Sampling techniques and microbial concentration measurements influence the results of microbiome studies

Most microbiome studies measure relative abundance of the various microorganisms in a sample. This study demonstrates the feasibility of large-scale measurements of absolute microbial concentrations. Moreover, it demonstrates how sample handling and storage methods can alter microbial measurements, potentially introducing bias in conclusions drawn about microbiome–host relationships.

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

Access options

Subscribe to this journal

Receive 12 print issues and online access

214,86 € per year

only 17,91 € per issue

Rent or buy this article

Get just this article for as long as you need it

$39.95

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

Fig. 1: Quantification of absolute microbial concentrations in microbiome samples.
41587 2023 1804 Fig1 HTML

References

  1. Jian, C., Luukkonen, P., Yki-Järvinen, H., Salonen, A. & Korpela, K. Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PLoS One 15, e0227285 (2020). This paper provides a workflow for 16S rRNA qPCR for quantification of microbial concentration.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  2. Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017). This paper provides a workflow for amplicon sequencing and flow-based quantification of absolute microbial concentration.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  3. Hagan, T. et al. Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans. Cell 178, 1313–1328 (2019). This paper reports microbial concentration variation in response to antibiotic treatment.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  4. Rao, C. et al. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature 591, 633–638 (2021). This paper provides a spike-in sequencing method for multi-kingdom count quantification.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  5. Oduaran, O. H. et al. Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. BMC Microbiol. 20, 330 (2021). This paper profiles the gut microbiomes of people in South African communities.

    Article 

    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: Maghini, D. G. et al. Quantifying bias introduced by sample collection in relative and absolute microbiome measurements. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01754-3 (2023).

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sampling techniques and microbial concentration measurements influence the results of microbiome studies.
Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01804-w

Download citation

  • Published:

  • DOI: https://doi.org/10.1038/s41587-023-01804-w

Read More