Overview of this Blog and the Microbiome

My ideas on this blog have evolved, as more and more information becomes available. This post is an attempt to bring readers up to date with my current thinking. I am striving to be transparent in my logic — showing the evidence I am working from, and my thought processes.

Notes to Treating Physicians     Quick Self Start on treating CFS

Analysis of Microbiome/stool with recommendations

Site: has moved to http://microbiomeprescription.azurewebsites.net

The data is available in an online collaborative python workbook for analysis. See this post.

Microbiome Definition of CFS/FM/IBS

A coarse condition that results from:

  • Low or no Lactobacillus, AND/OR
  • Low or no Bifidobacteria , AND/OR
  • Low or no E.Coli , AND/OR
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/suppress Lactobacillus, Bifidobacteria, E.Coli
    • Several are two or more times higher than normally seen
    • The number of bacteria genus goes very high (using uBiome results), but most of them are low amounts.
      (“Death by a thousand microbiome cuts” and not “Death by a single bacteria blow”)
  • The appearance of rarely seen bacteria genus in uBiome Samples.

A finer definition would be a condition with a significant number of abnormalities in the ‘Autoimmune profiles see this page for the current criteria (i.e. over 25%).

The specific genus and their interactions determine the symptoms seen — likely due to the over- or under-production of metabolites (chemicals). Other autoimmune conditions may share these core shifts. The specific high and low bacteria determine the symptoms if the person was the DNA/SNP associated with the symptoms.

Replace the metabolites produced by the missing bacteria

Replacing the metabolites should result in the reduction of symptoms associated with a deficiency of these metabolites.

See this post for the study references. These items should/could be done continuously.

Other Supplements Reported to Help

Bootstrapping Bifidobacterium and Lactobacillus

The items below were found in studies to increase bifidobacterium and lactobacillus:

Unless the bifidobacterium and lactobacillus (B&L) are human sourcedthere is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established. In fact, there are grounds to believe that most commercial probiotics actually reduce your  native B&L. You want to encourage your native B&L. See this post for citations.

Bootstrapping E.Coli

The E.Coli probiotics below are human sourced and known to take up residency in the human gut.

  • Core: D-Ribose a preferred food that it uses
  • Mutaflor probiotics — E.Coli Nissle 1917
  • Symbioflor 2 — multiple strains

Dealing with the other microbiome shifts

The other microbiome shifts appear to be in different clusters of microbiome shifts. This 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in its title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”.

The best way at present to proceed is to order an analysis from uBiome. (Disclosure: I have no financial interest in this company.) When your get your results back, log in, click on the “Compare” tab, then go to “Genus,” and click on “ratio” twice, so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk provides a nice summary of what we know about these. See, for example, Alistipes:

At this point, we run into a logistical challenge.  You want to avoid items that are “Enhanced By” (which is in common across all of the high items) and take the items that are “Inhibited By” (which are not on any of the “Enhanced By” lists).  You may also wish to reduce foods that are high in items listed in “Nutrients/Substrates.”  It becomes a jig-saw puzzle! I have done this exercise for many readers’ uBiome results:

I have discovered that DataPunk is not absolutely current, and have started creating posts based on its data, and then added studies from 2016 and 2017 to the page. Past pages are below, for current list MicrobiomePrescription site.


Src: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/

General Suggestions (no uBiome results)

Some of these items are contraindicated with a few uBiomes that I have reviewed. This likely is why person B reports no results while person A reports improvement. Example: Magnesium is usually very helpful — but there are a few cases where it encourages overgrowth of undesired  bacteria.


Most probiotics do not take up residency. They are “here today, gone tomorrow”. Their primary role in my model is producing natural antibiotics against other bacteria. For example:

Probiotics should be rotated: 2 weeks on a specific one, then several weeks off. As a general rule, you want about  6-12 B CFU taken three times a day (or 2-3 times the recommended dosage) — but work up slowly because you may get be a major herx! In general, do not take Lactobacillus with Bifidobacteria or with E.Coli etc. Keep to one family per cycle. You do not want them to kill off one another!

