A 90% recover patient with the Probiotics that helped her.

A reader is up to 90% recovered and shared her uBiome. Bifidobacterium and Akkermansia has returned; Lactobacillus has made a start. The reader also lists what helped her get there. Her Firmicutes:Bacteroidetes ratio is still off and she still has overgrowths of some bacteria genus (three of which I had to do deep dives on because they are not usual with CFS)

Reader Summary
  • Woman, 52 years old, Spain,
  • When I took the sample for Ubiome my situation was remission by 80-90%. I was asymptomatic and could lead an almost normal life.
  • I am now working to lower my bacteria over and I think I am walking backwards, I no longer feel with the energy and the spirit that I had. My intestinal problems keep well. It seems that some of these over bacteria are good for me.
  • And that my ubiome could represent in my case a marker very close to being
    healthy for me.
  • I have been ill for 12 years, diagnosed with breast cancer 7 years ago, Multiple Chemical Sensitivity severe degree three years ago
  • In the almost two years that I follow your blog I have improved up to almost 90%.
  • I have taken the following PROBIOTICS:
    • Lactobacillus plantarum (positive)
    • Presscrip Assist (unchanged) much anxiety
    • Symbioflor 2 (very positive)
    • Simbioflor 1 and 2 (positive)
    • Align (very positive)
    • Reuteri protectis and Prodentis (positive)
    • Culturelle (positive)
    • Lactobacillus fermentum M03 (excellent) Herx low doses to avoid progressive increased.
    • Others without significant results …..
  • I have taken the following Herbs:
    • Neem (positive)
    • Tulsi (unchanged)
    • Oregano (positive)
    • Thyme (positive)
    • Ashwaghanda (very positive)
    • Curcuma (positive)
      Others without apparent results ….
  • SUPPLEMENTS: (All recommended on your blog)
    • Vitamin D (very positive) taking a lot of sun.
      Other supplements (positive)
Standard Measures
  • Biodiversity: 82%ile
  • Bifidobacterium: 1.73x
  • Lactobacillus 0.02x
  • Firmicutes:Bacteroidetes ratio: 1.2 : 1 (normal 2.1:1)
  • Akkermansia: .48x (half the usual)
The microbiome appears to reflect the severity that is described above. If appears that Bifiobacterium and Akkermansia have managed to get established. On the opposite side, the Firmicutes:Bacteroidetes ratio being low suggests that we have not stabilized, that is “one set of demons have been tossed out of the house, but some new ones may start appearing!”

Overgrowth Bacteria Order
Erysipelotrichales: 2.17 X
Desulfovibrionales: 1.65 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.

  • Amoxicillin-Clavulanate antibiotics
  • Barley
  • Berberine
  • Bifidobacterium adolescentis Probiotics
  • Bifidobacterium animalis subsp. lactis B-12®) [See PDF where it was found to increase it 3 fold]
  • Bifidobacterium longum
  • Bifidobacterium pseudocatenulatum
  • Bile
  • Canola Oil
  • Clostridium butyricum (i.e. Miyarisan) probiotics
  • CVS Maximum Strength Probiotic
  • Dairy
  • Enterococcus probiotics
  • Fructooligosaccharides
  • Getting Cold
  • High Fiber Diet
  • Isoniazid-
  • Jerusalem artichoke, Inulin, Chicory
  • Lactobacillus fermentum
  • Lactobacillus paracasei
  • Lingonberries
  • Milk-derived saturated fat
  • Minocycline
  • Penicillin
  • Phosphorus containing food
  • Pyrazinamide
  • red wine (or grape seed extract or reservatol)
  • Resistant Starch
  • Resveratrol (Grapes, wine)
  • Rhubarb
  • Rifampin
  • Saccharomyces boulardii
  • Sleepless nights
  • VSL#3 Probiotics
  • Walnuts
  • Bacilus Coagulans probiotics
  • Bile salts
  • Capsaicin (chili peppers)
  • Chicory
  • Chitosans
  • E.Coli Probioitics
  • Flaxseed
  • Gallate – Green Tea is highest
  • gluten-free diet
  • Grapes (table) – likely grape seed extract will help
  • High-fat diet
  • Iron supplements
  • Ketogenic diet
  • Lactobacillus Casei
  • Lactobacillus kefiri
  • Lactobacillus plantarum
  • Lactobacillus reuteri
  • Lactobacillus salivarius
  • Low fiber diet
  • Metronidazole antibiotics
  • Navy bean (Cooked)
  • Omega 3 fatty acids (600 mg of omega-3 daily for 14 days cited in studies )
  • Polymannuronic acid
  • Resistant starch (type II & IV)
  • Tea
  • Thyme
  • Vitamin K2
Comment on the above
  • It was interesting that all of the specific strains of Bifidobacterium were on the Avoid list — given that there is a high(173%) amount of Bifidobacterium, that makes sense. Genus that may be encouraged by the Bifidobacterium are in the high list, and those discouraged have already dropped to normal or below.
  • No Dairy (i.e. no yogurt, cheese etc) seems indicated as well as No gluten. Start looking for recipes with Thyme, Chili Peppers.
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.


thanks for sharing this, ken! I really appreciate your work on the interplay between microbiome and CFS... I found this study that says OLE kills e. coli, and I believe that it would include the GOOD e. coli as well, which is low in CFS'ers... On the other hand, OLE is good for killing bad bugs, and is also a great antiviral... Do you have any recommendations for using OLE?

Olive leaf extract (OLE) can be considered a plant antimicrobial with both antimicrobial and antioxidant activities (Lee and Lee, 2010). OLE also has health benefits such as increasing energy levels, lowering blood pressure, and supporting the cardiovascular and immune systems (Khayyal et al., 2002; Visioli and Galli, 2002; Covas, 2007; El and Karakaya, 2009). OLE has been shown to have antimicrobial activities against foodborne pathogens such as Staphylococcus aureus, E. coli, Salmonella spp., and L. monocytogenes (Techathuvanan et al., 2014).
thank you, I'll come back to this ( and others) writing of yours.
Much appreciated!
My feeling is that it is more important to kill the bad ones then protect the good ones. So I would not hesitate taking OLE -- I would make sure that I am not taking E.Coli probiotics (Mutaflor, Symbioflor-2) at the same time.

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