Seeking Medical Professions willing to help with Microbiome results

In the past I have always kept myself under medical supervision. I have both a naturopath and a nurse practitioner. Both have prescribing authority in my jurisdiction — so if I can make a case for antibiotics, I can get them from at least one of them (I have not needed that for a few years).

The process is pretty simple with both of them:

  • Show them the science, that is:
    • Ubiome Results
    • PubMed articles if needed
  • Show them my action plan (I do NOT ask them to produce plan usually, and when there was a Lyme diagnosis for me, we negotiated which antibiotics).
  • Ask them to review the plan. In some cases, they want to run tests. Two examples:
    • 15,000 IU/day of Vitamin D — they wanted to make sure that I did not go out-of-bounds on the high level. 15,000 IU/day with malabsorption frequently results in modest raising of levels.
    • 2 gms of flushing niacin/day – they wanted to check liver function. (Pub Med)

For me, the key thing is to find professionals that accept that they do not know everything, do not have an ego problem and willing for patients to self-treat based on actual medical literature (as opposed to random information acquired from some user group), but under supervision to keep them out of trouble!

I have had medical professionals contact me for insights and to understand what I am trying to do with my site. I am very willing to spend time with professionals in this area to further their education.

Bottom Line

Over the last week, I have gotten two asks for who to contact about microbiome results. Many of my readers are ‘bio-hackers’ and are often self-guided (for better or worst).

If you are a medical professional willing to do telephone or email consultation with patients using their microbiome results — please drop me an email, or add a comment below.

I cannot guarantee the quality of these people — but medical professionals willing to try this area are very few.

InflamaZyme – review

A reader asked:
“Do know anything about the vitamin InflamaZyme by Biogeneis , my doctor told me to take it for thick blood, I have high fibrinogen. Thank you so much.”

90 capsules is 30 days. Serving is 30 capsules .
Amazon: $52 or $2/day

Requestor Beware

  • If you are trying to sell a product, I am likely the last person you want to be reviewing — I will try to find cheaper equivalents as well as challenge implications not backed up by science.


In the ingredient list are many of the known anticoagulant ones.

  • Pancreatin 4X Amylase (100,000 USP units/g), Lipase (8,000 USP units/g), Protease (100,000 USP units/g) 400 mg
  • Acid Protease (1,000 SAP/g) 300 mg
  • Bromelain (2,400 GDU/g) 250 mg
  • Bacterial Protease (100,000 PC/g) 240 mg
  • Papain (2,000,000 FCC PU/g) 120 mg
  • Superoxide Dismutase (SOD) (8,000 MFU/g) 100 mg
  • Cellulase (1,000 FCC CU/g) 100 mg
  • Nattokinase (20,000 FU/g) (soy) 50 mg
  • Trypsin (75,000 USP units/g) 40 mg
  • Chymotrypsin (25,000 USP units/g) 20 mg
  • Serrapeptase (2,000,000 SPU/g) 2 mg

My initial concern is that this may be the equivalent of a multivitamin formulation — that is maintenance dosages for healthy people but insufficient to be therapeutic for people with conditions. A few spot checks:

A few spotchecks

  • Bromelain: (2,400 GDU/g @ 250 mg –> 600 GDU, or 40% of single capsule [$0.09/day for same dosage via Amazon]
  • Nattokinease: (20,000 FU/g @ 50 mg –> 1000 FU, 50% of a single capsule [$0.05/day for same dosage via Amazon]
  • Serrapeptase (2,000,000 SPU/g @ 2 mg (2/1000 g) –> 4000 SPU. We see 10 times as much in individual capsules. [$0.11/day for same dosage via Amazon]
  • Pancreatin 4X Amylase: [Same dosage: $0.33/day]

I can go on, but the expected cost per day buying individually will likely be a bit over $1/day. They are selling at $2/day – so now the question becomes, is $1.0/day worth just taking 3 capsules from one bottle versus capsules from a dozen bottles.

