Sensitive detection of gene transfer in a microbial community

Sensitive detection of gene transfer in a microbial community
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Nature Biotechnology

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Gene transfer enables bacteria to adapt to their environment. To sensitively detect gene transfer, we created a synthetic biology tool that introduces an identifiable barcode into RNA when microbes exchange DNA. When applied in a wastewater community, high-throughput sequencing revealed which microbes in the community participated in gene transfer.

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Fig. 1: RAM, a synthetic biology tool to measure gene transfer.

References

  1. Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721 (2005). This review provides an overview of the mechanisms of horizontal gene transfer.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  2. Arnold, B. J., Huang, I.-T. & Hanage, W. P. Horizontal gene transfer and adaptive evolution in bacteria. Nat. Rev. Microbiol. 20, 206–218 (2022). This review describes the mechanisms and evolutionary theory of bacterial adaptation through gene transfer.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  3. Sheth, R. U., Cabral, V., Chen, S. P. & Wang, H. H. Manipulating bacterial communities by in situ microbiome engineering. Trends Genet. 32, 189–200 (2016). This review discusses approaches and applications for in situ microbiome engineering.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  4. Brito, I. L. Examining horizontal gene transfer in microbial communities. Nat. Rev. Microbiol. 19, 442–453 (2021). This review discusses laboratory techniques used to measure gene transfer.

    Article 
    CAS 
    PubMed 

    Google Scholar 

  5. Rubin, B. E. et al. Species- and site-specific genome editing in complex bacterial communities. Nat. Microbiol. 7, 34–47 (2022). This paper describes the environmental transformation sequencing (ET-Seq) method for mapping and quantifying gene transfer.

    Article 
    CAS 
    PubMed 

    Google Scholar 

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This is a summary of: Kalvapalle, P. B. et al. Information storage across a microbial community using universal RNA barcoding. Nat. Biotechnol. https://doi.org/10.1038/s41587-025-02593-0 (2025).

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Sensitive detection of gene transfer in a microbial community.
Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02639-3

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  • DOI: https://doi.org/10.1038/s41587-025-02639-3

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