16s Microbiome Tests

Many of the older tests, like those listed in Standard Gut Tests obtain their numbers by cultivating the bacteria. Unfortunately, many bacteria families do not cultivate, especially those that do not like oxygen.

For a more detail explanation, I have prepared this PDF.

16s takes the bits of Rna from the bacteria, multiple the Rna to measurable levels (without needing to cultivate), and then deduce the bacteria species involved. The key word is deduce. The same identical data going through uBiome, Thryve, Viome etc will likely give different reports. Why? Because each uses their own logic to deduce what bacteria is there.

Technical but understandable…

In short, 16S provides information on some bacteria that cannot be obtained in any other way.

The following article describes the technical aspect of how the tests are done and discusses why results from older traditional tests may disagree.

Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens [2015]

Accuracy of Tests

This is an area that can get into disputes, especially with some academics and researchers. For an excellent background article see: The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies (2018)

Trying to find consensus in the literature is challenging, with many studies producing conflicting evidence about the effects of various steps in the experimental process. It is therefore essential that consistency is maintained within a study, and there must be an acceptance that comparisons between studies may not be possible.

In short, keep to the same lab always. The vast majority of samples being uploaded are were from ubiome, but that is no longer in business.

ThryveAlive.com is the most common after ubiome.

Converting RAW Data (FASTQ) to bacteria

As promised, a walk thru using uBiome fastQ raw data( 480 MEGS when expanded!) and extracting the bacteria names from it. This may help to understand 16s tests.