Microbiome composition varies based on sampling time, mouse study finds | Hacker News Reader

Microbiome composition varies based on sampling time, mouse study finds

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23 pointswjb35 comments

I suspect chronomicrobiomics will be one of the next trends with wellness gurus given that newer research may take timing into consideration whilst a lot of prior research doesn't.

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?

The 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.

This 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

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.

If sampling time is effecting mice, good luck with Human Studies. It is not easy to get human gut microbiome samples in clinical trials especially when they are already suffering from disease. Even with longitudinal studies, patients can skip donating samples. Making it difficult to compare. Also diet (big factor) and genetics can impact your microbiome. Having said that, I am big fan of longitudinal microbiome studies with good metadata collection such as time of sample collection, Bristol stool scale, and diet(this is very difficult to quantify).

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