Another ubiome comparison with improvement except for FM

A reader wrote:

“As an engineer and accountant I have been so appreciative of the work you have done.  I found your site last June (2017) when looking for anything to help my daughter.  We did a UBiome in Oct and a second UBiome in March 2018… Today i finally  got back to see the changes you have made since the site was launched in January.  I am still working through interpreting the aggregated results. 

At this time I had one intriguing observation as it relates to my daughter’s results.  After 11 years she was finally been labeled as having fibromyalgia with 18 of 18 trigger points.  We had started doing some of your protocols in the fall and have gotten increasingly into the routine.  (It is hard for her to do it on her own …..)

Using the protocol many of her symptoms have improved, not tremendously, but improved. 

  • Migraines have gone from weekly to only one in the last 4 months,
  • light sensitivity has gone from not being able to comfortably go out during the day even with sunglasses to being able to be outside on the nice spring days. 
  • Anxiety much lessened.
  • Brain fog a little better.
  • Fatigue a little better.
  • Another symptom, which is observational, is that her lip and skin color is much improved.  It was not unusual for her to have while or blue lips most days.  Currently, she rarely has color that pale. I actually use that as my first assessment tool.  If she is looking a little grey or pale, I know she is having a poor day.

But, the one thing that has not improved are the FM symptoms of joint and muscle pain, still pretty severe.  Now the interesting observation, I just got done entering all of the 3/31/18 UBiome results.  And when I did the compare samples, the October test had a 0 for FM and the March test has a 1.  It just seems odd as her other symptoms (chronic fatigue, depression, digestive issues, etc) all had multiple hits.  

Just wanted to share with you as it was the first piece of information that appears to not match our situation.”

Standard Comparison

Overall, we have the significant improvement in the autoimmune profiles. The FM profile consists of only ONE item, so it is technically a 100% match! I just checked PubMed and there appears to be no further studies 😦 . We need to wait until someone does and publishes a study.

Measure   Oct, 2017     Mar, 2018  
* All Profiles 164 138
* All Profiles HIGH 61 31
* All Profiles LOW 103 107
* Metabolism Average 0.985922330097088 0.969174757281553
* Metabolism Std Dev 0.255159261658681 0.389777523954483
* Symptoms 4 0
ADHD 10 8
Allergies 6 6
Alzheimer’s disease 12 9
Autism 10 8
Autoimmune Disease 5 3
Brain Trauma 9 9
Chronic Fatigue Syndrome 12 11
Crohn’s Disease 7 8
Depression 12 10
Fibromyalgia 0 1
Gout 12 8
Hashimoto’s thyroiditis 3 3
High Blood Pressure 5 3
Histamine Issues 2 1
Histamine Issues From Ubiome 2 4
Inflammatory Bowel Disease 8 6
Irritable Bowel Syndrome 5 4
Metabolic Syndrome 4 3
Mood Disorders 7 4
Rheumatoid arthritis 11 9
Schizophrenia 0 0
Systemic Lupus Erythematosus 16 15
Type 2 Diabetes 6 4
Ulcerative colitis 0 1


The one FM taxonomy is low lactobacillus. Looking at the recommendations, the specific probiotics to try seem to be:

With CFS and FM — coagulation issues (past or present) is a factor. From my observation of myself, I believe microbiome plays a part — unfortunately, no studies could be found testing this hypothesis.

“Vasoconstriction occurs in the skin above tender points in FM patients, supporting the hypothesis that FM is related to local hypoxia in the skin above tender points.” [2000]

I said past or present, because the result of coagulation is typically fibrin deposit. It is likely that fibrinolytic may reduce or eliminate the pain points. Each of the items below work in slightly different ways.


a nattokinase/fibrinolytic enzyme and this enzyme may be considered as a new source for thrombolytic agents.” [2011]


The six lumbrokinase fractions (F1 to F6) with fibrinolytic activities were purified from ..“ [2004]


reports suggest it to possess anti-atherosclerotic effects also, due to its fibrinolytic and caseinolytic properties.” [2013]


studies demonstrate that bromelain exhibits various fibrinolytic, antiedematous, antithrombotic, and anti-inflammatory activities. “ [2012]


“Because clotting is an issue for my daughter.  The amount of bleeding she has after having blood taken for tests always surprises the techs as blood is streaming down her arm.”

