# Investigating the impact and patterns of homologous recombination and adaptive evolution on bacterial genomes

> **NIH NIH R01** · UNIVERSITY OF NORTH CAROLINA GREENSBORO · 2022 · $288,585

## Abstract

Project summary
In contract to sexual organisms, the mechanisms of population genetics in bacteria are far less
understood. Two fundamental aspects of bacterial population genetics remain sorely
understudied: i) the impact of DNA exchange on the evolution of bacterial genomes and
populations is largely unknown. ii) the prominence of adaptive evolution has not been
comprehensively assessed in bacteria. Determining how recombination and adaptive evolution
impact bacteria is key to understand the biology of these organisms and to develop relevant
models of their evolution. Although bacteria reproduce clonally, there is increasing evidence that
the vast majority of these organisms are capable of homologous recombination by exchanging
pieces of DNA in a process similar to gene conversion in animals and plants. This process
enhances microbial capacity to adapt to stresses or changing environments and the exchange of
DNA between bacterial strains is a major concern for human health as exemplified by the
transfer of virulence and antibiotic resistance genes. Despite the central role of this process, the
rates and patterns of recombination remain unresolved in bacteria. The extent of recombination
often varies greatly from one study to another and, as a result, the same bacterial species can
be perceived as clonal in one study and highly recombining in another. In this project, we
propose to re-evaluate the landscape of recombination rates and patterns along the genomes of
hundreds of bacterial species. Using new methodological frameworks based on Approximate
Bayesian Computation and Deep Learning, we will identify the factors shaping the variation in
recombination rate across bacteria. We will also uncover recombination rate variation across
bacterial chromosomes (i.e. hot spots and cold spots). Our rate estimates will also allow us to
study how recombination drives the evolution of genomic architecture of bacteria, including
turnover in gene content. Finally, we will quantify the impact of adaptive evolution in bacteria,
which may be substantially larger than in other organisms due to large bacterial effective
population sizes. We will also investigate the relationship between adaptation and
recombination, and identify the genes/pathways responsible for adaptation. In summary, this
study will evaluate the rates and patterns of recombination across hundreds of species,
determine the factors driving the evolution of the recombination process, reveal the role of
adaptive evolution in bacteria, and the interplay between recombination and adaptation.

## Key facts

- **NIH application ID:** 10360686
- **Project number:** 5R01GM132137-03
- **Recipient organization:** UNIVERSITY OF NORTH CAROLINA GREENSBORO
- **Principal Investigator:** Louis-Marie Bobay
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $288,585
- **Award type:** 5
- **Project period:** 2020-04-01 → 2025-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10360686

## Citation

> US National Institutes of Health, RePORTER application 10360686, Investigating the impact and patterns of homologous recombination and adaptive evolution on bacterial genomes (5R01GM132137-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10360686. Licensed CC0.

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