ArticleThe ISME journal2020
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Article in The ISME journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 146 citations in OpenAlex.
- Machine learning enables prediction of metabolic system evolution in bacteria.Science advances · 2023Pooled it
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- Article
- Genomic insights into the resistome, mobilome and functional adaptation ofMicrobial genomics · 2026Article
- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.Nature communications · 2026Article
- Community conservatism is widespread across microbial phyla and environments.Nature ecology & evolution · 2026Article
- Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota.ISME communications · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays.ISME communications · 2026Article
- Negative Frequency-Dependent Selection Promotes Strain Structure in a Plant Pathogen.Ecology letters · 2026Article
- Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.Scientific reports · 2025Article
- A human skin microbiome reference catalog and the skin microbial landscape of plateau adults.iMetaOmics · 2025Article
- Genomic and Pangenomic Insights intoPathogens (Basel, Switzerland) · 2025Article
- A blueprint for contemporary studies of microbiomes.Microbiome · 2025Article
- Microbial functional diversity and redundancy: moving forward.FEMS microbiology reviews · 2025Review
- Beyond H37Rv:Frontiers in microbiology · 2025Review
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.Microbiome · 2024Article
- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
9 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 at 8 institutions in 7 countries.
Funding
Abstract
Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.
Indexed as
Identifiers
What OpenQuestion holds
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.