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:

 

Psomagen

Thryve

Viome

Stool 1

(3/11/21)

1 Gene & GutBiome

1 GutBiome+

 

2 samples

Stool   2

(5/3/21)

1 GutBiome+

1 sample

1 sample

Stool   3

(6/27/21)

1 GutBiome+

2 samples

1 sample

Stool   4

(10/6/21)

1 GutBiome+

1 sample

1 sample

Stool   5

(12/11/21)

1 Kean Gut

1 Ombre

 

Stool   6

(5/6/22)

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)



Cost:

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.

Human Metagenomics Comp 2021/2022: Additional Viome Comparisons

To be clear, I did not take any action based upon these reports.

In this post, I present some additional measures that you can see compare between my Viome stool collections, under the following categories: i) dietary recommendations and ii) supplement recommendations.


Viome "Foods to Avoid":

 

Stool 1a

Stool 1b

Stool 2

Stool 3

Stool 4

Vegetables to Avoid

Bell Pepper


Broccoli


Brussels Sprouts


Cabbage


Mustard Greens


Tomato

Bell Pepper


Tomato

Bell Pepper


Sauerkraut


Tomato

Bell Pepper


Tomato

Bell Pepper


Cucumber


Tomato

Proteins and Fats to Avoid

Almonds


Chicken 
Egg Yolk


Pistachios

Almonds


Pistachios

Kefir (Cow Milk)


Yogurt (Cow Milk, Plain)

Almonds


Pistachios

Shrimp (Domestic)

Fruits and Grains to Avoid

None

None

Barley


Blueberry

None

Watermelon

Other Food Items to Avoid

None

None

Coffee

Turmeric

None

I do drink tea instead of coffee, since coffee can irritate my eyes (and, at least to some extent, my stomach).

However, I think these results were problematic overall:

  • It looks like the variation for the same stool is at least similar to the variation between stools.
  • I drink almond milk every morning, which I believe helps some with digestion (compared to diary milk).  I don't think my reaction to dairy is severe, but I am not going to stop drinking almond milk.  This was in multiple reports.
  • I also think it is helpful for me to eat Activia with lunch.  I am not completely sure how much eating regular yogurt helps, but I am certainly not going to stop easing any yogurt.
  • Shrimp and watermelon are among my favorite foods.  I don't typically encounter serious problems, and I think they might even help a bit with digestion (at least if the shrimp is cooked and fresh).  So, again, these are examples of food that I am definitely not going to stop eating.
I think that the formatting in the blog post is not great, but you can also see this in a PDF format here.

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.

Viome Supplement Recommendations:

I was not certain the best way to show these results in this blog post.

You can download the full Excel table as "raw" from the GitHub page.

You can also view the table in PDF format hereIf you want to see all 5 columns of results, then this is my recommended option.

I think that you can probably only clearly view the full content of the first 3 columns of results below (1a/1b and 2).  However, the 2 highlighted columns are for the collections from the same sample (for both this table as well as the "Food to Avoid" table above).  So, I think it is particularly useful to note when those are different.

Supplement

Stool 1a

Stool 1b

Stool 2

Stool 3

Stool 4

Acacia Fiber

 

 

1000 mg

 

 

Alpha-Lipoic Acid (ALA)

 

153 mg

 

 

 

Amylase

 

 

20 mg

 

 

Angelica Root Extract

 

 

87 mg

 

 

Astaxanthin

 

 

 

 

149 mg

B. animalis ssp lactis B420

 

270 million CFU

 

270 million CFU

500 million CFU

B. animalis ssp lactis BL-04

 

 

1.5 million CFU

 

 

B. animalis ssp lactis VK2

2 billion CFU

 

 

 

2.5 billion CFU

B. bifidum Bb-06

500 million CFU

 

 

1.4 billion CFU

500 million CFU

B. breve Bb-03

2 billion CFU

1 billion CFU

 

 

2.5 billion CFU

Bacillus coagulans SANK 70258

500 million CFU

 

