Sunday, December 12, 2021

Human Metagenomics Comp 2021/2022: Overall Summary

Inspired by an earlier post that I don't believe is currently accessible (from several years ago), I tested collecting stool samples at the same time for multiple companies.  This sometimes includes the same sample submitted the same company at the same time.

The sample collection can be summarized as follows:





Stool 1


1 Gene & GutBiome

1 GutBiome+


2 samples

Stool   2


1 GutBiome+

1 sample

1 sample

Stool   3


1 GutBiome+

2 samples

1 sample

Stool   4


1 GutBiome+

1 sample

1 sample

Stool   5


1 Kean Gut

1 Ombre


Stool   6


1 Ombre

 1 sample

 There are additional details (including the reports and data) on GitHub.

The sequencing performed can be described as follows:

Psomagen GutBiome (within combined "Gene & Gutbiome"): 16S (V3+V4 region, PE300 reads)

Kean Gut16S (V3+V4 region, PE300 reads)

thyrve/Ombre16S (V4 region, PE150 reads)

Psomagen GutBiome+"Shotgun" Metagenomics (DNA-Seq, PE150 reads)

Kean GutBiome+"Shotgun" Metagenomics (DNA-Seq, PE150 reads)

ViomeMetatranscriptomics (RNA-Seq, unknown read length)

As verified by Ombre technical support, you can view an alignment from my 5th paired sample here.  The other V4 sequences were downloaded from the GitHub repository for code associated with Johnson et al. 2019.

I have a couple paired posts (here and here), but I hope this can provide a fairly good summary of my overall experiences:

Individual assignments are not provided within the web interface for Kean Gut, but assignments can be made with re-analysis of the raw data and you can see some of such analysis with mothur here and Kraken2/Bracken here.

Raw Data Return:

1) thryve/Ombre - automatically provides raw FASTQ files as well as table with classifications at various levels

2) Psomagen/Kean - provides FASTQ files if e-mailed (but not automatically)

3) Viome - does not currently provide raw data (even if e-mailed) and classifications have discrete assignments (not percentages of reads)

When raw data was available (either automatically or by request), I have uploaded the data in public links on Google Cloud.  You can see a table of files to download here.

The samples and companies / organizations are different.  However, if it might help to see metagenomics samples that were collected before any of the samples described in this blog post, then you can see links to download raw data here.

Post-Collection Bacterial Growth Suppression:

1) thryve/Ombre - A liquid is included, but I have not yet verified the contents of that liquid.

2) Viome - liquid with preservative ("[bacteria] are not being killed nor growing").  I am not 100% sure about the implications for using RNA to study "active" bacteria, but I think it should help over adding nothing.

3) Psomagen/Kean - no liquid in collection tube to prevent / suppress bacterial growth

I only collected 1 BIOHM sample (10/6/2021), but there was no liquid (and therefore nothing to prevent / suppress post-collection bacterial growth)

Sample Collection Options:

1) Viome - originally provided 2 sizes of stool collector, but I think this is now reduced to 1 stool collector.

2a) Psomagen - 1 stool collector

2b) Kean -  tissue paper (0 stool collectors, if collected by itself)

3) thryve/Ombre - tissue paper (0 stool collectors, if collected by itself)


1) Psomagen - $149 (with discounts - I paid $83.49, including $8.99 shipping, for 1 of my samples)

Kean splits options into ability to purchase separate Gut Health (for $99) and Gut+ Health (for $169)

2) thryve/Ombre - $199 (with discounts - I paid $99 before taxes, with free shipping, for at least 1 of my samples)

If you count the re-test discount (and that is still offered through Ombre), then I paid as low as $74.32 for 1 kit (with taxes).

3) Viome -  $299 (with discounts - I paid $129 before taxes, with free shipping, for at least 1 of my samples)

Result Turn-Around Time:

I think there is a limitation or lowest raking for each company, depending upon whether you define "turn-around time" for the kit, the results, the raw data, or for answering questions.

If it takes weeks to receive results that I think should mostly be considered hypotheses, then I don't think the slightly faster arrival of materials is really helping very much.  However, I consider returning raw data for re-analysis and answering questions from consumers to be very important.