For one of my own daughters, she was found to have  three inherited coagulation defects. One from me, and two from her mother. I would press for a full inherited coagulation panel for you daughter. There may be multiple factors at play:

  • Fibrin generation
  • Absence of bacteria processing or producing Vitamin K (thus the blood streaming)

According to Wikipedia, E.Coli produces Vitamin K2 (desired form). So mutaflor and/or Symbioflor-2 should be considered also for probiotics.

Other bacteria producing Vitamin K include:

  • Enterobacter agglomerans,
  • Serratia marcescens and
  • Enterococcus faecium. [2006]

Bottom Line

As always, consult with your knowledgeable medical professional.

” The one thing I like about your site is that it presents possibilities.  The big problem for me is that I am an engineer and we are trained to only change one variable at a time.  You have now presented me with a number of new things to try and it will take a while to work through them.  I will let you know if anything seems to be significant.”

As a mathematician and statistician, I am similarly trained. When I started doing big data and fuzzy logic professionally the discipline of one item at a time was no longer possible. The result is I give choices and a fuzzy-logic probability of each having the desired  effect.

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 medici


2nd comparison with worst Autoimmune profiles

This is a followup to the last post. If things do not go ‘as expected’, I want to know so I can try discovering the root issue. I will not filter to only good or ideal reports. This is a process of discovery for my readers and myself.  The following comments are from a reader:

“Hi Ken,

I’ve uploaded a couple of ubiome samples but I can’t seem to access the suggestions and comparisons for them. I’m particularly interested in the newer feature where you can see if your profiles fit certain autoimmune or diagnostic profiles.
Since I’m writing you, let me give you a quick update. After trying to incorporate the changes from the last post you did about my ubiome, what little improvements I was seeing from my protocol seemed to disappear and I continued to get worse. In the last two months I’ve gone back to your older protocol of rotating through probiotics and herbs and I’m back to where I was prior. I know you often preach that CFS is a constantly moving target, but I haven’t found any relief and actually got worse following the diet recommendations and specific supplements and probiotics suggested. 
I’m curious what feedback you’ve had, if any, of readers going into remission following the suggestions on the new website? I’m thinking about going back on antibiotics to get relief though they are tough of my system, causing herx, etc.”

Standard Analysis

Sample Id   Older    Newer
* All Profiles 124 162
* All Profiles HIGH 23 42
* All Profiles LOW 101 120
* Metabolism Average 1.02087378640777
* Metabolism Std Dev 0.217666351962583
* Symptoms 83 0
ADHD 7 11
Allergies 4 6
Alzheimer’s disease 9 8
Autism 8 11
Autoimmune Disease 4 5
Brain Trauma 6 7
Chronic Fatigue Syndrome 11 14
Crohn’s Disease 5 10
Depression 12 16
Fibromyalgia 1 1
Gout 4 8
Hashimoto’s thyroiditis 2 4
High Blood Pressure 3 4
Histamine Issues 1 2
Histamine Issues From Ubiome 4 5
Inflammatory Bowel Disease 4 7
Irritable Bowel Syndrome 6 4
Metabolic Syndrome 2 4
Mood Disorders 5 8
Rheumatoid arthritis 5 5
Schizophrenia 0 0
Systemic Lupus Erythematosus 15 15
Type 2 Diabetes 4 6
Ulcerative colitis 2 1

As with the last post, the profiles An interesting comparison between 2 ubiome for the same person the profiles went up. A quick note to the reader to see if we have the same situation got this response:

