Triphala – an ancient medicine

Triphala is a mixture from Ayurvedic medicine has been mentioned in context of reducing high Streptococcus [2017] as well as in a patient report. It is cheap ($22 for 454gm/ 1 pound on Amazon — Organic)) and traditionally taken as a tea (a bit bitter – but tolerable). It was used since the Roman Period in the west [2015]

It contains equal parts of three herbs:

On pubmed,

I have taken to adding some to tea regularly and several people have been impressed by changes it has made.

So what do we know about each?

Amalaki (Emblica officinalis)


Bibhitaki (Terminalia bellirica)

Haritaki (Terminalia chebula)

  • “The highest antibacterial potentiality was exhibited by the methanolic leaf extract of T. chebula, followed by the aqueous fruit extract of T. bellerica. The leaf extract of T. chebula can be considered to be as equally potent as the most effective antibiotics, such as ciprofloxacin, gentamycin, kanamycin, ofloxacin and cephalexin.” [2008]

See this prior post.

THIS IS NOT MEDICAL ADVICE — this post is an education summary of what has been reported on PubMed. Always consult with a knowledgeable medical professional before changing diet, supplements and prescription drugs.

uBiome’s Clinical Report “Smart Gut”

uBiome has been offering clinical reports to MDs of some uBiome people.

Hi there,

We wrote you recently to invite you to the pilot program for SmartGut.  We are writing to let you know you are still invited to participate in the SmartGut pilot program.

If ordered, we will send you a clinical report on over a dozen common pathogens and commensals found in the human gut that affect your health with a clinical kit that we’ll send your way.

All you have to do is answer a few questions about your current health, and we’ll coordinate with your physician to request the test for you for your archived baseline if you have one as well as a new kit. It’s even covered by insurance. (As part of our pilot, we will not balance bill you for any amounts not paid by your insurance company.)

A reader has gotten their results, the “SmartGut” test report, show below.











Bottom Line

This report is designed to be typical physician friendly. Information is presented in a friendly (idiot) format. This is not my #1 choice for CFS patients, I believe GanzImmun Diagnostics AG report [GDs] that I reviewed in this recent post is better. Let us look at what is in these reports

  • Akkermansia muciniphila – both
  • Alistipes – both
  • Anaerotruncus colihominis – both
  • Bacteroides fragilis – both
  • Barnesiella – Smart Gut only
  • Bifidobacteria – Smart Gut: 1 measure. GD’s – 3 breakdowns
  • Butyrivibrio crossotus – both
  • Campylobacter Smart Gut only
  • Clostridium – both
  • Clostridium difficile – Smart Gut only
  • Collinsella aerofaciens – both
  • Desfulovibrio piger – both
  • Dialister – GD’s species, invisus Smart Gut
  • Escherichia spp – GD’s, Shigella Smart Gut
  • Fusobacterium – both
  • Fusobacterium nucleatum — GD’s
  • Lactobacillus – both
  • Odoribacter -both
  • Methanobrevibacter smithii – both
  • Oxalobacter formigenes – both
  • Prevotella – both
  • Roseburia – both
  • Ruminococcus – both
  • Ruminococcus albus – smart gut only
  • Salmonella enterica – smart gut only
  • Veillonella – smart gut only
  • Vibrio cholera  – smart gut only

I will refrain from listing the dozens other bacteria that GDs has. SmartGut gives a simple High, Low, Normal for each measure — perfect for a physician to look at and jump to conclusions (or dismissal — “you are fine! There are no microbiome problems!”). SmartGut does not provide treatment advice of any form. No pH is provided.

GD’s provide actual numbers and scales which provide a far more complete picture. Using the GD’s results and the information of what is significant in the Smart Gut report (which is based on studies cited at the bottom of their report)

Problem with both: There are no gender reference ranges.

This patient’s results

Recommendations are simple:

  • Bifidobacteria probiotics, no lactobacillus probiotics.
  • See increasing Akkermansia post (“pH 5.5–8.0, with optimum growth at 37 C and pH 6.5″ [2004]) – thus an alkaline environment would inhibit it some. This may be available as a probiotic in the coming months/years.
  • There was no report on E.Coli, just a report on “Escherichia-Shigella” which are overgrowths seen in Crohn’s disease.




