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

Analysis of Microbiome/stool with recommendations

Microbiome Definition of CFS/FM/IBS

A condition that results from:

  • Low or no Lactobacillus
  • Low or no Bifidobacteria
  • Low or no E.Coli
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/surppress 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.

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:

  • https://cfsremission.com/2017/09/11/ubiomes-before-and-after-a-fecal-microbiota-transplant/
  • https://cfsremission.com/2017/09/03/ubiome-result/
  • https://cfsremission.com/2017/09/18/another-ubiome-review-with-bifidobacteria-overgrowth/
  • https://cfsremission.com/2017/08/27/ubiome-of-a-mcs-with-cfs-person/

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. Current pages are below (I will add more links as I research other genus)

  • Acetitomaculum: https://cfsremission.com/2017/11/14/decreasing-acetitomaculum-genus/
  • Acidaminococcus: https://cfsremission.com/2017/11/01/reducing-acidaminococcus-genus/
  • Actinobaculum: https://cfsremission.com/2017/10/21/decreasing-actinobaculum-genus/
  • Actinomyces: https://cfsremission.com/2017/11/25/reducing-actinomyces-genus/
  • Adlercreutzia: https://cfsremission.wordpress.com/2017/10/14/decreasing-adlercreutzia-genus/
  • Akkermansia: https://cfsremission.com/2017/10/14/decreasing-akkermansia-genus/
  • Alistipes: https://cfsremission.com/2017/10/09/decreasing-alistipes-genus/
  • Anaeroplasma: https://cfsremission.com/2017/11/11/decreasing-anaeroplasma-genus/
  • Anaerosinus: https://cfsremission.com/2017/11/29/reducing-anaerosinus-genus/
  • Anaerotruncus: https://cfsremission.com/2017/11/19/reducing-anaerotruncus-genus/
  • Anaerostipes:   https://cfsremission.com/2017/10/07/decreasing-anaerostipes-genus/
  • Bacteroides: https://cfsremission.com/2017/10/20/decreasing-bacteroides-genus/
  • Barnesiella: https://cfsremission.com/2017/10/15/decreasing-barnesiella-genus/
  • Bilophila:   https://cfsremission.com/2017/10/14/decreasing-bilophila-genus/
  • Blautia:   https://cfsremission.com/2017/10/29/reducing-blautia-genus/
  • Brevundimonas:   https://cfsremission.com/2017/11/04/decreasing-brevundimonas-genus/
  • Butyricimas:  https://cfsremission.com/2017/10/14/decreasing-butyricimonas-genus/
  • Butyrivibrio Crossotus:  https://cfsremission.com/2017/12/15/increasing-butyrivibrio-crossotus/
  • Caldicoprobacter: https://cfsremission.com/2017/10/15/decreasing-caldicoprobacter-genus/
  • Candidatus Stoquefichus: https://cfsremission.com/2017/11/30/reducing-candidatus-stoquefichus-genus/
  • Catenibacterium: https://cfsremission.com/2017/11/18/reducing-catenibacterium-genus/
  • Citrobacter Freundii: https://cfsremission.com/2017/12/11/reducing-citrobacter-freundii/
  • Collinsella: https://cfsremission.com/2017/10/10/decreasing-collinsella-genus/
  • Coprobacter: https://cfsremission.com/2017/11/06/decreasing-coprobacter-genus/
  • Clostridium :  https://cfsremission.com/2017/10/07/decreasing-clostridium-genus/
  • Cronobacter:  https://cfsremission.com/2017/10/21/decreasing-cronobacter-genus/
  • Desulfovibrio:  https://cfsremission.com/2017/11/05/decreasing-desulfovibrio-genus/
  • Dialister:  https://cfsremission.com/2017/11/05/reducing-dialister-genus/
  • Dorea :  https://cfsremission.com/2017/10/18/reducing-dorea-genus/
  • Eggerthella: https://cfsremission.com/2017/10/19/decreasing-eggerthella-genus/
  • Eisenbergiella: https://cfsremission.com/2017/11/25/reducing-eisenbergiella-genus/
  • Enterococcus: https://cfsremission.com/2017/10/29/reducing-enterococcus-genus/
  • Enterorhabdus: https://cfsremission.com/2017/11/05/reducing-enterorhabdus-genus/
  • Erysipelatoclostridium: https://cfsremission.com/2017/11/14/decreasing-erysipelatoclostridium-genus/
  • Faecalibacterium: https://cfsremission.com/2017/10/11/reducing-faecalibacterium-genus/
  • Flavobacterium:
  • Flavonifractor: https://cfsremission.com/2017/11/05/reducing-flavonifractor-genus/
  • Fusicatenibacter: https://cfsremission.com/2017/11/03/decreasing-fusicatenibacter-genus/
  • Gelria: https://cfsremission.com/2017/12/22/reducing-gelria-genus/