Robustness of Results:

1) thryve/Ombre

2) Psomagen/Kean

3) Viome - noticeable variability results for samples collected at the same time

The explanation here is somewhat complicated.

As explained in a paired post, the signature/scores for collections from the same sample were better for thryve than Viome.  There are also some extra examples related to variability in the Viome results in this other paired post, but that is only for Viome.

Viome does not provide raw data and the data collected is different. So, only 2 signature/scores were available for thryve.  The Psomagen Gene & GutBiome kit used a different library design than the Psomagen GutBiome+ kit, so I don't have the replicates from the same sample that I intended.

There is also some information that I manually extracted from the 3 reports here (as well as on the highest level subfolder).  As mentioned earlier, you can also see some re-analysis of raw data (for Psomagen/Kean and thryve/Ombre, here and here).

Overall, I submitted an FDA MedWatch report Viome (for the currently commercially available tests described in this blog post), where the full draft is available to view here.  You can see the de-identified version in the MAUDE database under MW5106218.

To be fair, thryve/Ombre also have some food predictions that I would not place too much emphasis on.  However, Viome clearly has less consistency than the thryve/Ombre (positive and negative) recommendations.  If you download the thryve/Ombre PDF summary tables, then you should be able to access the links to the reports on Google Cloud (because they were too large for GitHub).

If you specifically purchase Kean Gut+, then there are some food recommendations.  I have not made changes based upon the results from any company, and I am not making any changes based upon any specific feedback from Kean either.  However, there were at least no recommendations to avoid eating food that I already find helpful or favorable.  I think the food recommendations also seem like mostly good ideas, regardless of any particular metagenomic result.  On the other hand, I am not certain what to say about the supplement recommendations for either Kean Gut or Kean Gut+.

A Note About Probiotic Detection:

The reason that I ordered a Viome sample for my 6th (but not 5th) paired sample is that I better understood the difference between the Kean Gut and Kean Gut+ kits, and I wondered if it was possibly useful to have a paired sample with untargeted DNA-Seq (for Kean Gut+) along with a Viome sample.

Viome still does not provide raw data, and I believe they only provide discrete specific assignments.  The Viome interface has changed recently, but I was still able to see those in a PDF file when I e-mailed myself to "Share My Results"  (under "Scores," and then at the bottom of the details for one of the scores)

Nevertheless, I could compare Kean Gut+ assignments and the "Active" status for Viome, and most assignments matched in that sense (everything above 1% listed in the table on this page match).

The one exception where I can have both Kean Gut and Kean Gut+ information for individual bacteria is for probiotics.  Lactobacillus was copied over from earlier collections, but I thought that might be interesting in that Ombre and Viome reported detection when both Kean Gut and Kean Gut+ reported a lack of detection.

I thought this was somewhat interesting because I have Activia with lunch on Monday to Friday.  The Wikipedia page mentions that other common probiotics are also present, but Bifidobacterium is mentioned as something specific to Activia.  So, I went back to check the original reports and update the GitHub table for the 6th paired collection, and all 3 companies report Bifidobacterium detection.

There are non-zero mothur read fraction assignments for Bifidobacterium for all samples except Psomagen for the 3rd paired collection (Psomagen3), and I can tell that Kraken2/Braken is also capable of making those assignments at the genus level.  I don't think this indicates what is present is specifically the proprietary strain, but I might guess eating yogurt on a regular basis might have some level of contribution.  I also don't think the bacteria has to be that proprietary strain in order to be helpful.

Closing Thoughts:

In general, my opinion is that is better to focus on a smaller number of things that are truly predictive than attempt to make a large number of claims (and have a lot of them not be valid).  I also think having access to raw data for re-analysis is very important.

I selected Psomagen because it was the company that purchased assets from uBiome.  However, there are notable differences in what Psomagen provides (such as no longer using a liquid to prevent post-collection bacterial growth).  Even though there were other ethical problems for uBiome, I think stopping post-collection growth was a good idea.  I also previously had the ability to sample multiple sites from uBiome, but that was not currently an option.  So, I don't think these company purchases/acquisitions necessarily mean that you can expect the same product.

