Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Briefing
  • Published:

Sensitive detection of gene transfer in a microbial community

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

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 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

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

Search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology