An interesting comparison between 2 ubiome for the same person

A reader wrote:

“Hi Ken,

I just got back my second uBiome result. I took the first in December and it indicated very high bifidobacteria and bilophila with lactobacillus and many others being very low. I followed my recommendations religiously, having eaten almost nothing I haven’t prepared myself since getting my recommendations in January (mostly curries and vegetable dishes high in fat since fats were highly recommended, especially saturated).
In terms of fatigue, I began feeling better almost instantly since a lot of the foods I was eating were contributing to my overgrowths and I have seen slow but steady improvement on this front since. To put it in perspective, the fatigue was so bad in December I had fallen into deep depression and was feeling truly hopeless for the first time since becoming ill. I’m a long way from that place now (though far from being healthy) and am on the cusp of looking for writing work I can do from home. Thank you so much for this.
My new April uBiome shows that my adherence has paid off as I appear to have wiped out my overgrowths, or so a quick glance would suggest. My problem now, however, is that my recommendation list is empty for my newly uploaded results unless I switch to “some evidence” under “restrict to items with”. I was hoping you might have some broad suggestions in terms of where to go from here. In addition, I want to ask if you would dive into my changes. I’ve attached my .json files below. #### is the older one, from December 9th 2017 and ###### is the new one from April 10.
Thank you again for the work you’re doing on your site. I’d be grateful for any insight you can offer. “

Standard Analysis

At a high level, we see metabolism has moved closer to normal but concerning:

  • symptoms have increased
  • all profiles have increased

despite the subject report of improvement.  Symptom reporting tend to be unreliable because if a few symptoms dominate in severity, less symptoms may be reported When Symptoms are less severe, more may be noticed.

Concerning profiles, see below:

Sample Id   Dec 2017   April 2018
* All Profiles 117 151
* Metabolism Average 0.96 0.98
* Metabolism Std Dev 0.20 0.21
* Symptoms 34 87
ADHD 10 5
Allergies 6 6
Alzheimer’s disease 5 9
Autism 6 10
Autoimmune Disease 3 4
Brain Trauma 6 9
Chronic Fatigue Syndrome 9 15
Crohn’s Disease 4 8
Depression 7 10
Fibromyalgia 1 1
Gout 4 8
Hashimoto’s thyroiditis 3 5
High Blood Pressure 3 3
Histamine Issues 2 2
Histamine Issues From Ubiome 5 5
Inflammatory Bowel Disease 4 5
Irritable Bowel Syndrome 4 5
Metabolic Syndrome 3 3
Mood Disorders 3 6
Rheumatoid arthritis 10 8
Schizophrenia 0 0
Systemic Lupus Erythematosus 14 15
Type 2 Diabetes 4 6
Ulcerative colitis 1 3

The only symptom that showed significant improvement was ADHD, a proxy for the ability to focus (which agrees with feeling good enough cognitively to seek writing work).

A followup email potentially explained what is happening.

“I stopped taking almost anything that wasn’t on my take list, especially vitamin d because I remember seeing it promoted bifidobacteria. I took melatonin and valerian throughout purely to help me sleep, a lot of monolaurin as it was a recommendation and for possible antiviral benefits, and curcumin (if I stop taking it I get really bad lower back pain). I took Lactobacillus gasseri for two weeks (made me feel great while taking it) and symbioflor 2 for 1 week which also made me feel better but less so.

I started taking niacin after the latest ubiome and it stopped my diarrhea for about 2 weeks, which has never happened before, and came with severe flushing.
When I took my December ubiome I was at a full 10, definitely worst cfs I’ve had. In April I was more like a 5 (and probably around 3 when I took the l gasseri in March.)”
This is the second uBiome comparison that I have seen worst profiles (I will be posting the other one shortly). BOTH had the same issue — stop taking everything on the general support list and keep only to the take/avoid list.
At the bottom of the recommendations/ suggestions, I stated:
Clearly I need to SHOUT THIS OUT — especially for the brain-fogged and distracted CFS reader.

Going forward Recommendations

#1 Get back on core set of recommendations for CFS/FM/IBS — click here to review

#2 For dealing with HIGH counts — there was nothing on the default recommendations. When I changed to LOW counts,  a lot of things appeared.  (Remember — the original recommendations ONLY dealt with High counts, the site has evolved from there).



REMINDER: the numbers are NOT the degree of effectiveness, they are the confidence that this would change bacteria based on the number of studies reporting it.  Olive Oil may be 100x better than inulin — but inulin has 4 times the number of studies!!! In general, relative effectiveness is not available in studies. Studies are usually, “Olive oil decreases…..”

As a result of this, I modified my profile summary page to report high and low separately, as shown below:


Clearly, most of the change was due to more bacteria dropping below normal, almost a 35% increase in low counts.

Hand Curated List

I am trying not to do this (time consuming and only benefits one person), but in this case it may be of general benefit.  The settings I used was LOW COUNTS, not aggregated, some evidence; then it’s common sense or remember this or that odd fact from reading.

  • Given some extract (often sold as a supplement) and the real whole food that contains it, I always favor the real whole food!


  • Apples — especially Pink Lady
  • Pomegranate
  • Blueberries
  • Black raspberry
  • Jerusalem artichokes / Inulin
  • Sea Weed — snacks or supplement
  • Walnuts
  • choline supplements
  • fish oil
  • barley and oats porridge for breakfast
  • Probiotics:
    • bacillus coagulans
    • clostridium butyricum miyairi probiotics
    • General Biotics’ Equilibrium
    • lactobacillus acidophilus
    • lactobacillus reuteri
    • Prescript Assist
    • saccharomyces cerevisiae


  • No Vitamin D (which is usually part of the standard recommendation 😦 )
  • Neem
  • Rosemary
  • Thyme
  • Triphala
  • L-Taurine supplements
  • Stevia, sulfites
  • Monolaurin
  • Probiotics:
    • bifidobacterium longum bb536
    • lactobacillus rhamnosus
 Remember — you should NOT view this as a “You must do everything on this list”, these are suggestions of modification you should do (keeping the core supplements unless there are explicitly excluded — like Vitamin D).
I have explicitly added the two soil based organism (which were not on the list) — Prescript Assist and Equilibrium. We are dealing with low counts across the autoimmune  board, and this ‘feels’ like a good way to address it.

Bottom Line

The earlier recommendation targeted at high counts only, appear to have worked based on two pieces of evidence:

  • Subjective report from reader (Improving from a 10 down to a 5 for severity)
  • No recommendations for high counts!

We are now moving over to repopulating the low counts. Once that is done, we may find that another adjustment is needed. It is not a one-step linear path to rebalance the microbiome.

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