Why 3x per day? Because almost none of them are detected after 12-24 hrs. So to keep them — and the production of natural antibiotics — going, you need to keep taking them during the day. See this post for citations.

The following probiotics commonly seem to help people with CFS/Lyme/Fibro:

Some probiotics, however, may make your symptoms worse! And, unfortunately, most commercial probiotics contains some of these. At the moment Bifidobacterium animalis, Saccharomyces boulardii and Lactobacillus acidophilus are on my best to totally avoid list.

  • “. The findings show that the six species of Bifidobacterium differed in their ability to relieve constipation. B. longum, B. infantis and B. bifidum were the most effective in relieving constipation, B. adolescentis and B. breve were partially effective and B. animalis was not effective. Furthermore, edible Bifidobacterium treated constipation by increasing the abundance of Lactobacillus and decreasing the abundance of Alistipes, Odoribacter and Clostridium. .” [2017]

On my neutral list (no clear benefit) is Lactobacillus Plantarum.


Some teas can also be antibiotics (among other roles). There are two teas that seem to produce significant results quickly:

Again, rotate and, if practical, change brands too. Their antibiotic compounds are different from different sources.

Herbs and Spices

The best choice needs examination of your microbiome (i.e. uBiome results) and doing the work cited above.  Survey results found:

  1. Neem and Oregano with 80% improving
  2. Olive Leaf and Licorice with 56% improving
  3. Thyme with 50% improving
  4. Wormwood and Tulsi with 33% improving

Other things

If you do not know your microbiome, then see https://cfsremission.com/reader-surveys-of-probiotics-herbs-etc/  for suggestions. Your results will vary because your microbiome vary.

Thick blood is an issue also — but here things gets more complicated and not suitable for this recap.

Antibiotics can have a role — but getting prescriptions for the right ones can be a major challenge.

Metabolism Shifts

From volunteered data, we can identify some distinctive shifts, see Metabolism Explorer Summary

Bottom Line

Working with the microbiome and autoimmune is like working with fragments of the dead sea scrolls. For many bacteria we can identify it — what inhibits or encourages it is not known to modern medical science.  We have extremely thin slices of knowledge –Almonds enhances Bifidobacterium, Lactobacillus (B&L)  as do sesame seeds. What about sunflower seeds? Peanuts? Cashews? We find that Walnuts help the bacteria that inhibits B&L — so we cannot safely generalize to “all seeds/nuts are helpful”.

In many cases, we find that healthy diet or supplements demonstrated to work for normal people have the opposite effect on CFS and other altered microbiome conditions. This is made even worst because most of the studies were done on males and most people with CFS are females. We end up having to swim up-stream thru good and valid suggestions — that are just wrong for us.

My model is simple to understand and allows us to filter many suggestions and candidates. With the availability of uBiome testing (without needing a prescription!) we have entered the age of explicit treatment based on your unique microbiome. We do not know the role of many bacteria involved. We do not know what will inhibit or enhanced all of these bacteria. Frustrating little knowledge!

On the flip side, many readers have reported significant improvement, reduction of prescription medication, etc. so the model and suggestions have potential and thus hope of remission! Microbiome studies are exploding on PubMed, a lot of research is being done and we can often borrow their results.

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.

DNA and Microbiome interplay….

A reader forwarded their report from NutraHacker (https://www.nutrahacker.com/). 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 http://microbiomeprescription.azurewebsites.net/ 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 http://microbiomeprescription.azurewebsites.net/  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…..do 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.


Revisiting obesity and leanness

We are aware that microbiome influence obesity, with charts like the one below [2015] [2017]



This last week a lovely study was published:

Citrus peel extracts attenuated obesity and modulated gut microbiota in mice with high-fat diet-induced obesity.[ June 1, 2018] which stated “Compared to the case of the HFD group, PMF B altered the gut microbiota by increasing Prevotella and decreasing rc4-4 bacteria.”

rc4-4 means a genus under Firmicutes; Clostridia; Clostridiales; Peptococcaceae; rc4-4;

Related under the Peptococcaceae family are:

As you can see, there are some 13% of this family that do not have a reported genus in uBiome results.