A possible explanation of how CFS gets started

My model is that CFS is a persistent shift of bacteria following some event (typically infection or stress).  In doing a reader microbiome analysis I focused on their high pH (alkaline). This lead to the following addition to the model. Back in 2001, pH was discussed on the old group that I was the moderator on, CFSFMExperimental with intermittent results

A light bulb went on reading a paper dealing with weaning babies on to cow milk. The chart below shocked me — because it looked like the shift seen in CFS!!!! Bifidobacterium dropped, Lactobacillus dropped and Escherichia Coli dropped — just like CFS!


  • “An increase in the relative abundance of Bacteroides spp., Blautia spp., Parabacteroides spp., Coprococcus spp., Ruminococcus spp., and Oscillospira spp. and a decrease of Bifidobacterium spp., Lactobacillus spp., Escherichia spp., and Clostridium spp. were observed during weaning. The change in microbiome composition was accompanied by a gradual increase of fecal pH from 5.5 to 7.” [2016] That is, the result from going from human milk to cow milk in humans. Human milk have a pH of 7.4 [1986] while cow milk has a pH of 6.5 [source] and milk from different mammals are significantly different in composition [2004]

At this point I need to make a table to clarify the relationship between the pH of the food intake and the fecal pH. It is an inverse relationship. Low pH food causes the body to make more acid to digest it, this increased acid production is not confined to just the stomach but across the entire digestive system.

Food Food pH Fecal ph
Human Milk 7.4 (milk alkaline) 5.5
Cow Milk 6.5 (mild acid) 7.0

From a veterinary study [2013]



“The onset of CFS was an event that resulted in the fecal pH increasing above the normal range (5.5-6.5) which resulted in bacteria composition changing [All bacteria are sensitivie to different pH ranes]. The shifted bacteria conspired to keep this more friendly-to-them pH value successfully.

Hypothesis Test

The above speculation means that we should find that believed triggering events for CFS may report in the literature a shift in fecal pH to a high (alkaline) value.

  • Giadia infections: see this post for literature on the outbreak with CFS seen in Norway.  ” infects the duodenum and upper intestine, which have a favorable alkaline pH, and gives rise to the clinical sequelae.” [2001]
  • Antibiotics Usage: “Stool with a high pH may mean inflammation in the intestine (colitis), cancer, or antibiotic use” [WebMd]
  • Lyme Disease: ” people with Lyme disease universally suffer from hyperammonemia [causing alkaline pH]” [source]
  • Virus:
    • ” Childhood episodes of hyperammonemia (high ammonia levels in the blood) may be brought on by viral illnesses including chicken pox, colds or flu, …. or even exhaustion.” [Source]

“Total organic acid was increased in acidic feces and decreased in alkaline feces. Lactic acid, succinic acid, and formic acid were the main contributors to acidity in acidic feces. In alkaline feces, acetic acid was significantly decreased. Propionic acid was markedly decreased in both acidic and alkaline feces compared with neutral feces” [2012]

Overall, there is little reported on PubMed (first choice of information) on Urine pH or Fecal pH or blood pH for the reported triggers of CFS.


“The following are some of the traditional causes of alkaline urine:

  1. urinary tract infections (Proteus and others)
  2. matabolic alkalosis (pyloric stenosis and ohters(
  3. failure of acidifications (renal tubular acidosis, chronic renal failure, or aldosterone abnormalities)
  4. ingestion (salicylate, sodium bicarbonate, acetazolamide, etc)
  5. respiratory alkalosis (hyperventilation)” [JAMA 1991]

Add in “acetazolamide, thiazide diuretics, potassium citrate, sodium acetate, sodium bicarbonate, sodium lactate” [Source]

  • “Infectious: Corynebacterium urealyticum, Klebsiella (rare), Proteus, Providencia, S. saprophyticus, Ureaplasma urealyticum” [2009]

Some drugs stay around in your system longer, which can result in adverse drug effects or hyper-sensitivity.


