uBiome result for a sample “left on shelf”

A reader wrote:

“I “pushed” smartgut into ubiome explorer and downloaded the CSV. Based on your comments, I am suspicious of how low things are. I am concerned that this is the result of degradation. It took them almost 5 months to run the sample, I actually had to contact them to ask them what the hell was going on. “

Several people have done smartgut (the professional version — which is focused on known and accepted microbiome shifts). I am not qualified to comment on degradation aspect – I understand that the techniques used is similar to recovering DNA, so gut feeling is that there may not be significant changes because of the techniques being used.

Reader Summary

11/5/2015 I woke up feeling like I was hit with mono overnight.

By 12/1/2015 I was on FMLA bed rest. Lots of pain, shaking, sweating, fever, exhaustion.

By mid December I was so run down that I could only shower every other day. The act of showering forced me back into bed. By the end of December the leg pain and muscle spasms started. I thought it was relapse remitting multiple sclerosis.

At the University Hospital an infectious disease specialist saw me twice and ran a lot of bloodwork, a large portion of which had to be completed at the Mayo labs at Rochester, MN. He concluded that I was not dealing with anything infectious and the department notified me that they would not schedule me for another appointment. (I was dismissed).

I saw a neurologist 5/2016 who said “sorry, its not MS, its CFS.” Which was the equivalent of telling me nothing at the time.
I woke up suddenly on 7/5/2016 with massive abdominal pain at 3am. I began voiding enormous amounts of fluid into the toilet from my GI tract. It was like my small intestine just stopped absorbing water and dumped it out. I struggled to get this under control for 6 weeks and did end up in the ER due to dehydration in the middle of the summer.
Following that episode, I demanded a screen of my ANA, which was positive. I was referred to rheumatology and a workup found positive anti phospholipid antibodies.
I was sent to digestive diseases and pressured into having an upper and lower endscopy, which found nothing. I tried, really tried, to explain that it was probably part of the hallmark “IBS” portion of CFS. The procedure left me with three herniated discs in my neck, which is just stacking disability onto disability at this point.
I’ve had two tests for mycoplasma. Unfortunately they both came back in the equivocal range. I do have antibodies against CMV, but they are the “old” ones, not the “recent” ones. The levels were off the scale of the lab test.
In 4/2017 my ANA was rechecked and it had “gone away,” which only frustrated my situation.
Since 8/2016 I have been having susceptible stap infections on my face, neck, torso. I shower with chlorhexidine and use mupirocin to treat it topically when it occurs. The primary literature suggests that this is cutaneous anergy, which is part of CFIDS.
Since 1/2017 I have had “rug burn” like rashes on my eyelids. They wax and wane unless I use an expensive topical steroid for around the eyes.
Also, my spleen is very large and often uncomfortable.
I am on the very long wait list to be seen at Stanford because no one here at Iowa wants to even see me, much less treat me.

Standard Items:

  • No Probiotics genus thus: no Lactobacillus or bifidobacterium.
  • No Akkermansia reported

Typical CFS profile

High Bacteria

Acidaminococcus: 7.11 X
Succinivibrio: 5.01 X
Catenibacterium: 4.38 X
Phascolarctobacterium 4.19 X
Haemophilus:  4.13 X
Peptoclostridium: 1.71 X
Sutterella: 1.70 X


Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.


  • Bacillus natto (likely all bacillus)
  • Berberine
  • BPA bottles
  • Cashews
  • Enterococcus faecium
  • Ginkgo
  • Glutamate
  • Lactobacillus acidophilus
  • Lactobacillus rhamnosus
  • Navy bean (Cooked)
  • Partial Sleep Deprivation [parent]
  • Polydextrose
  • Proton-pump inhibitors (PPI)
  • Soluble corn fiber
  • Thiamine supplements
  • Xylans


  • Acarbose
  • Cinnamon bark oil
  • Coriander oil
  • Cranberry bean flour [parent]
  • Flaxseed
  • Fructooligosaccharides (FOS)
  • Fumarate
  • Galactooligosaccharides (GOS)
  • High-protein, low-carbohydrate diet
  • Lactobacillus Casei
  • Lactobacillus kefiri
  • Lactobacillus paracasei
  • Lactobacillus plantarum
  • Lavender (spike) oil
  • Lemongrass oil
  • Peppermint oil
  • Perilla oil
  • Resistant starch (type II)
  • Saccharomyces boulardi
  • Sodium chloride (Table Salt)
  • Thyme oil
  • Vitamin D

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.