  • Gordonibacter: https://cfsremission.com/2017/10/09/decreasing-gordonibacter-genus/
  • Granulicatella: https://cfsremission.com/2017/11/25/reducing-granulicatella-genus/
  • Haemophilus: https://cfsremission.com/2017/11/19/reducing-haemophilus-genus/
  • Herbaspirillum: https://cfsremission.com/2017/10/12/reducing-herbaspirillum-genus/
  • Hespellia: https://cfsremission.com/2017/11/05/reducing-hespellia-genus/
  • Hydrogenoanaerobacterium: https://cfsremission.com/2017/12/22/reducing-hydrogenoanaerobacterium-genus/
  • Intestinibacter: https://cfsremission.com/2017/12/22/reducing-intestinibacter-genus/
  • Intestinimonas: https://cfsremission.com/2017/11/05/reducing-intestinimonas-genus/
  • Johnsonella: https://cfsremission.com/2017/11/04/decreasing-johnsonella-genus/
  • Kluyvera: https://cfsremission.com/2017/10/31/reducing-kluyvera-genus/
  • Lachnospira: https://cfsremission.com/2017/11/03/reducing-lachnospira-genus/
  • Lactonifactor: https://cfsremission.com/2017/11/29/reducing-lactonifactor-genus/
  • Leuconostoc: https://cfsremission.com/2017/10/26/reducing-leuconostoc-genus/
  • Marvinbryantia: https://cfsremission.com/2017/11/06/decreasing-marvinbryantia-genus/
  • Megasphaera: https://cfsremission.com/2017/11/18/reducing-megasphaera-genus/
  • Mitsuokella: https://cfsremission.com/2017/12/21/reducing-mitsuokella-genus/
  • Moryella: https://cfsremission.com/2017/11/11/decreasing-moryella-genus/
  • Odoribacter: https://cfsremission.com/2017/10/19/decreasing-odoribacter-genus/
  • Oscillospira: https://cfsremission.com/2017/10/15/decreasing-oscillospira-genus/
  • Oxalobacter-formigenes: https://cfsremission.com/2017/12/15/increasing-oxalobacter-formigenes/
  • Papillibacter: https://cfsremission.com/2017/11/06/decreasing-papillibacter-genus/
  • Parabacteroides: https://cfsremission.com/2017/10/17/decreasing-parabacteroides-genus/
  • Paraprevotella:https://cfsremission.com/2017/11/28/decreasing-paraprevotella-genus/
  • Parasutterella: https://cfsremission.com/2017/10/19/decreasing-parasutterella-genus/
  • Peptococcus: https://cfsremission.com/2017/11/28/decreasing-peptococcus-genus/
  • Peptoclostridium: https://cfsremission.com/2017/11/18/reducing-peptoclostridium-genus/
  • Phascolarctobacterium: https://cfsremission.com/2017/11/12/decreasing-phascolarctobacterium-genus/
  • Planomicrobium: https://cfsremission.com/2017/10/21/decreasing-planomicrobium-genus/
  • Prevotella: https://cfsremission.com/2017/10/14/decreasing-prevotella-genus/
  • Pseudoflavonifractor:https://cfsremission.com/2017/11/19/reducing-pseudoflavonifractor-genus/
  • Pseudobutyrivibrio: https://cfsremission.com/2017/10/15/decreasing-pseudobutyrivibrio-genus/
  • Robinsoniella: https://cfsremission.com/2017/10/12/decreasing-robinsoniella-genus/
  • Romboutsia: https://cfsremission.com/2017/12/09/reducing-romboutsia-genus/
  • Roseburia: https://cfsremission.com/2017/10/29/decreasing-roseburia-genus/
  • Rothia: https://cfsremission.com/2017/10/25/decreasing-rothia-genus/
  • Ruminococcus: https://cfsremission.com/2017/10/18/reducing-ruminococcus-genus/
  • Sarcina: https://cfsremission.com/2017/10/12/decreasing-sarcina-genus/
  • Senegalemassilia: https://cfsremission.com/2017/11/18/reducing-senegalemassilia-genus/
  • Shuttleworthia: https://cfsremission.com/2017/12/22/reducing-shuttleworthia-genus/
  • Slackia: https://cfsremission.com/2017/10/15/decreasing-slackia-genus/
  • Streptococcus: https://cfsremission.wordpress.com/2017/10/25/reducing-streptococcus-genus/
  • Subdoligranlum: https://cfsremission.com/2017/10/10/decreasing-subdoligranlum/
  • Succinivibrio: https://cfsremission.com/2017/11/05/decreasing-succinivibrio-genus/
  • Sutterella: https://cfsremission.com/2017/10/13/decreasing-sutterella-genus/
  • Terrisporobacter: https://cfsremission.com/2017/11/05/reducing-terrisporobacter-genus/
  • Thalassospira: https://cfsremission.com/2017/10/22/reducing-thalassospira-genus/
  • Veillonella: https://cfsremission.com/2017/11/29/reducing-veillonella-genus/
  • Victivallis: https://cfsremission.com/2017/11/11/decreasing-victivallis-genus/