More on Citrus Peels

So, it appears eating the peel of citrus fruit may have significant impact on obesity.

More on Prevotella

Bottom Line

Some people with various conditions will lose weight for years and then suddenly increase weight with the same, or even greatly reduced calories/diet.  The simple explanation is that their microbiome has shifted.  Correcting the shift by adding citrus peel to meals as a filler may both help with the weight issue and may even help with other health conditions.

Background on how suggestions are made

Creating suggestions on http://microbiomeprescription.azurewebsites.net/ is an art and not a science. I recently added choice of algorithms:


To illustrate, you have 4 bacteria:

  • A 2x normal
  • B 8x normal
  • C 1/2 normal
  • D 1/100 of normal

If A is normally  0.1% of bacteria and B is 10% of bacteria – do you treat them the same? B produces 100x more metabolites than A… so likely it is better to reduce B than reduce A.

Some herb reduces B (10% of population) and also reduces D which is 0.001% of the normal population and only 10% of patients have any of this bacteria. Do you take the herb or not?

The process of balancing factors such as:

  • Percentage of total bacteria
  • How often do people have this bacteria
  • Side-effects on other bacteria
  • How much shift we see

is what algorithms are about. If you restrict items to only what reduces your high bacteria OR encourages your low bacteria… you will have nothing in the suggestions.

A simple algorithm could be something like this for each substance

  • Sum up all of the high bacteria it reduces and the low bacteria it increases and use this to rank suggestions.
    • Problem: you are ignoring the low bacteria that may also be reduced and the high bacteria that may be further increased!
  • Sum up all of the high bacteria it reduces and the low bacteria it increases. Then subtract the high bacteria that it increases and the low ones that are reduced. Use this to rank suggestions.
    • Problem: A bacteria that is 10% of the bacteria is given equal weight to one that is just 0.00001% of the bacteria.
  • Sum up all of the high bacteria  it reduces and the low bacteria it increases using the expected percentage of the population. Then subtract the high bacteria that it increases and the low ones that are reduced using the expected percentage of the population. Use this to rank suggestions.
    • Problem: We are ignoring if the overgrowth is 10% or 800%!

Then we hit the question of — do we know anything abiut what this bacteria does? If this bacteria is not associated with any known condition and only occurs in 10% of the population…

Take: Propionibacteriaceae (14.35% of Samples) family a recent paper explains why — only 14% have it… so do we need to reduce or increase it??? Honestly, we do not know and I would exclude it from adjustments.

“For example, for SNP rs2297345 in the gene PAK7, we detected a correlation between genotype and a single microbial taxon, Propionibacteriaceae”

Formal Statement

  • S() returns a vector of factors
    • Output vector including, but not limited to
      • Taxonomy
      • Estimate of change for each taxonomy
      • Reliability of change for each taxonomy
      • DNA Snp factors
    • Input matrix including, but not limited to
      • Study
      • Study size
      • Study statistical significance
      • Shift reported by the study
      • Species involved
      • Background diet
      • Existing conditions or DNA
  • B() is a person matrix including, but not limited to
    • Taxonomy
    • Population size
    • Statistical error factors
  • R() is a reference matrix including, but not limited to
    • Taxonomy
    • Population size
    • Statistical error factors
    • Distributions broken down by:
      • Medical conditions
      • DNA
      • Age
      • Lab results
  • H() is a matrix of a person (the target), including, but not limited to
    • Medical conditions
    • Laboratory results
    • DNA
      • Ethnic background/heritage
    • Age
    • Normal Diet

Predictions are the output vector from   P(H(…),B(…), S(….), R(….))

The algorithms that I have implemented are Trade Secrets, do not ask me to disclose them.

Bottom Line

Suggestions come out of algorithms that attempts to balance a ton of different factors. The sequence of suggestions will likely change between algorithms and it is unlikely something would move between the take and avoid list.

There are two algorithms there at the moment, I will likely add more. Which one is best? We do not know.