The flip side is — do you know the precise nature of your coagulation and thus only need certain ones? Are those in this mixture? For example there is no Lumbrokinease (About $0.50/day) or Piracetam — items that I tend to use for my own coagulation issues.

Bottom Line

It’s a reasonable mixture if you have possible coagulation issues and do not know the specific nature of those issues.

In this case the reader states “high fibrinogen” which makes it easy to evaluate each of the ingredients by searching on PubMed. Some examples:

  • Pancreatin – nothing.
  • Bromelain – “unexpectedly Bromelain showed dual action on blood coagulation: at low concentration showed procoagulant effect and at high concentration anticoagulant effect.” [2016] – risk
  • Papain – nothing
  • Superoxide Dismutase ” show a complex covariation with many of the conventional cardiovascular risk factors.” [1997]
  • Cellulase – nothing
  • Nattokinase – valid for this.
  • Serrapeptase – nothing
  • Chymotrypsin – valid for this

My own take is simple: do the research, find the best ones and use them — change the MD to produce studies or evidence for their ‘cookbook guidance’ – often their cookbooks are out of date.

uBiome progression in ME Flare

This is a follow up to my earlier post: Sudden Onset ME Flare – uBiome One Week Later The purpose of this series is to gain insight on what happens during the early stages of Myalgic encephalomyelitis/chronic fatigue syndrome . A ME diagnosis takes at least 6 months after onset to get usually. In my case, I have been down the full route and I know the early symptoms (which allows rapid intervention).

Ubiome Results

Reports Showing Changes.

There was some improvement over the two weeks, but the lost of microbiome function continued in other areas. This is not unexpected because the microbiome state is a cascade of microbiome changes that takes time to resolve (a Markovian chain to any geeks reading this).

Good News 🙂

Serotonin produces have made a major improvement and GABA is starting to improve.

Bad News 😦

A delayed major collapse
Alcohol consuming bacteria – Interesting disappearance
Akkermansia continued its collapse
Decreased (more tolerant) – likely because of higher yogurt consumption.
This is likely good news…..

Reports with no change

Production of Vitamin K and Vitamin B9 — still at Zero: Supplement time!

Yogurt has no effect

Despite a liter of yogurt each day — no effect

Microbiome Prescription Site

Over on this site, our news is different from ubiome.

Bacteria Pattern matching conditions

The number of high bacteria associated with known conditions dropped back to almost my prior levels from a year ago. The number of low bacteria associated dropped significantly.

The associated conditions with the most significant drops are shown below:

End Products

In terms of End Products, a number of significant shifts (remember this is an experimental report)

  • INCREASE in:
    • 5-hydroxytryptamine (Serotonin)
      Bacteriocins (natural antibiotics)
      Biogenic amines
      Cobalamin (Vitamin B12)
    • Endocannabinoids
      Lactic acid
  • DROP in:
    • 3,4-Dihydroxyphenylacetic acid
    • Bicarbonate (to zero)
    • Methane

Bacteria Shifts

Remember that there are no ‘norm’, I have the left 2 columns from being in a full (symptomless) remission and the right 2 are from this flare.

The main class of concern is Fibrobacteria, a minor concern for Deltaproteobacteria
For what changes this, click here

At the Genus level,

  • low Staphylococcus is a concern (0,0 -> -98%, -98%)
  • low Anaerococcus also (0,0, -> -45%, – 65%)

Bottom Line

I will be doing another uBiome next week. Overall, I am positive.

  • I am up to 2 – 3 hrs/sessions with a break between for work (i.e. 75% time), using vacation time to keep me at full pay check.
    • Compare to my usual work day (3 hr of commute + 8hrs, I am at 55% of normal)
    • I have tried pressing to a 4 hr session once or twice a week, I can really feel it the next day — so 3 hr work-sessions is my safe zone.
  • Once a week, I do an ‘outing probe’ – that is drive or driven for a hour, then meet with friends for a few hours then head home.
    • Still have ‘day after payback’:
      • often with depression,
      • impaired cognitive function for the following day — which clears by the second day.
      • sleep pattern disturbances
    • This probe helps me keep real with the actual state of recovery (i.e. work from home is fine, a commute to work would worsen the situation).

