- Testing the drivers of environmental persistence in bacterial pathogens.Microbiology (Reading, England) · 2026Article
- Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.Nature communications · 2026Article
- Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmentalMicrobial genomics · 2026Article
- Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2026Review
- Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the Lactobacillaceae.The ISME journal · 2026Article
- Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.The ISME journal · 2026Article
- Genomic diversification and tailocin-mediated competition in animal-associatedISME communications · 2026Article
- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Complete genomes of Rickettsia typhi reveal a clonal population.PLoS neglected tropical diseases · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.
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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.