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[–]gwern[S] 4 points5 points  (2 children)

I am not really impressed by their title and other claims to environmental supremacy since they do not actually calculate SNP heritability for the whole gut microbiome (they only calculate a few subsets and don't combine them) nor how much of the gut microbiome is serving as mediation for genetics (since genetics is temporally and causally prior to gut microbiomes), but what I really like is their reuse of GCTA/variance component estimation, which fulfills my suggestion in https://www.reddit.com/r/Microbiome/comments/44j6zg/do_we_know_how_important_gut_microbiome/ :

We define the term biome-explainability as the variance of a host phenotype explained by the microbiome after accounting for the contribution of human genetics. Consistent with our finding that microbiome and host genetics are largely independent, we find significant biome-explainability levels of 16-33% for body mass index (BMI), fasting glucose, high-density lipoprotein (HDL) cholesterol, waist circumference, waist-hip ratio (WHR), and lactose consumption.

(The 'after accounting for the contribution of human genetics' bit is an example of their environmental supremacism as they don't seem to realize it's a mistake. That refers to the inclusion of the polygenic scores as covariates, which don't come remotely near to accounting for the full contribution of SNPs, never mind all genetics. So there is still a ton of genetic influence on the adjusted estimates.)

So this demonstrates that gut microbiomes really do have meaningful correlations with stuff like obesity, which is great to know. That provides reason to look more for causal relationships.

[–]MaximilianKohler 0 points1 point  (1 child)

Would a "causation" flair be appropriate for this submission?

[–]gwern[S] 0 points1 point  (0 children)

Well, it doesn't show causation, that's my point. Since a single cross-sectional snapshot of a gut microbiome could be caused by obesity or genetics or what have you. Showing a meaningful total correlation is merely the first step. Now that a decent quantity of smoke has been observed, it's more worthwhile asking what kind of fire is causing it. Before, I was unhappy because it wasn't clear that gut microbiomes had any consistent large correlation with anything at all because all the studies were small and done differently from each other.

[–]MaximilianKohler 2 points3 points  (0 children)

no statistically significant association between microbiome composition and ethnicity

Hmm, that's interesting considering how many papers I've seen showing differences in ethnicity.

our finding that microbiome and host genetics are largely independent

Lots of contrary data to this one as well...

There are a few using the flair search in the sidebar, but also additional ones via google/google scholar searches.