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.

Should you do uBiome before going on Antibiotics?

A reader on a local CFS group asked:

Ken Lassesen, can I enlist your expertise and help? First, I’ve been enema-dependent for a few years and I’m wondering if my Ubiome might give you some fascinating info. Second, I’m going to treat SIBO soon with vancomycin and Rifaxamin and I haven’t had antibiotics in many years — before being sick with ME. Could this give any interesting or helpful info (either for you or me) – if I did a Ubiome before and after treatment? Thanks for the help!

The Answer is very much a yes. Each of these antibiotics cause significant changes — the question arises — will the net change be for the better or the worst?

The following is the information (with sources) that have been assembled so far. I have seen some CFS patients with high Proteobacteria thus Rifaximin would be good, but not vancomycin. For other patients, the opposite is true.










Bottom Line

Most studies deal with a sample of patients that presents a condition.  The group as a whole may have positive results but individuals may not.  Working off your own uBiome may allow your likely response to be better predicted. More individual treatment based on your own reality.


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.

Gut Bacteria associated with Restless Leg

The following profile seems to occur with restless leg according to our explorer:

With high genus Oscillibacter being seen often.


The following should improve the bacteria shift seen above:

Walnuts 3.03
barley 2.02
Choline 2.02
Polymannuronic acid 2.02
Pomegranate ellagitannins 2.02
Bifidobacterium infantis 1.01


Acetic acid -2.02
Aspartame -2.02
Choline deficiency -2.02
Doxycycline -2.02
high-fat diet -2.02
Isobutyric acid -2.02
Isovaleric acid -2.02
macrolide -2.02
saccharin -2.02
vancomycin -2.02
vegetarian -2.02

Bottom Line

The following are likely to help

  • Supplement with choline
  • Eat Walnuts and Pomegrantes
  • Barley porridge

Do not use Saccharin or Aspartame

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.

Dioxin degradation and CFS

For the third item from the Metabolite Explorer, we return to a LOW item, Secondary metabolite degradation: Dioxin degradation. Here we see

  • Low 8/14
  • High 1 /14
  • Normal 5/14

We all know the term dioxin and usually associate with man-made evil chemicals associated with PCBs. This reduced ability to degrade dioxin may means increase culmination of dioxin in the body for some (not sufficient clearance for the intake).

“The terms ‘dioxins’ and ‘dioxin-like compounds’ are used in literature when referring to a large family of chemical compounds that are found in trace amounts in nearly all realms of the environment….Dioxins are the byproducts of both anthropogenic activity and natural processes. “[src]

What is the main source of dioxin in the environment, according to the EPA, Backyard burning of refuse accounts for 35%!

The World Health Organization(WHO) writes

  • “Dioxins are found throughout the world in the environment and they accumulate in the food chain, mainly in the fatty tissue of animals.
  • More than 90% of human exposure is through food, mainly meat and dairy products, fish and shellfish.
  • Once dioxins enter the body, they last a long time because of their chemical stability and their ability to be absorbed by fat tissue, where they are then stored in the body. Their half-life in the body is estimated to be 7 to 11 years. In the environment, dioxins tend to accumulate in the food chain. The higher an animal is in the food chain, the higher the concentration of dioxins.
  • Long-term exposure is linked to impairment of the immune system, the developing nervous system, the endocrine system and reproductive functions.
  • Trimming fat from meat and consuming low fat dairy products may decrease the exposure to dioxin compounds. However, the possibility for consumers to reduce their own exposure is somewhat limited.”

Some Literature

Bottom Line

If you have a low Dioxin degradation, then the best information appears to suggest:

  • Reduce food and supplements (i.e. Fish Oil, some Omega-3 and 6) higher in dioxin. Trim fat off meat. Low fat dairy products.
  • Resveratrol supplementation
  • Folic acid supplementation
  • Activated charcoal

Do not expect quick results. To reduce half of the existing dioxin is 7 to 11 years, with a low degradation it may be even longer without some of the above.

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.


Stilbenoid, diarylheptanoid and gingerol impact on CFS/IBS

The highest average value on the symptom-metabolites explorer at present is from “Secondary metabolite biosynthesis: Stilbenoid, diarylheptanoid and gingerol biosynthesis” with an average of 2.1 with

  • 8/14 HIGH
  • 4/14 low
  • 2/14 Normal.

This is biosynthesis — the body producing this group of compounds, not metabolism (using and recycling) like in my last post

What are these?

Three new words for our vocabulary:


Wikipedia provides a list of examples which gives a good idea –> Resveratrol, Grape Seed Extract,  Red Wine etc.



  • Astringin in the bark of Norway spruce
  • Piceid is a resveratrol derivative in grape juices


Again, Wikipedia gives some good examples “The best known member is curcumin, which is isolated from turmeric (Curcuma longa). Some other Curcuma species, such as Curcuma comosa also produce diarylheptanoids. Other items include ginger

” are mainly distributed in the roots, rhizomes and bark of Alpinia, Zingiber, Curcuma and Alnus species. They have become of interest in natural product research over the past twenty years because of their remarkable anti-cancer, anti-emetic, estrogenic, anti-microbial and anti-oxidant activity. This paper compiles all 307 naturally occurring diarylheptanoids from 46 plants as reported in 137 references with their distributions, physiological activities and 13C-NMR spectral data.” [2010]


From wikipedia

  • Gingerol, properly as [6]-gingerol, is the active constituent of fresh ginger.”
  • [6]-Gingerol administered by intraperitoneal injection has been used to induce a hypothermic state in rats.[4]
    • Is this the cause of low body temperatures seen in many CFS patients?
  • Gingerol seems to be effective in an animal model of rheumatoid arthritis.[5]

The Literature

  • “PICRUSt analysis revealed that metabolic pathways such as “stilbenoid, diarylheptanoid, gingerol biosynthesis” were enriched in high weight rabbits, and pathways related to “xenobiotics biodegradation” and “various types of N-glycan biosynthesis” were overrepresented in rabbit soft feces. ..41 bacterial taxa were significantly more abundant in high weight rabbits (e.g. YS2BacteroidalesLactococcus spp.Lactobacillus spp.Prevotella spp.Sutterella spp.Acinetobacter sppp <0.05)," [2015]

What could this abnormally high biosynthesis mean?

My first impression is that we are talking about items, when taken as supplements, causes blood thinning. Do CFS patients have thin blood? No, the opposite — so is this the body response to hypercoagulation? The microbiome may be sensing the thick blood and to protect it’s host, responding by trying to thin things out.

The nasty question: What to do?

The body is spending resources on this biosynthesis, likely because it needs the resulting compounds. My take is this, if you are high then supplement with the items cited above, i.e.

The body may shift it resources elsewhere (because the supplements are delivering the desired items).