Two Approaches to suggestions

The normal approach is to upload the ubiome.json to the analysis site and see the suggestions. After doing the above analysis, I can get suggestions based solely on the areas of my concern:

  • low Staphylococcus
  • low Anaerococcus
  • low Fibrobacter

by going to the All Bacteria [Genus] Reported page and just entering those 3. This approach excludes the shifts from population norms, which may be natural shifts (due to DNA) for me. For example, Fibrobacter only occurs in 30% of people — but it was there always prior to this flare — so it’s loss is likely significant .The results are shown below — and very interesting

Looking at probiotics only:

Using the full set of bacteria:

Mixture of Probiotics Ratio

A reader wrote with an interesting question:

I want to create 2 probiotic formulas for myself but need help in determining approximate percentages of each of these strains.
% of: B-Bifidum, B-Breve, L-Salivarious etc

The question is how to answer this!

Ways of Determining Ratios

Looking at this question, I see several logical roots:

  • A proprietary blend (keep secret on the ratio – more below)
  • The percentage seen in appropriate human samples (usually healthy controls)
  • Result of experiments with different ratios and picking the ratio with the best results.

I will deal with the first and last approach first, and then go on to the middle one.

A proprietary blend

Unfortunately, there are no published studies in this area – proprietary means not public. Existing formulation on the market appear to be based on proprietary processes. In better cases it is likely to get past a min level (i.e. reported in some study) for each individual probiotic and then ‘pad’ with the cheaper ones until they hit a BCFU that was determined by marketing studies. In the worst case, it is determined by a marketing study of competitors.

Base on Human Studies with different mixtures

I have never seen such a study done. I recall a very few where there are three groups: {Control, Mixture of A and B, just A}. This does not answer the percentage question at all.

This is further complicated because of some studies reporting no results for a probiotic and another study reporting positive results. Doing a proper valid study is both very time consuming and very expensive.

Based on observed ratios in Human Samples

This is the simplest to do. It has two challenges:

  • Defining the target population
  • Insuring that the testing (usually 16S) methodology measures all of the candidate strains.

I do have a contributed set of human samples and let us see what the results are assuming this is the target population.

Proposed Bifidobacterium Ratios

The numbers below are the result of a little data manipulation (any one proficient in R can repro these numbers

Looking at the common species likely to be available for probiotics

Proposed Lactobacillus Ratios

The numbers produced are very interesting – Lactobacillus acidophilus is far very down the list!

Looking at the common strains, we see a very interesting set of ratios:

Some 114 taxonomy units of Lactobacillus are currently in the sample

Bottom Line

Well, I did create one possible answer to the question that the user asked. A firm like Thryve or Ubiome can likely produce more definitive data. If either firm care to share their numbers with me — I would be glad to share they results here.

Firms like CustomProbiotics or Seed may wish to produce mixtures matching the above ratios (or obtained in the same way elsewhere). Lactobacillus and Bifidobacterium appear to be close to a 1:1 ratio.

What I found especially interesting is that there appear to be some species that IMHO should be more available as probiotics — but are not. Especially the following:

Dry Eye Disease/Syndrome

A reader asked me review the treatment options and risk. DED is often associated with Sjogren’s syndrome which is frequent with
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)  [1999]

  • “Asian ethnicity is a mostly consistent dry eye disease (DED) risk factor.” [2019
  • The prevalence of DED is high, with global estimates ranging from 5 to 50% of the adult population [4], and the economic burden from the disease is expected to riseas populations age [5]. 

Sjogren’s syndrome has distinctive microbiome shifts [2019] [2018] [2017]. A 2018 study on mice found that DED reversed with a fecal transplant.

