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Cited by 57Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsBacterial Genetics and Biotechnology

Bacterial lifestyle shapes pangenomes

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Dewar, Anna E., Hao, Chunhui, Belcher, Laurence J., Ghoul, Melanie, West, Stuart A.·2024·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2320170121PMC PMC11126918
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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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  • The problem of non-independence can be exacerbated when examining genomes or genes.

    “This problem of non-independence can be exacerbated when examining genomes or genes.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [24]

    The Abstract says that species and genomes can share characteristics through common descent and therefore cannot always be treated as independent data points. It does not say that non-independence is exacerbated when examining genomes or genes, or make that comparison explicitly. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • The problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes and genomes of the same or closely related species.

    “In genomic datasets, data points can correspond to genomes or even individual genes, meaning the problem of species not being independent can be exacerbated by additional levels of non-independence, including genes within genomes, such as those carried on the same replicon, and genomes of the same or closely related species16,19,21–26.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [24]

    The Abstract (page unavailable) says that species and genomes can share characteristics through common descent and that species cannot be treated as independent data points. This supports non-independence among related species and genomes, but our copy does not address non-independence of genes within a genome or genes carried on the same replicon. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Bacterial species with more fluid pangenomes have both more variable lifestyles and larger effective population sizes; a phylogenetic path analysis supported the hypothesis that this was due to lifestyle traits together influencing gene gain and loss, and that effective population size did not have a casual influence on pangenome fluidity.

    “As another example, bacterial species with more fluid pangenomes have both more variable lifestyles and larger effective population sizes; a phylogenetic path analysis supported the hypothesis that this was due to lifestyle traits together influencing gene gain and loss, and that effective population size did not have a casual influence on pangenome fluidity24.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [24]

    Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

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  • In cases where complications arise, analysing the data with multiple methods can test the robustness of conclusions.

    “In cases where complications arise it can be extremely useful to analyse the data with multiple methods to test the robustness of conclusions24,126.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [24]

  • A lack of variation in a potential explanatory variable (X), while the response variable (Y) does vary, is an important result, not a failing of the dataset.

    “A lack of variation in a potential explanatory variable (X), while the response variable (Y) does vary, is an important result, not a failing of the dataset24.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [24]

    The Results section, “Variation across Host-Associated Species” (page unavailable), reports substantial variation in pangenome fluidity and finds that varying lifestyle traits explain some of it. I searched for a lack of variation in an explanatory variable and for whether that would be an important result rather than a dataset failing; no passage in our copy addresses that methodological claim. (LLM, conf=0.73)

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Cited by

Sorted by citations

Authors
Dewar, A. E., Hao, C., Belcher, L. J., Ghoul, M., & West, S. A.
Affiliations
University of Oxford (GB)
Corresponding author
Dewar, Anna E.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2024-05-14
Volume
121
Issue
21
Pages
e2320170121-e2320170121
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.2320170121
PMC
PMC11126918
OpenAlex
W4396887303
Cited by
57
References
5
Citations by year
2026: 30 · 2025: 22 · 2024: 5
FWCI
7.37
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by-nc-nd)
Funders
EC | ERC | HORIZON EUROPE European Research Council (834164)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
bacterial pangenome, bacterial lifestyle, host-associated bacteria, free-living bacteria, effective population size, bacterial pathogenicity, bacterial motility, intracellular bacteria, host dependence
MeSH terms
Bacteria, Phylogeny, Genome, Bacterial

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