CFS Process

Once an alkaline environment has been established, alkaline friendly bacteria become established and attempt to maintain the alkaline state.  My original model assumed that the metabolites and natural antibiotics produced by different species helped to maintain the dysfunctional shift. This model may still be true, but a shift of pH is a simpler model that is consistent with the shift of bacteria seen.

Bottom Line

Assuming (moderate assumption) that alkaline urine/fecal plays a significant role in the dysfunctional shift seen in CFS/IBS/FM etc. then an alkaline shifted diet with probiotics and herbs would be a logical path.  Remember to reduce the alkaline urine, we want to eat alkaline foods — not acid foods! See the studies cited above.

What is an alkaline shifted diet? There are many sites on the web..  a few are below:

Many of the alkaline items match other recommendations on this site, for example

REMEMBER: there is a reversed relationship — to reduce acid, more acid food. to reduce alkaline, more alkaline food.

You do not want (because they are acid food): Cow Milk, Eggs, Cheese, Cream, Yogurt, Ices cream.

  • Goat milk is 6.4 – 6.7 [1921] — too acid
  • Soy and milk beverages at a constant pH of 6.5 or 5.5 — too acid again
  • Almond milk appears to be mildly alkaline and would be preferred.

THIS IS NOT MEDICAL ADVICE — this post is an education summary of what has been reported on PubMed. Always consult with a knowledgeable medical professional before changing diet, supplements and prescription drugs.


Another reader lab report

In an earlier post this week, I mentioned that a single patient microbiome can often be fuzzy to interpret. Regional lab reports where the patient is a match for the general population interms of genetics and diet is the exception.  An example: Estonia and Sweden are a short boat ride away from each other but for L. Fermentum, this species was found only in Estonian children but not in Swedish children [2009].

A reader in Germany sent their result from a German Lab, GanzImmun Diagnostics AG.

The lab report has a nice presentation of how their results compared to a German reference population. The width of analysis was also good.  Examples are below:






Compared to Other Reports

How does this compare to Lipkins results (for those reported above) and other results

And for the classic pattern reported in the 1998 Australian Study and others?

  • Escherichia Coli etc: Study – Low, Patient – Low  🙂
  • Bifidobacterium: Study – Low, Patient – Low 🙂
  • Lactobacillus: Study – Low, Patient – Low 🙂
  • Klebsiella/Enterbacter: Study – High, Patient – Normal 😐
  • Enterococcus: Study – Low, Patient – Normal  😐
  • Firmicutes: 2016 Study – Low, Patient – Low 🙂
  • Bacteroides: 2016 Study – High, Patient – High 🙂

The model postulates that symptoms and microbiome shifts are likely associated. For the classic patterns, we have a good match. For Lipkin’s study, we have a much poorer match, causing the useful of that study further into question.

Checking for Infections

All negative, but an impressive list of items.


Additional Charts

Another chart was very interesting because it shows high histamine (Histaminbildner) producers — a frequent issue with CFS. Fäulnisflora (rotting flora) I suspect is SIBO, again common with CFS. Säuerungsflora(acidifying bacteria) is low  And high pH (alkaline) as the consequence.


Bottom Line

The first thing that struck me was to reduce pH. A shift in pH results impacts a lot of bacteria (increase or decreases growth).

pH Factors

Normal pH is 5.5 to 6.5, this patient is 7.0. A shift outside of the normal range is usually viewed as an indicator of bacteremia [2012]. Based on Bile Acids: A pH Dependent Antibacterial System in the Gut? [BMJ 1972], bile acid supplementation should be discussed with your medical professional. Drinking diluted vinegarhas often been suggested on alternative-medicine sites. For myself, I prefer eating pickled herring – Bismarckhering because it is natually rich in all of the recommended supplementations for CFS