The administration of probiotics strains was effective in reducing DES. In light of these results, we have identified our probiotic (Saccharomyces boulardii MUCL 53837 and Enterococcus faecium LMG S-28935) activity integration with the action of tear substitutes, along with standardization of clinical parameters of the tear film and microbiological activity in restoring of the microbiota ocular surface subject with DES.

Aging Eye Microbiota in Dry Eye Syndrome in Patients Treated with Enterococcus faecium and Saccharomyces boulardii. [2017]

 a combined dietary supplement containing fish oil, lactoferrin, zinc, vitamin C, lutein, vitamin E, γ-aminobutanoic acid, and Enterococcus faecium WB2000 on dry eye. .. Supplementation improved objective and subjective dry eye symptoms.

Dietary Supplementation with a Combination of Lactoferrin, Fish Oil, and Enterococcus faecium WB2000 for Treating Dry Eye: A Rat Model and Human Clinical Study. [2016]
  • “A moderate daily dose of both forms of long-chain ω-3 EFAs, for 3 months, resulted in reduced tear osmolarity and increased tear stability in people with DED.” [2017]  [2017] [2015]

Prescription Interventions

“Twenty-six unique trials investigating 13 ophthalmic drugs were identified, including trials of the approved drugs cyclosporine A, cyclosporine A cationic emulsion, diquafosol, rebamipide and lifitegrast. ….
 Publications on lifitegrast reported statistical superiority in a symptom or sign endpoint versus the control group in a large (N > 200), multicenter trial, with results repeated in trials of similar design.  ” [2019 – long full text article]

  • Xiidra (lifitegrast ophthalmic solution) 5% is a lymphocyte function-associated antigen-1 (LFA-1) antagonist indicated for the treatment of the signs and symptoms of dry eye disease (DED).
    • “The most common adverse reactions reported in 5-25 % of patients were instillation site irritation, dysgeusia and reduced visual acuity.” [FDA]
    • “In vitro studies demonstrated that lifitegrast may inhibit T-cell adhesion to ICAM-1 in a human T-cell line and may inhibit secretion of inflammatory cytokines in human peripheral blood mononuclear cells. The exact mechanism of action of lifitegrast in dry eye disease is not known. ” 
    • “Self-reported adverse reactions were noted in 31.4% of patients.” [2019

Bottom Line

My preference is usually non-prescription approaches — especially an avoidance of new drugs where long term consequences are still to be determined. Xiidra was approved in 2016, so it is just 3 years on the market. Some of the reaction listed on suggests that people with histamine or mast cells issues may have issues.

Enterococcus faecium probiotics and omega-3/fish oil combination appears to be demonstrated to help. I know of two (only) Enterococcus faecium probiotics:

  • Symbioflor-1 (Available from the German Apotheke in the US)
  • Bioflorin ( Enterococcus faecium SF68 or E. faecium NCIMB 1041 or Streptococcus faecium SF68)

We also have

New Biofermin S Granule Powder 45g Lactic Acid Bacteria Japan TAISHO

There were no probiotic studies for Sjogren’s syndrome that I could locate. There was some work to engineer a probiotic (A Novel Probiotic for the Treatment of Sjogren’s Syndrome).

High Mercury (and Uranium!) spells Selenium Deficiency

A good friend for almost two decades also writes a blog Cort Johnson (HealthRising) and is attending the National Institute of Health ME/CFS conference and giving regular reports on his notes (the above link goes to one of them). Several of them caught my eye — today, I will look at the report of high uranium levels being detected in ME/CFS patients.

Early hair analysis results highlight increased mercury and uranium (!) levels associated with decreased selenium levels. The sample size is small, however….
Then came a preliminary but really weird finding – elevated levels of mercury (not so weird) and high levels of uranium (really weird) associated with low selenium levels in the hair analyses of a significant subset of patients. Both the mercury and uranium issues derive from low selenium levels. Selenium, interestingly, also plays a role in the conversion of T4 to T3 in the thyroid. (Chris Kressler recommends getting your selenium levels tested and, in general, using
 dietary methods (not selenium supplementation) to safely 
increase selenium levels in hypothyroidism.)

