Time of Sample Collection Critical for Microbiome Replicability
Allaband, C.; Lingaraju, A.; Ramos, S. F.; Kumar, T.; Javaheri, H.; Tiu, M. D.; Machado, A. C. D.; Richter, R. A.; Elijah, E.; Haddad, G. G.; Leone, V. A.; Dorrestein, P. C.; Knight, R.; Zarrinpar, A.
Show abstract
Although many aspects of microbiome studies have been standardized to improve experimental replicability, none account for how the daily diurnal fluctuations in the gut lumen cause dynamic changes in 16S amplicon sequencing. Here we show that sample collection time affects the conclusions drawn from microbiome studies and are larger than the effect size of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups are unique to each experiment. Sample collection times as short as only four hours apart lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. Without looking at other data, the impact on other fields is unknown but potentially significant. One-Sentence SummaryIf we are not controlling for host circadian rhythm time in microbiome studies when performing experiments, it is like trying to measure sea level rise while not knowing that tides or waves exist.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans 94%
- Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics 94%
- Projection of gut microbiome pre and post-bariatric surgery to predict surgery outcome 93%
Similar papers in this journal
- Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism 95%
- The gut commensal Blautia maintains colonic mucus function under low fiber consumption through short-chain fatty acid-mediated activation of Ffar2 95%
- A Novel Index for Predicting Health Status Using Species-level Gut Microbiome Profiling 95%
Similar papers in this journal
Similar papers in this journal
- Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment: a randomized trial of preterm infants 94%
- The Gut Microbiome of Exudivorous Marmosets in the Wild and Captivity 93%
- Understanding artificial mouse-microbiome heterogeneity and six actionable themes to increase study power 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.