  • “Pickled herring is one of the best sources of natural vitamin D3. It is also an excellent source of selenium and vitamin B12. 100 grams may provide 680 IU of vitamin D or 170% of the DV, as well as 84% of the DV for selenium and 71% of the DV for vitamin B12. [5][6]” – Wikipedia
  • “Increasing levels of the primary bile acid cholic acid (CA) causes a dramatic shift toward the Firmicutes, particularly Clostridium cluster XIVa” [2013][2017]
  • Western diet deregulates bile acid homeostasis, cell proliferation and tumorigenesis in colon [2017]. “Western-style diets (WD) high in fat and scarce in fiber and vitamin D”
  • “Pickled herring is one of the best sources of natural vitamin D3. It is also an excellent source of selenium and vitamin B12. 100 grams may provide 680 IU of vitamin D or 170% of the DV, as well as 84% of the DV for selenium and 71% of the DV for vitamin B12. [5][6]” – Wikipedia

I will revisit pH (Acid/Alkaline balance) in a future post — there are some complexities (fecal pH versus blood pH) and few studies to reference. A high stool pH is seen with non-specific diarrhea, crohn’s disease, ulcertative colitis, ileostomy [1970], the general spectrum of autoimmune conditions that CFS patients could drift into over time.  Giadia infections (cause of a CFS outbreak in Norway) appears to result in an increase of pH [2001] — suggesting a possible mechanism for CFS onset. The triggering event caused a pH shift which resulted in a change of bacteria. The change of bacteria seized the opportunity to keep the pH favorable to these bacteria. For example, ammonia producing bacteria would cause pH to increase.

  • “A shift to an alkaline environment stressful for bacteria as shown by how Escherichia coli responds to alkali with SOS and heat shock-like responses [18]; [19] ;  [20].”
  • B. subtilis initially grows rapidly and acidifies the medium.” [2005]

“An increase in the relative abundance of Bacteroides spp., Blautia spp., Parabacteroides spp., Coprococcus spp., Ruminococcus spp., and Oscillospira spp. and a decrease of Bifidobacterium spp., Lactobacillus spp., Escherichia spp., and Clostridium spp. were observed during weaning. The change in microbiome composition was accompanied by a gradual increase of fecal pH from 5.5 to 7.” [2016] That is, the result from going from human milk to cow milk in humans. Human milk have a pH of 7.4 [1986] while cow milk has a pH of 6.5 [source] and milk from different mammals are significantly different in composition [2004]



The reader asked about antibiotics. I have done some very rough charts on antibiotics and what they work against. The general group that this patient is high in are Bacteroides spp, with specific members being low — adding some complexities. Using Trends in antimicrobial resistance among Bacteroides species and Parabacteroides species in the United States from 2010-2012 with comparison to 2008-2009 [2017].Which suggest metronidazole or chloramphenicol or Carbapenem or beta-lactam/beta-lactamase inhibitor combinations. Based on the CFS patients survey on response to antibiotics, I would opt for metronidazole(a.k.a. Flagyl) as the first choice.

Bottom Line

Doing this analysis, I came across the pH aspect of CFS and will do further digging in the literature. My suggestions to discuss with a medical professional are:

  • Regular intake of food that are high in acid (which is different from food causing an “acid stomach”)
  • Metronizalole
  • Bacillus probiotics, see this post — some may not be suitable for everyone



Bacteremia and death from Probiotics

In the interest of full disclosure — there is a risk of bacterial infection from probiotics and yogurt, even death. The odds appear to be very low (likely a lot lower than many prescription drugs). In some cases, a single case of an issue have been circulated into a alternative-medicine legend that one or another probiotic should be avoided.

Some articles:


Animal Probiotics are called Direct-fed microbials

A reader forward me a link to the USA FDA approved probiotics for animals [FDA page]. The official list for humans is likely further restricted.  There are web-sites that specialize in the sale of these DFMs for animal use.