I think I might have purchased a Viome kit because of an advertisement, but I believe that I am less likely to make future Viome purchases (if similar to what is currently provided).  I also do not plan to make additional BIOHM purchases.  My overall impression for Psomagen/Kean was somewhere in the middle, but I would guess that I am most likely to purchase Ombre in future.  For example, I posted Trustpilot reviews for all 3 companies: 4 stars for Ombre, 3 stars for Kean, and 2 stars for Viome.  However, to be clear, that is largely because of the automatic return of the raw data and the presence of some sort of liquid that I assume helps reduce post-collection growth.  That does not mean that I like or approve everything within the Ombre results.

For example, I am not sure if I support the Ombre supplement recommendations, and I don't remember seeing anything that I considered particularly helpful among the food recommendations.

From a technical standpoint, my critiques were mostly for Viome.  Of course, anybody can submit FDA MedWatch reports for a technical issue with a diagnostic (as I did).  However, if other consumers do plan on taking supplements recommended by the company, then I hope that they use FDA MedWatch if they encounter any adverse events I did this for an earlier human genomic test, but I am hesitant to try recommendations from the multiple other companies.  So, I hope that customers for all 3 companies are aware of resources like this and take the time to provide important feedback as relevant.

Unfortunately, I don't think have enough specialized background to gauge the relative importance of various options for specific diseases (such as those offered by a given company, versus other options that might even be free).  So, if you are well aware of the common best practices (as either a physician or possibly as a patient with a chronic condition), then please provide feedback if you notice any claims that might either over-emphasize the benefit of a supplement from a given company or if enough emphasis on other available/established options is not adequately described.  I think there are reporting systems for advertising, but I am not sure of those can be recommended by somebody else.  I think critical evaluation of claims is important, and I think e-mails to the company and discussion with your general or specialized physician are probably a good starting place.

Again, I did not make any changes based upon any results from any of the companies.  I only used this for research purposes to gain a better appreciation for the bacterial metagenomic analysis, which would allow me to do things like study microbiome changes over time.  In the future, I might also make changes based upon independent physician advice and see what happens in my metagenome (mostly as a matter of curiosity), but I consider that different than starting from recommendations based upon the metagenomic data.

I hope others find this helpful, and I would certainly encourage feedback! I think the blog post comments section has been OK in the past.  However, if there is any possible benefit to using the GitHub discussion (which can include images and code), then that is also an option.

Change Log:
12/12/2021 - public post date
12/13/2021 - various wording revisions/corrections
12/14/2021 - change wording for last change log entry; additional revisions
12/19/2021 - add Viome response + additional links
12/29/2021 - thryve/Ombre food recommendations
1/22/2022 - add FDA MedWatch report
5/2/2022 - change title and add additional sample information
6/18/2022 - after receiving results from all companies, add collection date for 6th sample.
6/19/2022 - add links for raw data
6/27/2022 - revise closing thoughts and add some additional details (such as re-analysis and Bifidobacterium detection)
6/28/2022 - add link to GitHub disucssion
7/16/2022 - add Trustpilot review links, and re-arrange content.

For example, I have moved the content below out of the main post for brevity, but I am keeping the comments below for reference:

When I asked Viome for feedback regarding the extra discordance that I believe I saw in my samples (including those collected at the same time), I was directed to this page.  I am not sure if I see the assessments currently being provided to consumers.  However, if that represents the response, then perhaps it can be mentioned that I think it is important to emphasize that the "FDA Breakthrough Device Designation" for a different application that I believe is not available to consumers is not in fact FDA approved (matching the bar chart in the provided link, if you look carefully - however, it was an issue that I separately reported for regulatory misconduct, with draft available here that is a follow-up from discussion with other FDA that informed me about the regulatory misconduct reporting system). That said, I wish to emphasize that it is important that each claim be evaluated independently (within and between tests).


I believe this article references low consumer reviewers for Viome.   As of 12/19/2021, I see 1.28 out of 5 from the BBB, and 3.2 out of 5 from Trustpilot.

No comments:

Post a Comment

Creative Commons License
My Biomedical Informatics Blog by Charles Warden is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 United States License.