Units differ between VMH diets and others?

[nickp60]

Hello! I am trying to wrap my head around the diet component of these sorts of analyses, and I'm confused about the units. I downloaded the Western Diet Gut AGORA qza file and the VMH EU Average Agora qza file, to get a sense of how different the two were. The units don't seem comparable at all though -- the water fluxes are 10.0 and 33178.46850 respectively; sucrose EX_sucr(e) 0.0074493 vs 40.4766 . Is this expected, and are these normalized internally? The units from VMH are mmol/(person*day). The Western Diet ones are listed as (mmol/gDW/h) in https://www.nature.com/articles/nbt.4212. Which set of units should be used when creating custom diet media?

Thanks so much!!

Nick

[cdiener]

Hi Nick, the western diet came from https://doi.org/10.1038/nbt.4212. Though it used a similar design as the VMH diets this one contained more metabolites and was already in units of mmol/gDW/h. The VMH ones are limited to some 80 metabolites or so if I remember correctly.

You could adjust the per person/day by dividing by 24h and even adjust for the microbial biomass (around 200g per person). But for most VMH diets that results in very slow growth rates. So we sometimes just convert to hours and rather set growth rate constraints in the completion step. In the end the best validation is probably to simulate a few samples with it and check if the community doubling time after tradeoff is around 12h (average bowel movement frequency).

If you look in the recipes folder it illustrates how those are converted etc.

The water flux is pretty arbitrary. 10 mmol is already quite a lot but it is essentially unlimited. Some media limit the maximum flux and others don't.