Approved Probiotics DFM

FDA and Association of American Feed Control Officials (AAFCO) approved microbial species are:

  • Aspergillus niger
  • Aspergillus oryzae
  • Bacillus coagulans
  • Bacillus lentus
  • Bacillus licheniformis
  • Bacillus pumilus
  • Bacillus subtilis
  • Bacteroides amylophilus
  • Bacteroides capillosus
  • Bacteriodes ruminicola
  • Bacteroides suis
  • Bifidobacterium adolescentis
  • Bifidobacterium animalis
  • Bifidobacterium bifidum
  • Bifidobacterium infantis
  • Bifidobacterium longum
  • Bifidobacterium thermophilum
  • Lactobacillus acidophilus
  • Lactobacillus brevis
  • Lactobacillus bulgaricus
  • Lactobacillus casei
  • Lactobacillus cellobiosus
  • Lactobacillus curvatus
  • Lactobacillus delbrueckii
  • Lactobacillus fermentum
  • Lactobacillus helveticus
  • Lactobacillus lactis
  • Lactobacillus plantarum
  • Lactobacillus reuteri
  • Leuconostoc mesenteroides
  • Pediococcus acidilactici
  • Pediococcus cerevisiae (damnosus)
  • Pediococcus pentosaceus
  • Propionibacterium freudenreichii
  • Propionibacterium shermanii
  • Saccharomyces cerevisiae
  • Streptococcus cremoirs
  • Streptococcus diacetilactis
  • Streptococcus faecium
  • Streptococcus intermedius
  • Streptococcus lactis
  • Streptococcus thermophilus

There is no normal or reference microbiome!

One of the common misconception is that there is a “normal” microbiome that can be used as a reference.  Below is a chart from “Metagenomic sequencing of fecal DNA“. Diet makes a major impact on the distribution and volume of the bacteria.

  • “In a study of gut bacteria of children in Burkina Faso (in Africa), Prevotella made up 53% of the gut bacteria, but were absent in age-matched European children.”[2010]

The chart below is for healthy individuals in 12 different countries.  In some cases neighboring very similar countries (Sweden [SE] and Denmark [DK]) have very different compositions.


This great variation means that testing the microbiome can only be done as group of individuals living in the same area with similar eating habits…. An individual result without reference from people with the same eating habits and possibly ethnic background is very fuzzy to interpret. Yes, highlights may be common — like low E.Coli, Lactobacillus and Bifidobacteria….  but they likely apply to no more than 80-90%, the other CFS patients may have different shifts.

People have asked me, “Did you get your microbiome done, what was it?” My honest answer was “No, such testing was not available when I last had CFS. I simply assumed that my pattern would be an appropriate match to that reported from the 1998 Australian studies”

Some Population Studies

“We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides– or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the “enterotypes” hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples’ Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the “enterotypes” and is not associated with other taxa across studies.” [2016]

” All Egyptian gut microbial communities belonged to the Prevotella enterotype, whereas all but one of the U.S. samples were of the Bacteroides enterotype.

  • The intestinal environment of Egyptians was characterized by higher levels of short-chain fatty acids, a higher prevalence of microbial polysaccharide degradation-encoding genes, and a higher proportion of several polysaccharide-degrading genera.
  • Egyptian gut microbiota also appeared to be under heavier bacteriophage pressure.
  • In contrast, the gut environment of U.S. children was rich in amino acids and lipid metabolism-associated compounds; contained more microbial genes encoding protein degradation, vitamin biosynthesis, and iron acquisition pathways; and was enriched in several protein- and starch-degrading genera.
  • Levels of 1-methylhistamine, a biomarker of allergic response, were elevated in U.S. guts, as were the abundances of members of Faecalibacterium and Akkermansia, two genera with recognized anti-inflammatory effects.
  • The revealed corroborating differences in fecal microbiota structure and functions and metabolite profiles between Egyptian and U.S. teenagers are consistent with the nutrient variation between Mediterranean and Western diets.” [2017]

“This suggests that similarities between the Inuit diet and the Western diet (low fiber, high fat) may lead to a convergence of community structures and diversity. However, certain species and strains of microbes have significantly different levels of abundance and diversity in the Inuit, possibly driven by differences in diet.” [2017]

Bottom Line

IMHO: There is no clear definitive benefit from doing an individual microbiome testing — there is no reference that is reliable for it on an individual basis at a fine level of details. On the other hand, having results showing abnormalities help in several ways:

  • It encourages you to make changes in eating which will usually be for the better
  • It confirms that you have significant shifts and supports the concept that the gut is causing your symptoms.