1.3 billion CFU

 

1 billion CFU

Bacillus subtillis DE111

1 billion CFU

 

750 million CFU

 

 

Beet Root Juice

700 mg

 

700 mg

600 mg

 

Benfotiamine

 

 

101 mg

 

122 mg

Berberine

 

515 mg

 

 

 

Beta-Glucan

 

1000 mg

250 mg

750 mg

 

Bilberry Extract

 

79 mg

 

 

 

Boswellia Serrata Gum Extract

 

 

140 mg

120 mg

 

Butterbur Root Extract

62 mg

60 mg

59 mg

 

59 mg

Capsicum Extract

 

24 mg

 

 

 

Caraway Seed Extract

 

 

161 mg

 

 

Cellulase

 

 

74 mg

 

 

Chamomile Flower Extract

 

 

45 mg

 

 

Chromium

 

2 mg

 

 

 

Citicoline

149 mg

 

124 mg

 

149 mg

Curcumin

200 mg

200 mg

 

 

107 mg

Dandelion Root Extract

 

 

454 mg

 

 

Deglycyrrhizinated Licorice (DGL) Root Extract

 

 

31 mg

 

 

Elderberry Extract

 

 

 

 

208 mg

Feverfew Extract

 

 

239 mg

 

239 mg

Fisetin

70 mg

 

 

60 mg

 

Forskohilli Root Extract

 

 

 

21 mg

 

Fructo-oligosaccharides (FOS)

 

 

3250 mg

 

 

Garlic Extract

 

 

 

 

306 mg

Greater Celandine

 

 

76 mg

 

 

Inulin

1900 mg

 

 

 

2400 mg

L. acidophilus DDS-1

 

 

1.3 billion CFU

 

 

L. acidophilus NCFM

 

 

200 million CFU

 

 

L. casei Lc-11

 

 

200 million CFU

 

 

L. delbrueckii ssp bulgaricus Lb-87

500 million CFU

 

 

 

 

L. delbrueckii ssp bulgaricus LE

500 million CFU

 

 

 

500 million CFU

L. fermentum LF61

 

 

400 million CFU

 

 

L. gasseri Lg-36

 

 

 

270 million CFU

500 million CFU

L. helveticus VPro13

 

 

 

1.4 billion CFU

 

L. paracasei Lpc-37

 

 

 

270 million CFU

 

L. plantarum 299v

 

 

750 million CFU

1.4 billion CFU

 

L. plantarum LM

500 million CFU

 

 

270 million CFU

500 million CFU

L. plantarum Lp-115

500 million CFU

 

 

 

500 million CFU

L. reuteri 1E1

500 million CFU

 

 

270 million CFU

500 million CFU

L. rhamnosus GG (ATCC 53103)

 

 

1.4 billion CFU

 

 

L. rhamnosus LB3

500 million CFU

 

 

 

500 million CFU

L. rhamnosus Lr-32

 

 

200 million CFU

 

 

L. salivarius Ls-33

 

 

200 million CFU

 

 

Lactase

 

 

1 mg

 

 

Lactobacillus acidophilus La-14

500 million CFU

 

200 million CFU

 

500 million CFU

L-Arginine

 

 

 

124 mg

 

Lemon Balm Extract

 

 

76 mg

 

 

L-Glycine

152 mg

 

126 mg

177 mg

152 mg

L-Lysine

 

 

 

 

406 mg

L-Tyrosine

152 mg

 

126 mg

177 mg

152 mg

Lutein

59 mg

 

49 mg

 

59 mg

Magnesium

758 mg

735 mg

727 mg

727 mg

 

Mastic Gum Extract

257 mg

 

 

257 mg

 

Mulberry Leaf Extract

 

1000 mg

 

1000 mg

 

N-Acetyl-L-Cysteine (NAC)

509 mg

 

 

509 mg

 

Nettle Extract

 

 

 

 

209 mg

Olive Leaf Extract

 

 

