
The Integrative Human Microbiome Project - pseudolus
https://www.nature.com/articles/s41586-019-1238-8
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heymijo
Collecting stool is one of the main data gathering tools for the gut
microbiome. For the this study, the portion that studied inflammatory bowel
disease relied on 1,785 stool samples (self-collected and sent by mail every
two weeks) for the temporal period.

Now, they did get intestinal biopsies at baseline and took quarterly blood
draws so it's not exclusively stool based data.

However, recent work from Dr. Mark Pimenthal's lab at Cedars Sinai says
something that could shake this data to its core:

"The gut microbiome is NOT represented by stool! The longest segment of the
gut (20 ft of small bowel) is completely different."

They haven't released a paper yet, this was on a poster at a recent seminar,
but if true, it could have huge implications for just about all of the gut
microbiome research out there today as it uses stool samples as the workhorse
for data collection and analysis.

This is still a nascent field and one I have experience in myself.

I saw first hand while at a biosciences startup how the tests we were using
for stool samples of the microbiome were statistically unreliable calling in
to question the validity as well.

After researching other labs practices at the time, it left me questioning the
best practices of the day as well as the worth of the data being collected and
reported.

Combining what I have seen personally combined with the implications of Dr.
Pimenthal's lab's research and I have to wonder if there is any reliable and
valid data out there on the gut microbiome yet.

~~~
ramraj07
Frankly I've never seen a single massive data collection project since the HGP
that has had made any real consequential contribution worth it's investment
since. That modencode fiasco still leaves a bad taste in my mouth.

