Example of doing an Analysis of a uBiome Report

Symptoms:
Extreme fatigue,brain fog,adrenal fatigue/low cortisol,high th2,constipation alternating to loose stools,bloating,depression,underweight. High levels of klebsiella pneumoniae found in stool test. All of the the typical CFS symptoms.

Standard Elements

• Firmicutes to Bacteroidetes: 0.2:1 (normal 2.1:1) thus a TEN FOLD shift.
  • Bacteroidetes 2.71x
  • Firmicutes: 0.22x (5 fold decrease)
  • Definitely check out this post
• Akkermansia 41% of reference:
  Lactobacillus 0x
• Bifidobacterium 0x
• Diversity: 2% (unusually low)

Overgrowths of Bacteria Genus
Bacteria
Ratio
Alistipes: 2.95 X
Bacteroides: 2.71 X
Parabacteroides: 2.52 X
Sutterella: 2.02 X
Barnesiella: 1.70 X
Reference Deep Dives

• Alistipes: https://cfsremission.com/2017/10/09/decreasing-alistipes-genus/
• Bacteroides: https://cfsremission.com/2017/10/20/decreasing-bacteroides-genus/
• Parabacteroides: https://cfsremission.com/2017/10/17/decreasing-parabacteroides-genus/
• Sutterella: https://cfsremission.com/2017/10/13/decreasing-sutterella-genus/
• Barnesiella: https://cfsremission.com/2017/10/15/decreasing-barnesiella-genus/

Rare Bacteria Genus
Nothing below 5%

Bottom Line
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.

Avoid

• Amoxicillin-Clavulanate antibiotics
• Aspirin (other NSAID’s are fine)
• Bacillus probiotics
• Bacillus subtilis
• Bifidobacterium Animalis subsp. Lactis BB-12
• BPA bottles
• Broad beans and lupin seeds
• Canole Oil
• Cranberry
• Fructo-oligosaccharides
• Gallic acid
• Glutten
• Gum arabic
• High meat diet
• Lactobacillus acidophilus La-5
• Lactobacillus Fermentum
• Lactobacillus paracasei
• Lactobacillus rhamnosus GG
• Lactobacillus plantarum
• L-citrulline
• Lingonberries
• Low fat diets
• Melatonin
• Oligofructose
• Pea Fibre
• Proton-pump inhibitors (PPI)
• Red wine, Grape Seed Extract
• Resistant starch (type IV)
• Resveratrol (Grapes, wine)
• Rhubarb
• Saccharin
• Stevia
• Tannic acid

Take

• Bacillus licheniformis
• Bacillus subtilis natto (or nattokinease supplements)
• Bifidobacterium Longum probiotics
• Bifidobacterum Bifidum
• Bifidobacterum Infantis
• Bifidobacterum Longum
• Bile supplements
• Capsaicin (chili peppers)
• Dairy Products
• Faecalibacterium prausnitzii
• Garlic
• High Fat diet
• Lactobacillus kefiri LKF01
• Metronidazole antibiotics
• Polymannuronic acid
• Sucralose (Splenda)
• Tannin and Gallate — green tea see this web page.
• Walnuts
• Whole-grain barley
• Xylitol
• β-Glucan

The Compounded Probiotic Dilemma!
The reader asked about taking Megaspore (which he just received). Checking my post for Bacillus probiotics that I know about, we find that it is the only one containing

• Bacillus licheniformis [TAKE]

But it also contain

• Bacillus subtilis [AVOID]

This leaves us with a dilemma which people will resolve different ways. Being aware of patients financials and that probiotic potency decreases over time, I would proceed for myself as follows:

• Use the Megaspore but do not reorder. Keep one week supply for a re-trial later.
• While not doing other changes, slowly ramp up and see if it has any impact

Once exhausted (except for the one week retrial amount) stay off it for at least 6 weeks and see if there are any changes from stopping it. Do a retrial of it for a week and see if the earlier changes repeat or not. Re-evaluate based on your actual experience.

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.