” Yes and No. When incorporating the specific changes I stopped rotating herbs and probiotics from your past general recommendations (Prescript Assist, Symbioflor, Olive Leaf, Neem, etc). I did stay on the basics (B vitamins, etc)

The ubiomes are about a year apart. I’m not surprised to see things going the wrong way. I’ve definitely been getting worse overall. So I guess it’s a good thing that your site and the results are reflecting that, at least in terms of your overall theory and the value of the website

So unlike the last reader who following my suggested practise:

  • Got a uBiome results
  • Looked at the suggestions and made a selection
  • Kept on them for 3 months
  • Redid the uBiome to find the next set of changes

This reader started with an out of date ubiome, The microbiome is constantly changing…

Bottom Line

There are words of caution from this post:

  • Make sure that your ubiome results are current.
  • Do not take the suggestions as a REPLACEMENT, they are a list of suggestions which:
    • Likely good to do most of the avoid
    • Likely good to do the easy/cheapest ones of the take

I ran two sets of recommendations thru — one focused only on high bacteria and one focused on low bacteria only. It is interesting to note that there is a lot of overlap between the two — despite having no bacteria in common with either group. This illustrate how bacteria tend to have a Ying-Yang aspect.

High Low
low drew1

This list of items is similar to the last post with a few minor changes.

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.

New recommendation options: For autoimmune bacteria only

From doing the reviews this weekend, I realized that adding a filter to ignore all taxonomy (bacteria types) that are not associated with any autoimmune condition may give a more effective and targeted set of recommendations.

This is at (if you are interested and have not done a ubiome and uploaded it, a sample login in on this page for you to use).

In short, if the taxonomy is not associated with a known autoimmune condition, we will ignore it (high or low).


Often they will be the same, but as we see below:

  • Coconut products disappeared
  • Bacillus probiotics appeared
  • Soy appeared
All Bacteria Taxonomy Autoimmune associated

bacteria taxonomy

off on

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.

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.


Adding Common Name to Drugs and anti-viral reflection

From medical literature I have added several hundred drugs and their likely impact on the microbiome. A common problem with CFS patients is that they are only aware of some trademark name and not the standard scientific name.

I have started (it’s a long process) adding the common or trademark names to various drugs — for example Antivirals:


Now becomes


This process will likely take a few weeks to complete.

Antivirals and CFS

I have posted about this in the past ,”Valganciclovir antiviral and CFS[2016]” and  “Valacyclovir, EBV and CFS [2016]”.

I decided to look at the microbiome shifts seen with the valacyclovir hydrochloride  antiviral,  And was quite surprise to see a high number of bacteria taxonomy are reduced — which may account for the success reported in the above post “All patients were treated subsequently with valacyclovir, with 93% having a positive response” [2014]. The other antiviral, Valcyte or Valganciclovir, is not in my sources.

So, the question must be asked — was it’s antiviral nature OR microbiome modification nature that causes the reported improvement?

