ubiome analysis of a friend in Seattle

Reader Summary


Gradual onset (or as I call it, “Gradually Sudden”).

  • Began high-stress job 9/1994 managing a large old apartment building where I worked with pesticides, fungicides, paints, paint thinners, and was exposed to mold from plumbing leaks on many occasions.
  • 4/1996: Came back from Mexico w/montezuma’s revenge.  Noted ‘never felt this weak in my entire life’ a week later, before herbs (haritaki, etc) stopped it.  But didn’t really recover 100%.
  • Continued with stressful 24/7 job, managed to stay afloat, but stressors took theirtoll by fall ’97 and I ended up in ER June 3rd, 1998.
  • After that got worse each year until a little rebound in early 2015, and a distinct one in March 2016 (thanks mainly to niacin – a two-edged sword – helps w/triglycerides, but can make histamine issues worse). I was so bad in Feb 2016 that I needed a cane to get out of bed, and after falling into the bedroom window, used a walker – inside my apartment – probably 85-90% of the day, as I was just unbelievably weak and my balance unstable.  After 2 weeks of niacin, I needed the walker maybe 20-25%…)
  • Hindsight is always 20/20.  I started to develop reddish-brownish, semi-crusty patches/rashes in a couple spots on my legs in early 2008.  By late 2010-early 2011, I stopped sweating and my skin started really drying out.  By late 2011 to present day, I have at times overall body dandruff – mostly on my lower legs though, but can be anywhere.  This is no doubt due in part to not being able to bath or take a shower since about mid-2012 – so I dry brush or do spot bathing – but it’s mainly due to insulin resistance/metabolic syndrome/pre-diabetes. No one could tell me what the patchy reddish-brown areas were, so I googled and came to a site w/55 different types of rashes.  The one that matched my main ‘patch’ was called “stasis dermatitis”.
  • More googling revealed stasis dermatitis is connected to venous insufficiency, which can be connected back to diabetes, along with other vascular issues.  It might be a tiny bit better than a year ago – I’ve been taking quercetin w/vitamin C and the main spot doesn’t seem to be so bad, but the circulation to my feet is still BAD.
  • Rich Van Konynenburg reviewed for me back in September of 2010(!).  And my muscle has definitely broken down.  My calves are basically jelly-like, what’s left of them anyway.
  • And Medicaid doc agrees I definitely have developed fatty liver.  My legs are like sticks, but my gut looks like I’m six months pregnant(Update, now I’m maybe 4 months pregnant.)  B. longum to the rescue?:
  • I also had a test for gluten sensitivity back in 2007.  Looking at it in hindsight,only one of the four-part test was positive, and mildly so.
  • Can only tolerate a few spices, mainly because of the histamine issue.  But nothing pungent (dries me out, and sometimes causes severe muscle cramps) or anything too bitter (makes me constipated).  But can do dill, some small amounts of basil from time to time, small, very small amounts of onion.
  • Also, in addition to the l. plantarum for histamine and dust mites above, I want to mention two other probiotic strains that I know have been helpful:  b. infantis, and b. longum BB536.  Both helped w/histamine issues.  And now in 10/2017, the b. longum – at a higher dose – 4-6 10billion caps/day – seems to be helping w/the chronic constipation.

Standard Items:

  • Diversity: 76%ile
  • Lactobacillus:  0.19x
  • Bifidobacterium: 0x
  • Akkermansia: 0x
  • Firmicutes:Bacteroidetes: 2.8:1 (Normal  2.1:1)
    • More bacteriodetes undergrowth than firmicutes overgrowth.

Typical CFS profile

Uncommon Bacteria

None – 8.6% common was the rarest (threshold is 5%)

High Bacteria

Sarcina: 2.23 X
Phascolarctobacterium: 3.03 X
Dorea: 2.51 X
Sutterella: 2.04 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.


  • Animal-based diet
  • Barley
  • Berberine
  • BPA bottles
  • Helminth infections
  • High Fat Diet
  • Lactobacillus rhamnosus
  • Polydextrose
  • Saccharomyces boulardii
  • Soluble corn fiber
  • Stress
  • Walnuts (and likely pomegranates)


  • Acarbose
  • Bifidobacterium Longum
  • Enterococcus  faecalis
  • Fennel
  • Flaxseed
  • Fructooligosaccharides (FOS)
  • Fumarate
  • Galactooligosaccharides (GOS)
  • Gluten free diet
  • High Protein Diet
  • High resistance starch
  • Lactobacillus Casei
  • Lactobacillus paracasei
  • Lactobacillus plantarum
  • l-glutamine
  • lycheerambutanguaranakorlanpitomba, Spanish lime and ackee. [fam-Sapindaceae]
  • Metronidazole
  • Oral Iron Supplements
  • Polymannuronic acid
  • Resistant starch (type II)
  • Sodium chloride (Table Salt)
  • Vitamin D3
  • β-glucan

Personal Comment

The reader has self-discovered two probiotics that helped him: (Bifidobacterium Longum and Lactobacillus plantarum) — both were on his Take list, as well as three more suggestions:

  • Enterococcus  faecalis
  • Lactobacillus Casei
  • Lactobacillus paracasei

Other easy supplements are: L-Glutamine, Vitamin D3, oral Iron Supplements, beta-glucan. He should see if he tolerate Fennel and Flaxseed in low dosages and work up.

  • Acarbose is a prescribed medication that is often used with pre diabetes — he may be amble to get a physician to prescribe it.

I should note that some of the studies found that 24 BCFU/day of a specific probiotic was often needed to get effective results — you need enough of them to overwhelm the cartels (at least temporarily).

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.