ArticleNature methods2019
Inferring bacterial recombination rates from large-scale sequencing datasets.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Comparative population genomic analysis of Brevibacterium casei isolated from a tuberculosis patient.Folia microbiologica · 2026Article
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.eLife · 2025Article
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- From Microbial Switches to Metabolic Sensors: Rewiring the Gut-Brain Kynurenine Circuit.Biomedicines · 2025Review
- Unraveling the tempo and mode of horizontal gene transfer in bacteria.Trends in microbiology · 2025Review
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.bioRxiv : the preprint server for biology · 2025Article
- Article
- Whole-Genome Sequencing Analysis Revealed High Genomic Variability, Recombination Events and Mobile Genetic Elements inAntibiotics (Basel, Switzerland) · 2025Article
- Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.Molecular biology and evolution · 2025Article
- Hotspots of genetic change in Yersinia pestis.Nature communications · 2025Article
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- Comparative genomics reveal a novel phylotaxonomic order in the genus Fusobacterium.Communications biology · 2024Article
- Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient.Nucleic acids research · 2024Article
- Detecting co-selection through excess linkage disequilibrium in bacterial genomes.NAR genomics and bioinformatics · 2024Article
- Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations.PLoS genetics · 2024Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Patterns of Change in Nucleotide Diversity Over Gene Length.Genome biology and evolution · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- First report on in-depth genome and comparative genome analysis of a metal-resistant bacteriumFrontiers in microbiology · 2024Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a robust, computationally efficient method ( https://github.com/kussell-lab/mcorr ) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.
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