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 here.  If 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)