ArticleNature microbiology2021
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 102 citations in OpenAlex.
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- Citywide metagenomics reveals microbial community and resistome dynamics in urban wastewater.Nature communications · 2026Article
- Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.Nature genetics · 2026Article
- Host adaptation drives genome evolution and virulence diversification in a bacterial zoonotic pathogen.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the pangenome of the shellfish pathogenMicrobial genomics · 2026Article
- Phylogeographic clustering ofApplied and environmental microbiology · 2026Article
- Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems.The ISME journal · 2026Article
- Microbial Contamination Risks From Adjacent and Nearby Land: Evidence and Implications for Produce Safety.Journal of food science · 2026Review
- Genomic plasticity and mobilome architecture ofMicrobial genomics · 2026Article
- Pangenome-GWAS analysis ofCanadian journal of microbiology · 2026Article
- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- Hotspots of Bacterial Pathogen Abundance and Exposure Risk in Soils of the Contiguous United States.GeoHealth · 2025Article
- Low-Coverage Whole-Genome Analysis of Population Structure, Bottlenecks, and Selection in Indiana Bats Before and After White-Nose Syndrome.Molecular ecology · 2025Article
- Genomic and spatial heterogeneity of Brucella melitensis underscores latent brucellosis risks in non-endemic zones in Southwest China.Communications biology · 2025Article
- Population structure and gene flux ofMicrobial genomics · 2025Article
- Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems.Nature communications · 2025Article
- Whole-genome sequencing and metagenomics reveal diversity and prevalence ofMicrobiology spectrum · 2025Article
- Fitness consequences of structural variation inferred from a House Finch pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria.Nature communications · 2024Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural bacterial populations can display enormous genomic diversity, primarily in the form of gene content variation caused by the frequent exchange of DNA with the local environment. However, the ecological drivers of genomic variability and the role of selection remain controversial. Here, we address this gap by developing a nationwide atlas of 1,854 Listeria isolates, collected systematically from soils across the contiguous United States. We found that Listeria was present across a wide range of environmental parameters, being mainly controlled by soil moisture, molybdenum and salinity concentrations. Whole-genome data from 594 representative strains allowed us to decompose Listeria diversity into 12 phylogroups, each with large differences in habitat breadth and endemism. 'Cosmopolitan' phylogroups, prevalent across many different habitats, had more open pangenomes and displayed weaker linkage disequilibrium, reflecting higher rates of gene gain and loss, and allele exchange than phylogroups with narrow habitat ranges. Cosmopolitan phylogroups also had a large fraction of genes affected by positive selection. The effect of positive selection was more pronounced in the phylogroup-specific core genome, suggesting that lineage-specific core genes are important drivers of adaptation. These results indicate that genome flexibility and recombination are the consequence of selection to survive in variable environments.
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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.