Skip to main content

Thank you for visiting 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.

  • Comment
  • Published:

Translating microbiota analysis for clinical applications

Harnessing the potential of microbiota analysis creates new opportunities in diagnosing diseases, improving treatment efficacy, reducing treatment complications and preventing disease recurrence. However, microbiota analysis has not yet been integrated into clinical management workflows. Here, we discuss crucial characteristics of microbiota analysis systems for clinical translation.

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: Clinical translation of microbiota analysis.


  1. Sender, R., Fuchs, S. & Milo, R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164, 337–340 (2016).

    Article  Google Scholar 

  2. Talebian, S., Dehghani, F., Weiss, P. S. & Conde, J. Evolution of CRISPR-enabled biosensors for amplification-free nucleic acid detection. Trends Biotechnol. 42, 10–13 (2023).

    Article  Google Scholar 

  3. Dar, D., Dar, N., Cai, L. & Newman, D. K. Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. Science 373, eabi4882 (2021).

    Article  Google Scholar 

  4. Shi, H. et al. Highly multiplexed spatial mapping of microbial communities. Nature 588, 676–681 (2020).

    Article  Google Scholar 

  5. Takahashi, M. K. et al. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat. Commun. 9, 3347 (2018).

    Article  Google Scholar 

  6. Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K. & Dorrestein, P. C. Mass spectrometry-based metabolomics in microbiome investigations. Nat. Rev. Microbiol. 20, 143–160 (2022).

    Article  Google Scholar 

  7. Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).

    Article  Google Scholar 

  8. Lin, D. B. & Medeiros, D. M. The microbiome as a major function of the gastrointestinal tract and its implication in micronutrient metabolism and chronic diseases. Nutr. Res. 112, 30–45 (2023).

    Article  Google Scholar 

  9. Man, W. H., Piters, W. A. A. D. & Bogaert, D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat. Rev. Microbiol. 15, 259–270 (2017).

    Article  Google Scholar 

  10. Karstens, L. et al. Community profiling of the urinary microbiota: considerations for low-biomass samples. Nat. Rev. Urol. 15, 735–749 (2018).

    Article  Google Scholar 

  11. Sekirov, I., Russell, S. L., Antunes, L. C. & Finlay, B. B. Gut microbiota in health and disease. Physiol. Rev. 90, 859–904 (2010).

    Article  Google Scholar 

  12. Ben-Amor, K. et al. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl. Environ. Microbiol. 71, 4679–4689 (2005).

    Article  Google Scholar 

Download references


This research was supported, in part, by the National Institutes of Health (NIH), grant number R01AI153133.

Author information

Authors and Affiliations



All authors contributed equally to the preparation of this manuscript.

Corresponding authors

Correspondence to Joseph C. Liao, Samuel Yang or Pak Kin Wong.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lee, JH., Chin, S.M., Mach, K.E. et al. Translating microbiota analysis for clinical applications. Nat Rev Bioeng 2, 284–286 (2024).

Download citation

  • Published:

  • Issue Date:

  • DOI:


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research