If you are low or normal, see if:

  • any of these items are on your recommendation list from your ubiome
  • there is any significant cognitive improvement from taking themway

There are a dozen step in the coagulation cascade, I speculate that if the above thinners have no effect on the step causing coagulation, then biosynthesis will be normal or even low.

 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.

D-Arginine and D-ornithine metabolism in CFS/IBS

The data from 14 people to date reporting in the microbiome metabolism explorer has a high percentage with a very low metabolism for D-Arginine and D-ornithine (10/14). There are a few others that are high (4/10). None normal. This variation is expected because everyone’s shift is different.

At face value,  this means that both arginine and ornithine that is taken into the body is not effectively processed and suggest high levels of both would be in the body OR low levels of chemicals they produce.

Diagram from Arginine Metabolism: Boundaries of Our Knowledge [2007]


This agrees with other findings:


  • “These results indicated that L-Arg induces iNOS and generates NO, which inhibits EBV reactivation in EBV-positive cells.” [2002]
    • With a low metabolism, the amounts of  inducible nitric oxide synthase (iNOS) and nitric oxide (NO) produce would drop considerably and EBV would become re-activated! The mechanism of inactivation of  EBV cells is lost.  You are EBV positive/reactivated? this is likely the why!
    • Also it explains low iNOS and NO reported from studies.
      • Decreased nitric oxide-mediated natural killer cell activation in chronic fatigue syndrome [1998] “These results demonstrate that the L-Arg-induced activation of NK activity is mediated by NO and that a possible dysfunction exists in the NO-mediated NK cell activation in CFS patients.”
      • “There were significant and positive intercorrelations between COX-2, iNOS and NFkappabeta and between COX-2 and iNOS, on the one hand, and the severity of illness, on the other. The production of COX-2 and iNOS by PBMCs was significantly related to aches and pain, muscular tension, fatigue, concentration difficulties, failing memory, sadness and a subjective experience of infection. ” [2007] – lower iNOS => more severe.


Again, the products produce from this amino acid will be greatly reduced.

  • “From these findings, we speculated that L-ornithine may play a role in the relieve of stress and improve sleep and fatigue symptoms in humans. Through a randomised, double-blind, placebo-controlled clinical study, we asked if L-ornithine could be beneficial to stress and sleep in healthy workers…. L-ornithine supplementation has the potential to relieve stress and improve sleep quality related to fatigue, both objectively and subjectively.” [2014]
  • l-Ornithine affects peripheral clock gene expression in mice. [2016] “. l-Ornithine also increased plasma levels of insulin, glucose and glucagon-like peptide-1 alongside mPer2 expression, suggesting that it exerts its effects probably via insulin secretion. Collectively, these findings demonstrate that l-ornithine affects peripheral clock gene expression and may expand the possibilities of L-ornithine as a health food.”

Leaky Gut

“Arginine and ornithine are precursors of nitric oxide and polyamines, respectively. These metabolites intimately participate in permeability and adaptive responses of the gut. The liver possesses high arginase activity as an intrinsic part of urea synthesis and would consume most of the portal supply of dietary arginine. The gut reduces this possibility by converting dietary arginine to citrulline, which effectively bypass the liver and is resynthesized to arginine in the kidney. Dietary ornithine supplementation, in the form of ornithine alpha-ketoglutarate (OKG) can be considered as an arginine precursor. Several supplement studies have shown both amino acids to promote growth hormone and insulin secretion with anabolic effects in postoperative patients. Their intermediary metabolites (for example, glutamine, proline) may also be of benefit in trauma metabolism. Specific effects of either amino acid on the gut are poorly reported.” [1994]

Bottom Line

Remember that this estimation of D-Arginine and D-ornithine metabolism is based off your gut bacteria nothing else is known about you, no blood sample etc.

  • We see that this explains EBV reactivation
  • “aches and pain, muscular tension, fatigue, concentration difficulties, failing memory, sadness and a subjective experience of infection.” for low arginine
  • ” to relieve stress and improve sleep quality related to fatigue” and likely sleep reversal and insomina — for low ornithine

With time, I hope to have this pattern confirmed from the uBiome and symptoms shared on our analysis site.

I was unable to identify from scanning the literature, the bacteria that are important for this metabolism (hopefully a reader will find such!).

