From new scientist today

This describes how ubiome and other gut bacteria work… And more important, what they totally miss.

To identify microbial species, researchers usually look for a particular gene that acts as a genetic barcode for bacteria and archaea. Different species have subtly different DNA sequences in this gene, so reading the sequence can tell you what microbes are present in a sample.

Moissl-Eichinger and her colleagues have shown that the standard sequencing method often detects no archaeal species, or just one, in samples taken from people’s bodies. But when her team used a version of the sequencing method optimised to detect archaea in the same samples, it revealed that there were in fact dozens of these species present.

Each part of the body seems to be home to characteristic species of archaea, as with bacteria.

What’s more, in the nose and appendix, individual archaea cells outnumbered those of bacteria. “We did not expect that,” says Moissl-Eichinger. Because we have only just discovered them, we don’t know what most of the archaea in our bodies do.”

From A huge number of mystery microbes are living on your skin

Hay fever and thick blood — the connection

A reader wrote about this year being very bad for allergies/hay fever for her. DAO, REAL sudafed, etc only made a small dent in it. She tried niacin (the flushing type) and fibrinolytics (bromelain, serrapetase, lumbrokinease, nattokinease) which made a much bigger improvement …. what gives?

For back references:

Allergy and Coagulation

Different Allergy Mechanisms

  • “The immune-mediated adverse reaction to food is defined as food allergy (FA) which is roughly divided into IgE mediated or non-IgE mediated FA (NFA)… there is far less of an understanding of NFA than IgE-mediated FA and its clinical relevance is likely under-estimated in most cases…The lack of easily accessible diagnostic measures also contributes to the problem.  ” [2008]
    • This also applies to Hay Fever and other allergies
  • “Although pathogenesis of NFA is still not well understood, recent studies indicate widely variable clinical manifestations of NFA…This review discusses recent progress in our understanding of the regulatory mechanisms of gut immune homeostasis and recently revealed widely variable clinical presentations of NFA with respect to it pathogenesis.” [2012]
  • Inhibition of IgE- and non-IgE-mediated histamine release from human basophil leukocytes in vitro by a histamine H1-antagonist, desethoxycarbonyl-loratadine. 1994
  • “Nonallergic rhinitis represents a non-IgE-mediated group of disorders that share the symptoms of nasal congestion, rhinorrhea, sneezing, and/or postnasal discharge but not pruritus that characterizes allergic rhinitis…. skin testing for aeroallergens is negative.” [2012]

Of special interest (especially for MCS folks)
“The classic symptoms of idiopathic nonallergic rhinitis are nasal congestion, postnasal drip, and sneezing triggered by irritant odors, perfumes, wine, and weather changes.” [2012]

“: Idiopathic nonallergic rhinitis (iNAR) has been difficult to define because of the long differential diagnosis of rhinopathy in the absence of allergic rhinitis. iNAR has traditionally been a diagnosis of exclusion with no clear unifying pathophysiology. Increased sensitivity to triggers such has climate changes, cold air, tobacco smoke, strong odors, and perfumes have been thought to be characteristic, but recent studies do not support this hypersensitivity hypothesis. New investigations of the local nasal environment and systemic “functional” syndromes have offered new insights into this condition. iNAR may be a heterogenous disorder that includes (1) anatomic abnormalities requiring nasal endoscopy for diagnosis, (2) incipient, local atopy (entopy), (3) dysfunction of nociceptive nerve sensor and ion channel proteins, and (4) autonomic dysfunction as found in chronic fatigue syndrome and other functional disorders.” [2009]

Bottom Line

If you are having bad hay fever and the “standard popular knowledge” is not doing it for you, you may wish to discuss coagulation as being part of it with your medical professional.



DNA and Microbiome interplay….

A reader forwarded their report from NutraHacker ( They offer free reports and more advanced paid reports.  Their reports also contain Encourage and Avoid items.

What is interesting is when you combine recommendations from with their recommendations. In some cases they corresponds and in other cases disagree. DNA says one thing, existing microbiome says another thing.

Simple Example for Vitamin E


So this person with AG should NOT be supplementing with Vitamin E because it will increase inflammation. What about the case of a high Vitamin E take by diet?