299 mg

 

 

Oregano Leaf

 

 

 

 

74 mg

Panax Ginseng Root Extract

 

 

99 mg

139 mg

119 mg

Phosphatidylcholine

 

 

304 mg

 

 

Phosphatidylserine

92 mg

 

76 mg

 

92 mg

Phygeum Bark Extract

99 mg

 

 

 

 

Psyllium Husk Fiber

2000 mg

 

 

 

2000 mg

Pumpkin Seed

385 mg

330 mg

385 mg

330 mg

 

Pygeum Bark Extract

 

 

 

99 mg

 

Rhodiola Root Extract

149 mg

 

124 mg

174 mg

149 mg

Saccharomyces boulardii DBVPG 6763

500 million CFU

 

 

279 million CFU

500 million CFU

Sage Leaf Extract

 

209 mg

 

 

 

Saw Palmetto Berry Extract

224 mg

192 mg

224 mg

 

 

Schisandra Berry

239 mg

 

199 mg

279 mg

239 mg

Serrapeptase

 

 

17 mg

 

 

Spirulina Extract

 

 

 

34 mg

 

Streptococcus thermophilus St-21

1 billion CFU

470 million CFU

 

470 million CFU

1 billion CFU

Thyme Leaf Extract

 

 

 

 

79 mg

Tinospora Cordifolia Extract

 

 

 

 

419 mg

Tribulus Terrestris Extract

356 mg

 

 

356 mg

 

Turkey Tail Fruit Body Extract

124 mg

 

 

124 mg

 

Vitamin B5 (Panthoenic Acid)

 

 

 

20 mg

 

Vitamin B7 (Inositol)

 

 

 

257 mg

 

Vitamin B8 (Biotin)

 

99 mg

 

 

 

Vitamin C (Ascorbic Acid)

 

 

 

 

353 mg

Xylo-oligoaccharides (XOS)

1550 mg

 

 

750 mg

1000 mg

Zeaxanthin

59 mg

 

 

69 mg

 

Zinc

 

 

 

 

59 mg

 

 

 

 

 

 

Total Supplements

28

30

37

34

30

Total Probiotics

19

18

18

18

19

 The units for the supplements above are the dosage per day.

I am manually copying over the information from printed PDF files that I have saved (from the Viome web interface).  I think sometimes information might have gotten cut-off (and/or the screenshot did not contain all of the recommendations), since the sum don't exactly match the numbers that I recorded closer to the time when results were returned.  However, I did confirm the numbers themselves at the beginning of what was saved (and available on the GitHub page), which is what I report at the bottom of the table above.

If I test any of these recommendations and I have adverse reactions, then I will submit separate FDA MedWatch reports.  In my previous experience, when I tested a subset of a much smaller number of recommendations (blog post and MAUDE report for Theanine), I had some adverse reactions to supplements recommended based upon my genotypes.  However, I am currently hesitant to test any of these supplement recommendations from Viome.

I believe that I previously got headaches with high doses of zinc, and I noticed some amount of recommended zinc from my 4th stool sample (but not any of the other stool samples).  I noticed some other metals (like magnesium and chromium), but I hope somebody with more of a medical background might have more of an ability to guess the chances of causing harm before doing any testing.

Either way, you can certainly see noticeable changes in the recommendations, including the 1st 2 measurements from the same sample.

I believe somewhat more complicated machine-learning methodology is used for these predictions.  While I am not 100% certain, results like this wonder if there could be some sort of over-fitting.  If that is true, then the helpfulness/utility in independent samples may be lower for the machine learning model than a simpler model.  However, the only thing that I can say for certain is that there is noticeable variation without implementing any changes in my diet or medication,  and I am hesitant to test any of these predictions.


Please click here to return to the overall summary.


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 revision
12/29/2021 - add thryve/Ombre food recommendations
5/2/2022 - modify title to match new main post (even though I am currently only planning to update GitHub with details for the Viome sample for my 6th paired colleciton)
 
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