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This study found that the microbiome composition varies based on the time of sampling. How do you think this variability might affect the reproducibility of mic
by wjb3 2y ago
This study found that the microbiome composition varies based on the time of sampling. How do you think this variability might affect the reproducibility of microbiome research? What are some practical ways researchers could standardize sampling times to improve consistency across different studies?
- adrian_b 2y agoThe food available to the microbiome varies during the day, according to the feeding schedule and to the kind of food that is provided to the mice. Because the generation time of the bacteria is very short, e.g. fractions of an hour, it is normal for the quantities of each kind of bacteria to vary during the day, following the fluctuations in the concentrations of various nutrients in the intestine. For a constant microbiome composition, one would have to feed the mice with exactly the same food at the same hours each day, and sample the microbiome also at fixed hours that are the same each day.
- nextos 2y agoThis was obvious to any statistician working in the area, as the same thing happens with gene expression in virtually any tissue. There are also seasonality effects in gene expression, and even in microbiomes: https://doi.org/10.1126/science.aan4834 https://doi.org/10.1126/science.aan4834 Accounting for these covariates is important. But with larger sample sizes, they might cancel out anyway. IMHO, larger studies will be reproducible. There are other much more serious technical issues.