uBiome with low diversity and significant recovery

Most CFS uBiomes show high diversity — but CFS can be a progressive condition which would imply that the uBiome can change it’s profile over time.

Patient History

  • A year of antibiotics for a prostate infection was the probable cause
  • Fatigue, tendonosis, exercise fatigue, muscle twitching, dry eyes, joint pain, ibs, mcs.  The worst of which is the fatigue.
  • What helps:
    • Tai chi,
    • Sleep,
    • Equilibrium,
    • Align (B. infantis),
    • Amino acids (Tyrosine in particular),
    • 5htp,
    • Vitamin D (but causes sleep problems, so can’t take),
    • Regactive [Lactobacillus Fermentum (but causes sleep problems–probably the b vitamins?),
    • cocoa powder,
    • low starch diet (helps with pain, but carbs give more energy so I avoid most carbs and live with the lower energy).
    • Mutaflor helps but can make sleepy.
    • Bifido strains make sleepy.
    • L. Acidophilus makes dry eye worse.
  • State:
    • I would say that I’ve recovered about 40%, which has allowed me to work every day but hasn’t allowed me to have the energy to socialize, exercise or stand for long periods of time.
    • My IBS symptoms have been cured, however.

Basic Criteria for CFS/FM

E.Coli’s Parent:

Conclusion: Every basic criteria is a match. The low diversity is not typical but has been seen in some other uBiomes.

Overgrowth of Bacteria Genus


Rare Bacteria

Analysis of Over Growth

  1. Holdemania (genus) 
  2. Bacteroides (genus) 
  3. Akkermansia (genus) 
  4. Lachnospira (genus) 
  5. Bilophila (genus) 
  6. Anaerotruncus (genus) 
  7. Bacillus (genus) 

Items struck out below appear on both inhibits and enhances — so a toss up!





Bottom Line

My first question was why was there low diversity, there is no report of taking antibiotics? A good night sleep revealed the probable cause – because the right probiotic to reduce the high diversity was taken. The one that I suspect most as being the cause was:

  • RegActiv (Lactobacillus Fermentum)
    • “Up to the present no strain of lactobacilli with an extensive anti-microbial effect against numerous pathogens and opportunistic pathogens has been described.” – this one does!!!!
    • “The innate resistance of Lactobacillus fermentum ME-3 against antimicrobial preparations (TMP-SMX, ofloxacin, aztreonam, cefoxitin and metronidazole) allows to use it as a preparation accompanying antibiotic treatment in case of gastrointestinal and uroinfections”
    • Mutaflor is also possible, but seems less probable.

Wish List: Some patient with high diversity in uBiome try Lactobacillus Fermentum for 4-6 weeks and then get another uBiome done. This will provide some evidence if the above speculation is correct. If it is, then we may have discovered a key probiotic for remission.

Unexpected Scattering

Usually I have seen clustering (multiples) of some items across the bacteria genus. In this case, there is little, what there is:

One interpretation of the lack of clustering in the overgrowth is that the microbiome is moving towards normal. The highest overgrowth is just 2.74x well below most CFS uBiome results.

Patient Reports

I suspect that the sleepiness is a form of herx. RegActiv (Lactobacillus Fermentum) produced strong antibiotics and does Mutaflor. If there is an opportunity to take a week+ off from work for a ‘sleep vacation’, I would suggest loading up on one of them to try to the corner (but do not take together — they will disagree with each other). I recalled sleeping 12-14 hrs a day during my second episode from antibiotics for a few weeks, then it stopped.

An alternative would be to use Symbioflor-2 (US Source, World Wide Source) , another E.Coli probiotic and slowly work up the dosage – balance the dosage with the amount of sleepiness.

Dry eye: I have had dry mouth, and found that mastic gum cleared it up within a few days (not permanently). A reader provided an interesting comment on an earlier post:

“a treatment I developed for myself decades ago. During my late teens and early twenties I suffered from chronic ear infections. I eventually discovered that if I broke open an acidophilus capsule and left the contents between my cheek and gum overnight after brushing my teeth when I first felt an infection coming on, it would be cleared up by morning. Eventually, after a couple of years, I noticed that I no longer suffered from chronic ear infections.”

  • A very unorthodox approach (definitely needs medical review) is to use Symbioflor-1 or Symbioflor-2 as eye drops….

CAUTION: With prescription antibiotics, if you stop then the herx effect disappears within 24 hrs. With bioactive antibiotics (i.e. probiotics), a herx can go on for weeks. See this patient experience post and also this post.

As always, this is strictly an informational/education post of items that should be discussed with your knowledgeable medical professional before starting.