Looking at a list of foods that are HIGH in vitamin E, we see:

  • Almonds
  • Hazelnuts
  • Sunflower Seeds
  • Avocado
  • Mango
  • Abalone
  • Salmon
  • Wheat Germ Oil

Looking at this person’s suggestions from the Microbiome, we see Almonds listed.


This suggests that almonds should be excluded (mainly because there are lots of other suggestions) because of DNA and not microbiome.

Bottom Line

DNA and microbiome interacts.





Looking at Urine Element Profiles

A reader forwarded their Comprehensive Urine Element Profile from Genova Diagnostics. with some questions. This is an area that I did not expect to find much or anything.

The reports had high:

  • Antimony
  • Copper
  • Lead
  • Thalium
  • Zinc

A 2008 study was interesting and may be related. Humans were given bismuth supplements and the results were:

“The upshift of the bismuth content also led to an increase of derivatives of other elements (such as arsenic, antimony, and lead in human feces or tellurium and lead in the murine large intestine). “

Bismuth or it’s salts are in a fair number of supplements, for example:

WebMD states:
“People take bismuth salts by mouth for inflammation of the lining of the colon(colitis), constipationdiarrheaindigestionHelicobacter pylori (H. pylori) infection, odor caused by an opening in the belly wall during surgery (ileostomy odor), stomach problems caused by nonsteroidal anti-inflammatory (NSAID) drugs, stomach ulcers, stomach flu, and preventing traveler’s diarrhea.”

Additionally, “Many epidemiological studies have shown an association between Parkinson’s disease  and exposure to metals such as mercury, lead, manganese, copper, iron, aluminum, bismuth, thallium, and zinc. ” [2018] We know that Parkinson’s has a distinctive microbiome shift too.

High Copper (Cu) Possible Consequences

“high-copper diets led to liver injury in high-fructose-fed rats, and this was associated with gut barrier dysfunction, as shown by the markedly decreased tight junction proteins and increased gut permeability. … [2018]

High Lead(Pb) Possible Consequences

” For the gut microbiota, at the phylum level, the relative abundance of Firmicutes and Bacteroidetes changed obviously in the feces and the cecal contents of mice exposed to 0.1mg/L Pb for 15weeks” [2018]


High Zinc (Zn) Possible Consequences

“dietary Nano-ZnO increased the bacterial richness and diversity in ileum, while decreased both of them in cecum and colon. Specifically, the relative abundances of Streptococcus in ileum, Lactobacillus in colon were increased, while the relative abundances of Lactobacillus in ileum, Oscillospira and Prevotella in colon were decreased (P < 0.05). I” [2017]

Bottom Line

We have some interesting questions to ask:

  • Was this person recently consuming any supplements containing bismuth?
    • There was no detectable bismuth in the results
    • If so, some of the test results could be due to that
  • Did the person take EDTA or other biofilm breakers — or fibrinolytics recently?
    • These could release the above into the blood system, resulting in higher urine levels
  • We know almost nothing about which bacteria uptake these mineral
  • We see that some of these elements are known to influence the microbiome.

In short, no answers and many questions. What we did find is that bismuth compounds are likely significant microbiome modifiers — in some case this may be by an indirect route (i.e. increasing lead and arsenic)

“At the end of bismuth therapy, the relative abundances of Bacteroidetes and Actinobacteria decreased to 0.5% (P < .001) and 1.3% (P = .038), respectively. Additionally, the relative abundance of Verrucomicrobia also decreased from 3.2% to 1.11E-3% (P = .034). In contrast, the relative abundances of Proteobacteria and Cyanobacteria increased (P < .001 and P = .003, respectively). ” [2018]

“we report that the production of methylated bismuth species by the methanoarchaeum Methanobrevibacter smithii, a common member of the human intestine, impairs the growth of members of the beneficial intestinal microbiota at low concentrations. The bacterium Bacteroides thetaiotaomicron, which is of great importance for the welfare of the host due to its versatile digestive abilities and its protective function for the intestine, is highly sensitive against methylated, but not against inorganic, bismuth species. The level of methylated bismuthspecies produced by the methanoarchaeum M. smithii in a coculture experiment causes a reduction of the maximum cell density of B. thetaiotaomicron. ” [2011]




A reader’s experience

Hi Ken
Just wanted to update you on the excellent results I am having using you site. My main condition was microcolitis, and I had just a little help with prescription drugs from gastroenterologist, with unpleasant side effects.