Taxonomy Rank Effect
Bacteroidaceae family Decreases
Bifidobacteriaceae family Decreases
Clostridiaceae family Decreases
Coriobacteriaceae family Decreases
Desulfovibrionaceae family Decreases
Enterobacteriaceae family Decreases
Eubacteriaceae family Decreases
Fusobacteriaceae family Decreases
Lachnospiraceae family Decreases
Peptostreptococcaceae family Decreases
Porphyromonadaceae family Decreases
Prevotellaceae family Decreases
Ruminococcaceae family Decreases
Streptococcaceae family Decreases
Veillonellaceae family Decreases
Verrucomicrobiaceae family Decreases
Akkermansia genus Decreases
Bacteroides genus Decreases
Bifidobacterium genus Decreases
Bilophila genus Decreases
Blautia genus Decreases
Clostridium genus Decreases
Collinsella genus Decreases
Coprococcus genus Decreases
Dorea genus Decreases
Eggerthella genus Decreases
Escherichia genus Decreases
Eubacterium genus Decreases
Fusobacterium genus Decreases
Odoribacter genus Decreases
Parabacteroides genus Decreases
Peptoclostridium genus Decreases
Prevotella genus Decreases
Roseburia genus Decreases
Ruminococcus genus Decreases
Streptococcus genus Decreases
Veillonella genus Decreases
Akkermansia muciniphila species Decreases
Bacteroides caccae species Decreases
Bacteroides fragilis species Decreases
Bacteroides ovatus species Decreases
Bacteroides thetaiotaomicron species Decreases
Bacteroides uniformis species Decreases
Bacteroides vulgatus species Decreases
Bacteroides xylanisolvens species Decreases
Bifidobacterium adolescentis species Decreases
Bifidobacterium longum species Decreases
Bilophila wadsworthia species Decreases
Clostridium perfringens species Decreases
Collinsella aerofaciens species Decreases
Dorea formicigenerans species Decreases
Eggerthella lenta species Decreases
Escherichia coli species Decreases
Fusobacterium nucleatum species Decreases
Lactobacillus paracasei species Decreases
Odoribacter splanchnicus species Decreases
Parabacteroides distasonis species Decreases
Parabacteroides merdae species Decreases
Peptoclostridium difficile species Decreases
Roseburia hominis species Decreases
Roseburia intestinalis species Decreases
Streptococcus parasanguinis species Decreases
Streptococcus salivarius species Decreases
Veillonella parvula species Decreases
Lactobacillus casei group species_group Decreases

Contradicting Antibiotics and Prescription Impact on the Microbiome

I am just finishing a course of high dosage antibiotics for cellulitis that sent me to the hospital last week. With the website data, I realized that I do not need to do random things to recover from the antibiotics.

First, the antibiotic that I was using was a cephalosporin i antibiotics that antibiotics and many many antibiotics and prescription drugs are listed at

Clicking on it showed what changed:

cephalosporin i antibiotics

The following are impacted

Taxonomy Rank Effect Citations Links
Enterobacteriaceae family Increases Studies Also modified by
Pseudomonadaceae family Increases Studies Also modified by
Streptococcaceae family Increases Studies Also modified by
Citrobacter genus Increases Studies Also modified by
Kluyvera genus Increases Studies Also modified by
Pseudomonas genus Increases Studies Also modified by
Streptococcus genus Increases Studies Also modified by

I just added a link below the table:

Recommendations to contradict the shifts

When I click this, it takes me to the recommendations page.

Recommendations from cephalosporin i antibiotics Lab Results

Item    Action    Confidence value
bacillus probiotics Take 14.341
herb Take 8.041
gallic acid and tannins Take 3.507
fruit Take 3.396
antiseptics Take 2.911
triphala herb mixture Take 2.842
vitamin d cholecalciferol Take 2.773
lactobacillus casei probiotics Take 2.585
fungus Take 2.585
lactobacillus rhamnosus probiotics Take 2.585
low/no meat diet Take 2.495
neem herb Take 2.426
lactobacillus plantarum probiotics Take 2.426


Bottom Line

I have recommendations of what to take and to avoid that are specific to the antibiotic / prescription drug that I took! No random picking of stuff from the air.

In the near future, I will extend this to allow microbiome information from ubiome to be incorporated (i.e.  if you are low, and the prescription item increases it — then we attempt no correction).

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.



Brain Trauma’s Microbiome

On my commute today I had a conversation with an old colleague whose teenage daughter had a physical brain trauma(included cerebral ischemia) in January. As she described her symptoms, I recognized a lot of symptoms that are often seen with CFS. I also recall reading some articles about gut shifts seen with physical trauma.

Cognitive impairment is common with CFS and other autoimmune conditions.

Bottom Line

The number of bacteria taxonomy identified is lower than with other conditions but it is definitely work creating a profile on. An example with the demo ubiome result is shown below.


Analysis Web Site:

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.