Sunday, December 12, 2021

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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