Why 16s

This is a recent Blurb that I wrote in response to some questions in the FB Gut Group - It gives a good background as to WHY 16s test is my preferred testing.!  Why 16s Testing

Debunking Culture Based Testing

Dr. Jason Hawrelak who is a well accomplished microbiome specialist has commenet extensively Culture Based testing

Here is an interview where Dr. Hawrelak briefly comments on 16s type testing vs Culture testing @ about 5 minutes in

https://www.youtube.com/watch?v=flQLdtlI2tg

If you register for his courses on the microbiome, you will encounter some experiments where he had sent stool sampling to several labs and compared the results. There is a brief mention of that in this interview below with regard to the inaccurcies of Culture Based testing (Doctors Data Type) @ around 8 minutes into the interview. https://www.youtube.com/watch?v=6nOFfmtoxXs

Here is a another good lecture, @ about 3 minutes in he discussing testing types.

https://www.facebook.com/AutismResearchCoalition/videos/513101566399062

Specifically, culture based testing relies on the sample to be grown in the lab. That depends on the following factors

Transit time for your sample to get to the lab (its growing this whole time in a non uniform way)

Temperature that your sample is maintained at before being processed

Culture mediums used to culture certain microbes tested for.

These tests only can test for what they can grow, so there is limited us, the levels can not be well compared for abundances, and they are time and temperature dependent (anything could grow out of proportion). They are extremely unreliable.

You can also checkout the information that Lucy Mailing has provided on microbiome testing

Lucy specifically comments on how Culture Based Testing is not useful

https://www.lucymailing.com/a-comprehensive-guide-to-stool-and-microbiome-testing/

It's not a question of consistency or reproducibility for the culture methods. Reproducibility is important but if your process changes the distribution or it is incomplete or it is not useful. In order to grow the microbe (a requirement for culture testing) it needs to be alive, the fact that it's alive means it can grow in transit at different rates subject to heat, pressure and time changes. This means variation from true state.

In order to grow the microbe you need a medium. Not all microbes grow with the same medium,  and at the same rates, either some are anaerobic. This means more variation. Testing for these requires time delay,  heat, variation etc. Not 2 samples taking the same journey.

So it's much trying to guess the ecosystem by growing things,  some things only and, not all and not evenly.

the DD test is not reliable for obtaining useful or relevant abundances, 16s v4 is currently the best when factoring in all aspects for taxonomy... and the best for clinically helping the patient. 

Why 16s over Shotgun Sequencing?

Why 16s rRNA and not Shotgun Metagenomics?

https://en.wikipedia.org/wiki/16S_ribosomal_RNA