Based on the suggestions from your site, started using b longum and b plantarum from custom probitocs, and acidophilus from Solgar, and my symptoms were resolved within a week.

I’m still amazed by this, after almost two years of great discomfort.

It’s been two months now, and I am still symptom free. Again, thank you, so grateful for the work you do!

One question, for the avoid items, they are listed from low to high values, so if
clostridium butyricum is  avoid -1.127
vsl #3 probiotic           is  avoid -4.442
it would be more important to avoid the vsl #3 correct?”

Thank you for sharing.

On the analysis site  the numbers in the confidence column reflect the number of studies reporting the change. It is the confidence of the recommendation.  Some items have positive effects reported in some studies and negative in others. The cause may be because one study looked at the impact with people with disease X and the other with people with disease Y.

As always — these are suggestions based on pubmed studies and are strictly theoretical. These have not been validated in any clinical trial. There is no need to do all of the suggestions, it is more a “Guide book”. If you buy a guide book on London, you do not visit every place listed;  you visit the places that interest you, at a reasonable cost, in the time you have.

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.

Emotional Lability

A friend in dealing with a difficult person noticed a change of some microbiome associated symptoms (6-10 bowel movements a day, increased night sweats). He asked me about his dramatic increase of emotional lability he has seen recently. SPECT scan studies indicate that CFS includes acquired brain injury. From Australia Health department – a good PDF on it is here and some quotes:

“Emotional lability refers to rapid, often exaggerated changes in mood, where strong emotions or feelings (uncontrollable laughing or crying, or heightened irritability or temper) occur. These very strong emotions are sometimes expressed in a way that is greater than the person’s emotions. “

“Emotional lability occurs because of damage to parts of the brain that control:

  •  Awareness of emotions (ours and others)  Ability to control how emotions are expressed – so ability to inhibit or stop emotions coming out
  • Stronger emotional responses”

The medical term is Pseudobulbar affect since the term emotional lability has been used in multiple ways. “It is hypothesized that these primary neurologic injuries and diseases affect chemical signaling in the brain, which in turn disrupts the neurologic pathways that control emotional expression.[21][22][23]

A change of microbiome will impact chemical signaling.

Microbiome Connections?

It has been demonstrated in the literature that microbiome shifts are associated with many neurological conditions — so can we find any literature dealing with emotional lability. A PubMed search suggested the following studies:

This area appears to be understudied – but we do see a frequent reference to streptococcal infections, which are often reported in association with flu.

A Perfect Storm: Increased Colonization and Failure of Vaccination Leads to Severe Secondary Bacterial Infection in Influenza Virus-Infected Obese Mice [2017].

“Our studies utilized a coinfection model to show that obesity increases mortality from secondary bacterial infection following influenza virus challenge through a “perfect storm” of host factors that lead to excessive viral and bacterial outgrowth. In addition, we found that vaccination of obese mice against either virus or bacteria failed to confer protection against coinfection, but antibiotic treatment did alleviate mortality.”

Bottom Line

For some people it is hard to say “I have infection acquired brain trauma, one of the symptoms is emotional lability” and then ask people for their assistance by handing them a print out of the lovely Australian PDF above.

Looking at contributed microbiome with “Neurological: emotional overload” – an easier to understand symptom than “Pseudobulbar” or “lability” we have 38 samples with 16 of these having metabolism data.

Looking at the data

  • We observe these patterns frequently:
    • Bacterial Abilities: Flagellar assembly – LOW
    • Lipid metabolism: alpha-Linolenic acid metabolism LOW
    • Lipid metabolism: Arachidonic acid metabolism LOW
    • Lipid metabolism: Ether lipid metabolism LOW
    • Secondary metabolite degradation: Dioxin degradation LOW
    • Secondary metabolite degradation: Xylene degradation LOW

Going over to the Bacteria explorer

Symptom modification suggestions:

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.







