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.
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References
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.
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.
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.
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.
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.
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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).
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Sampling techniques and microbial concentration measurements influence the results of microbiome studies. Nat Biotechnol 42, 194–195 (2024). https://doi.org/10.1038/s41587-023-01804-w
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DOI: https://doi.org/10.1038/s41587-023-01804-w
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