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Microbiome

You are what you excrete

Nature Microbiology (2023)Cite this article

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Residual human DNA reads in sequenced faecal samples may allow some individuals to be identified.

Privacy is a concern in human microbiome research. Identifying an individual using microbial DNA present in a sample that they provide is predicated on the relative stability of any given microbiome, its uniqueness to an individual, and the nature of the residual microorganisms that we leave in the environment. A growing body of evidence suggests that these three features of microbiomes could be exploited for forensic applications1,2,3. However, any human sample collected for microbiome analysis contains more than just microorganisms, because we shed human cells constantly, and human DNA sequences are often present in microbiome datasets. To allay privacy concerns in the National Institutes of Health’s Human Microbiome Project, removal methods for human DNA reads were pioneered4. These methods use computational screening of sequences against a human reference genome to identify and remove them. Although such methods are in use today, we need a comprehensive database to capture the unique variation that exists among human populations to be certain that all human DNA sequences have been removed. Such a database does not exist. Now writing in Nature Microbiology, Okada and colleagues5 report that there is substantial potential for identification of participants using metagenomes sequenced from human faecal samples.

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Fig. 1: Human DNA in stool samples contains personal information. Collection of stool samples is a common procedure in human microbiome studies.

References

  1. Fierer, N. et al. Proc. Natl Acad. Sci. USA 107, 6477–6481 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Kodama, W. A. et al. J. Forensic Sci. 64, 791–798 (2019).

    Article  PubMed  Google Scholar 

  3. Franzosa, E. A. et al. Proc. Natl Acad. Sci. USA 112, E2930–E2938 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Methé, B. A. et al. Nature 486, 215–221 (2012).

    Article  PubMed Central  Google Scholar 

  5. Tomofuji, Y. et al. Nat. Microbiol. https://doi.org/10.1038/s41564-023-01381-3 (2023).

  6. Nurk, S. et al. Science 376, 44–53 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Denny, J. C. et al. N. Engl. J. Med. 381, 668–676 (2019).

    Article  PubMed  Google Scholar 

  8. Joh, E. E. Notre Dame J. Emerg. Technol. https://doi.org/10.2139/ssrn.3742320 (2021).

  9. Borodulin, K. et al. Int. J. Epidemiol. 47, 696–696i (2018).

    Article  PubMed  Google Scholar 

  10. Ramirez, A. H., Gebo, K. A. & Harris, P. A. JAMA 325, 2441–2442 (2021).

    Article  PubMed  Google Scholar 

  11. Poore, G. D. et al. Nature 579, 567–574 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Pediatrics, University of California San Diego, La Jolla, CA, USA

    Caitlin Guccione, Daniel McDonald & Rob Knight

  2. Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Caitlin Guccione & Kit Curtius

  3. Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA

    Caitlin Guccione

  4. Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA

    Rebecca Fielding-Miller

  5. Center on Gender Equity and Health, School of Medicine, University of California San Diego, La Jolla, CA, USA

    Rebecca Fielding-Miller

  6. Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA, USA

    Rebecca Fielding-Miller

  7. Department of Bioengineering, University of California San Diego, La Jolla, CA, USA

    Rob Knight

  8. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA

    Rob Knight

  9. Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA

    Rob Knight

Authors
  1. Caitlin Guccione
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  2. Daniel McDonald
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  3. Rebecca Fielding-Miller
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  4. Kit Curtius
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  5. Rob Knight
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Corresponding author

Correspondence to Rob Knight.

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The authors declare no competing interests.

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Guccione, C., McDonald, D., Fielding-Miller, R. et al. You are what you excrete. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01395-x

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