20 month later – an update and request

“Know of a doctor in the Philadelphia region who has a good track record with CFS patients?” – from reader below

In December 2015 a reader emailed me describing the results of selectively following suggestions from this blog.  She did an update in April, 2016

“At the time I found your blog, these were my symptoms, all of which, disappeared or diminished within days  of taking action based on reading your blog (except for the asthma and allergies, which nonetheless somewhat better)”

I just got an update with a request that I am sharing with my readers in the hope that they can help:

“Hi, Ken! I don’t know if you remember me as it has been a couple of years since I’ve been in touch. I continue to read your blog often and still really appreciate the work you are doing (though it is a bit over my head lol).

I am writing both to update you on my situation, and to ask if you have any words of wisdom.  I can write a background summary for you again if you need it, but the best summary is probably the one that you posted back in December 2015.

Anyway….the good news is that since my “miraculous recovery” that I wrote you about, my CFS has been *pretty much* managed in that the physically painful symptoms are still gone, though they will start to come back if I discontinue treatment with supplements, probiotics, etc.

But….I still haven’t found a doctor to treat me and at present I fear that I may be on the verge of a relapse. I am having a lot of trouble with motivation, energy level, planning, and some brain fog. And after about 18 months or more with no upper respiratory infections, I have now had 3 since December, all of them going to bronchitis. My health collapse previously was preceded by chronic upper respiratory infections. 

I have moved from …..  to Philadelphia last fall… you by chance know of a doctor in the Philadelphia region who has a good track record with CFS patients?

At present I am working at trying to get a referral through my primary care doctor, but I am not hopeful because on my “get to know you” visit with him in January I presented him with my CFS history and asked about a referral and his response was “it seems like that was in the past and you are doing really well now.”

Two places here that pop up when I search “CFS Philadelphia” are The Marcus Institute for Integrative Health and the Garabedian Clinic, if you have ever heard of them.

Thank you so much for all you do. If it wasn’t for you I think I would probably have been virtually bedridden for the past three years. As it is I still am living a limited life and would like to broaden that.

Take care,

November 2016

Hi, Ken!! I hope you are well!! 

Even though I have been out of touch I am still reading your blog and appreciating it greatly, and have shared it with others.

I wanted to give you another update….the last time I wrote you, I had just tried Symbioflor II, which really didn’t work for me, and I also asked you about how you defined “remission” and I followed your advice and got a really undemanding part-time temp job which lasted couple of months and which I enjoyed a lot but which let me know I didn’t have as much stamina as I thought I did because I got sick the first week in and then was back to sleeping whenever I wasn’t at work. There was also a lot of family upheaval and stress ……

Anyway, all that is background to the fact that I am actually doing pretty well in many ways, much thanks to you, plus a couple of other things that I have started doing that seem to be shoring up my results. I would say that I am at 60 – 70 percent energy most days, with that being pretty steady. In other words, without the energy surges and crashes I used to have before I got sick. I’m not taking naps, and all in all I’d say I have enough energy to get by on except the one deficit I really still have is in drive and motivation and the ability to concentrate (I sort of think of those three combined as one thing)


Here’s what I am doing:

