Definition of western and non-western samples in CuratedMetagenomicData
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pd378 • 0
@d725d772
Last seen 10 weeks ago
United States

Hello,

I'm hoping that someone could help me understand how western and non-western samples are defined in the curated metagenomic datasets from the Waldron lab (https://waldronlab.io/curatedMetagenomicData/).

Each individual sample is marked as western and non-western; however in the case of India and Mongolia, some samples are western and some are non-western. All the other countries are exclusively one or the other.

I originally assumed that western and non-western was based on the country of origin, but now I'm wondering if it's based on each sample regardless of country (i.e. some samples in India came from subjects with western diets while others came from subjects with non-western).

Whether based on country or individual samples, I'm also interested to know how these designations were assigned. Is it income, diet, geography or something else?

Thank you to anyone who can provide some insight! -Peter

curatedMetagenomicData • 139 views
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@schifferl
Last seen 10 weeks ago
New York, NY

Hi Peter,

I don't do the curation of metadata myself, but I asked a few team members who do – according to them, non_westernized "is not based on geography only, but associated with the lifestyle that we extrapolated from the original paper(s)." I realize that remains a bit ambiguous, but I hope it helps clarify the assignment some.

Regards,

Lucas

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I received a bit more of an update:

Non-westernized lifestyle is defined as not impacted by factors typical of modern society, with particular reference to the gut microbiome, in particular antibiotics usage and other medical treatments that impact the microbiome and a subsistence strategy that does not involve heavily treated food-chain products such as in urban contexts. The definition is of course somewhat "continuous", but it applies well to the microbiome, which is undoubtably more complex and less studied in hunter-gatherers or shepherds in highly rural contexts.