Time of sample collection is critical for the replicability of microbiome analyses, Allaband et al, 2024

Published in Nature Metabolism, 1 July 2024 (received 27 October 2022, accepted 8 May 2024)

Authors from the Knight Lab at University of California at San Diego

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As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur.

One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5,6,7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions.

Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.

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Closed access link: https://www.nature.com/articles/s42255-024-01064-1

 

Feels like common sense really...many hormone tests differ across a day and many illnesses only show up on tests when you're in crisis!

 

I agree that it's an official statement of basic common sense. I expect that right now, there isn't even adequate data on how long various factors affect microbiome populations. I've noticed my last meal come out the next morning (carrot chunks, poppy seeds, both obvious markers), but just what effects does eating a carrot have on the gut microbiome, and how long do those effects last, and how much does that vary between individuals? Do the effects of a cheese-rich meal vary depending on the fibre or nutritional content of the rest of the meal? Comparing microbiome samples, or even studies, is like those blind men trying to describe an elephant.