The NIH ME/CFS Conference II: Lipkin’s Possibilities, Prusty’s Big Idea, Oh’s Search and Ron Davis on ALWAYS Moving Forward, Apr 15, 2019

I have selenium as one of my core recommendations – which the above reinforces. The reasons that I cite on earlier posts (see prior link for more studies)

  • 78% of IBS patients examined showed selenium insufficiency [2007],
  • Low selenium is associated with hypothyroidism [2015]
  • FM has lower selenium levels [1998]
  • Selenium supplement improved the condition of CFS rats [2018]

Uranium and mercury is frequently found in trace amount in drinking water [2018], as well as in human placenta [2016] and US children [2010]. It appears, for reasons not currently understood, that the body retains more of those two minerals when it is short of selenium. (“Significant pairwise correlations were observed for a number of metals.” [2010]) Some additional interesting studies:

Bottom Line

Preferred sources are from food (a list here) but not that malabsorption does occur with gastrointestinal condition (i.e. microbiome dysfunction).

Selenium Toxicity does occur with supplements — so the safest course is to get measured and under medical supervision for supplementation.

The source of the outbreak was identified as a liquid dietary supplement that contained 200 times the labeled concentration of selenium. Of 201 cases identified in 10 states, 1 person was hospitalized. The median estimated dose of selenium consumed was 41 749 μg/d (recommended dietary allowance is 55 μg/d). Frequently reported symptoms included diarrhea (78%), fatigue (75%), hair loss (72%), joint pain (70%), nail discoloration or brittleness (61%), and nausea (58%). Symptoms persisting 90 days or longer included fingernail discoloration and loss (52%), fatigue (35%), and hair loss (29%). The mean initial serum selenium concentration of 8 patients was 751 μg/L (reference range, ≤125 μg/L). The mean initial urine selenium concentration of 7 patients was 166 μg/24 h (reference range, ≤55 μg/24 h).

Acute Selenium Toxicity Associated With a Dietary Supplement 2010

Cardiac Disease and the Microbiome

A reader who has several family members with conditions that have microbiome shifts associated asked about cardiac disease, which is frequent in one side of the family.

Below is what I could find. This is a new area of research that I expect to explode in the next few years.

” Dysbiosis of the intestinal flora has been associated with insulin resistance, diabetes mellitus and cardiovascular diseases, such as atherosclerosis and heart failure. ” [2019]

” In the recent years, both human and animal experiments have revealed that alterations in the composition and function of intestinal flora, recognized as gut microflora dysbiosis, can accelerate the progression of cardiovascular diseases. “[2019]

The gut microbiomes of VC and CAD patients were significantly different in terms of beta-diversity. Bacteria from Veillonella dispar, Bacteroides plebeius and Fusobacterium were enriched in the VC group, while members of Collinsella aerofaciens, Megamonas, Enterococcus, Megasphaera, Dorea and Blautia were decreased. According to the association with dyslipidemia, seven operational taxonomic units (OTUs), including Parabacteroides distasonis, Megamonas, Fusobacterium, Bacteroides sp., Bacteroides plebeius, Lactobacillus and Prevotella copri, were regarded as potential pathogens for CVDs. Additionally, Prevotella copri might be a keystone of CVDs, especially in VC patients, while Collinsella aerofaciens is a possible keystone of CAD, based on the multi-correlations of these bacteria with other OTUs in microbial communities.

The intestinal microbiota associated with cardiac valve calcification differs from that of coronary artery disease[2018].

Bottom Line

You will note that almost all of the studies cited above were done this year and last year. This is an area that is actively being researched because the evidence indicate strongly that there is a relationship.

Endocrine organs of cardiovascular diseases: Gut microbiota [2019]

Because cardiac disease has many divisions and the amount published on each is sparse, I will not include this on my analysis site yet.