If your metabolism function is estimated to be low, then supplementation with both Ornithine and arginine seems to be suggested. With arginine, convention wisdom is that lysine should be taken with it.

There is no clear study dealing with low metabolism. Ornithine occurs is very low amounts in food and thus with a reduce metabolism, taking more may produce more end products.

If you have herpes, care need to be taken:

“In the studies conducted, arginine deficiency suppressed herpes simplex virus replication in tissue culture. Lysine, an analog of arginine, as an antimetabolite, antagonized the viral growth-promoting action of arginine. The in vitro data may be the basis for the observation that patients prone to herpetic lesions and other related viral infections, particularly during periods of stress, should abstain from arginine excess and may also require supplemental lysine in their diet.” [1981]

In this case zinc supplements with Glutamine may be an alternative approach.

In the case of arginine, we read of additional side-effects from too much. From livestrong.com

Digestive Problems

L-arginine can increase levels of stomach acid, particularly gastrine. Too much gastrine can result in stomach pain and nausea. You may also experience bloating, cramps and diarrhea.

Allergic Reactions

Some people experience anaphylaxis, or an allergic reaction, to L-arginine. The severity of anaphylaxis increases with dosage. Symptoms include itches and skin rashes, swollen eyes, and in the worst cases, shortness of breath. People with asthma may be especially prone to this.

Blood Pressure

Because of L-arginine’s properties as a vasodilator, low blood pressure can be a side effect of supplementation. If you experience low blood pressure, you may notice dizziness, fainting or blurred vision. Contact your doctor immediately if you experience these or other associated symptoms.”

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.



We need more data…

But a symptom of hair loss has some strong trends (3/3) had

  • Low Amino acid metabolism: D-Arginine and D-ornithine metabolism .233
  • Low Bacterial Abilities: Bacterial chemotaxis .658
  • Low Bacterial Abilities: Bacterial motility proteins .658
  • Low Bacterial Abilities: Flagellar assembly .575
  • Low Secondary metabolite degradation: Dioxin degradation .74
  • Low Secondary metabolite degradation: Xylene degradation . 825

See http://ubiomecfsweb.azurewebsites.net/Metabolite/Explorer?filter=,116

Data Downloads are now available

All of the user entered data is available for citizen scientists (as well as some AI scientists and statisticians with significant others having CFS). This was a promise that I made in collecting the data — make the data freely available without any human identifying information.

On the menu, you will see an Advance tab.


The first three are reference tables which will be similar from day to day. The 2nd three should always be downloaded/updated as a set (I randomize the SampleId daily to insure privacy).

I show an example of the data in each one below. Yes, for your data nerds, the data structure has been normalized.

Taxonomy CSV

Taxonomy id,Parent id,name,rank

Symptoms CSV

Symptom id,Symptom Name
134,Asymptomatic: Live in house with person with probable microbiome dysfunction
132,Asymptomatic: Minor Health Issues (a few symptoms only)
131,Asymptomatic: No Health Issues
25,Autonomic Manifestations: nausea
29,Autonomic Manifestations: bladder dysfunction
31,Autonomic Manifestations: cardiac arrhythmias
124,Autonomic Manifestations: Cortisol disorders or irregularity
22,Autonomic Manifestations: delayed postural hypotension

Metabolites CSV

Metabolism id,Metabolism Name
39,Amino acid metabolism: Alanine aspartate and glutamate metabolism
35,Amino acid metabolism: Arginine and proline metabolism
49,Amino acid metabolism: beta-Alanine metabolism
34,Amino acid metabolism: Cyanoamino acid metabolism
45,Amino acid metabolism: Cysteine and methionine metabolism
48,Amino acid metabolism: D-Alanine metabolism
50,Amino acid metabolism: D-Arginine and D-ornithine metabolism
32,Amino acid metabolism: D-Glutamine and D-glutamate metabolism:

Sample To Symptom CSV

Sample id,Symptom Id

Sample to Metabolism CSV

Sample id,Metabolism Id,Value

Sample to Taxonomy CSV

Sample Id,taxonomy id,Count Norm

Bottom Line

The data is there for any professional or amateur research to use. The greatest value comes when people provide their symptoms and copies the function/metabolites numbers into this shared repository.