  1. Using the CFS Remission model – I will send you a detailed list of what I am taking in a day or two. I made changes based on your suggestion that I alternate between Prescript Assist and Equilibrium, which worked well (and if you have another broad spectrum probiotic to recommend I would be interested in hearing about it). I also tweaked my herbs based on the results of your reader survey, and added in D-Ribose at the suggestion of a friend with fibromyalgia (and then I saw that you had written about it though I somehow missed it).
  2. I finally saw a naturopath in October who said the CFS/ME diagnosis was pretty obvious. I printed out my initial letter to you and the other posts of mine you included on your blog, as well as your disease model. I gave them to her when I saw her but she hadn’t read them at the time – perhaps she’ll comment when I see her next. She did look at my supplement list, though, and gave it the thumbs up. She also made some diet recommendations. Here’s where it gets pseudo-science-y. She recommended the Blood Type diet, which I am aware has been debunked. I am blood type O. What I noticed about food lists for me is that many of the foods were those I had already been avoiding from the histamine restricted diet. Also, I had noticed that I felt a lot better when I ate beef, which according to the BTD is probably the best source of protein for me. It also recommended against grain (which you have also) and dairy. So I just chose to interpret her recommendation primarily as keep avoiding histamines, keep eating beef, and cut out milk and most grains, and of course most sugar and that seems to be working for me. I would say it has made the difference between having steadier energy vs. surges and crashes, which I was still having up until I started eating this way. I have also lost a little bit of weight, which I am happy about though I wasn’t really trying to do that.
  3. I have gradually started exercising again. As you know it’s hard to exercise with CFS, not to mention contraindicated, so I had cut way back and was pretty inactive and deconditioned as a result of basically sleeping a whole year, and then when I got whooping cough you basically can’t exercise without triggering a fit that makes you feel like you are going to die. I literally once turned blue from doing the kind of yoga where you do nothing but lay on floor and breathe; it was terrifying. So despite the fact that exercise has always been my go-to for managing my depression, I was scared to start exercising again. I started with walking (since I have a dog) and using Audible and or/ talking to my husband on a headset while I walk, and I am enjoying it immensely, averaging about 8,000 steps a day, and sometimes a lot more – I got lost when I visited my husband and walked 11.5 miles and expected a crash afterwards, but none came. Yay! I have also started swimming twice a week (deliberately doing it *much* less strenuously and with less duration than I used to, because I think over-swimming was part of what triggered my CFS or mono or whatever my initiating event was) and rather than having to nap after a workout I feel energized. I want to do yoga again but the turning blue scare is still holding me back a bit even though I know I am recovered from whooping cough…if my heath holds up I will ease my way into that too.
  4. This is something that I haven’t mentioned before, I don’t think….I have had depression on an off since adolescence, sometimes acute, sometimes low-grade, and have been off and on antidepressants since my twenties. Most recently, I was on them for about 10 years, and at the time I got whooping cough I had three prescriptions going. While acutely ill with whooping cough, I was too sick to take them and thus went off them without intending to. I didn’t want to start them again without talking to my prescriber, but, meanwhile, between the herbs and probiotics etc., which I did restart when I was able,  my mood problems diminished drastically. I never did go see my prescriber and now have been off for almost a year, and feel better than I did when I was taking the meds (even though they helped and I am not an anti-med person at all). Often, if I go through a patch of getting tearful easily, adding in or increasing the Miyarisan takes care of it within 24 hours.
  5. As I mentioned above, the thing that keeps me from being what I think of as functional is my lack of focus of motivation, which no longer rises to the level of brain fog but which really holds me back. Coffee and tea disagree with me. But one energy drink, or even half of one, and BAM! I am good for the day. My drink of choice is organic Rock Star, which contains sugar, green coffee extract, guarana, ginseng, vitamin B12 and taurine. Of course the naturopath told me not to do this, and I have been saving it for days when I really have to get a lot accomplished, but it would be nice to be able to be more productive all the time. So far, there doesn’t seem to be a big downside (except when I drank three whole cans three days in a row – some of my symptoms returned) and I’m considering using it more consistently, half a can per day, though it is basically  just enhanced soda and I have always disapproved of soda. I tried taking ginseng pills and also guarana pills with relatively little effect, haven’t tried green caffeine or taurine. What do you think? It would make life easier for my husband, my other families, and not to mention me if I could be a more productive version of me on a regular basis.  Alternatively, I have found that chocolate sometimes has the same effect, either the 85% kind from Trader Joes, or these dark chocolate covered almonds they have at Costco. There is something unnerving in trying to fuel my ability to concentrate with, essentially, candy and soda when I am trying so hard to be healthy in other ways and putting a lot of work into it.

 Anyhow….I wanted to let you know I am still around and still “working the program” and very grateful to you.

 Happy Thanksgiving!!

Bottom Line

This person has not done ubiome yet, and I would strongly urge it. They were working off the earlier post before I started detail analytics of microbiome. Ubiome with the new site would give very specific advice which have a good probability of improving the remaining symptoms.

REMEMBER: Those suggestions are NOT a replacement, but additional fine tuning.

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.