Where do I go from Here – Part #2

Synopsis To Date

Patient “M” has had progressive deterioration over 8 years with a single respite caused by the first of three fecal transplants. The relief lasted for only a few weeks.  To quote their own words:

The extreme severity of the condition combined with acknowledging:

  • my long history of complex and involved GI problems,
  • the fact I have now entered my eighth year of this illness
  • have been and remain in a free-falling overwhelmingly steep and ongoing decline
  • the evidence of the most ‘wrong-in-every-way’ stools of my life (indescribable but newish, hitherto unseen strands/strings of more jelly like stool amidst undigested matter and a mass of other ‘just wrongly’ textured mess’ )
  • near daily gut-pressure attacks that prevent eating for 17+ hours  and so much more

The goal of this post is try modelling the current state and thus the best path forward — suggestions to discuss with their health professional, not guaranteed solutions. Does the patient has Chronic Fatigue Syndrome — I really do not care, they have a gut dysfunction, a severe deteriorating dysfunction.


The simplest model is that a particularly virulent infection has became established in the mouth. Bacteria produces toxins against other bacteria and this bacteria toxins (sometimes called antibiotics – which is what they are) seems very effective against normal healthy bacteria. Usually evil bacteria tolerate each other, that is, are often immune to the toxins of each other. It is simple a case of like supporting like. This bacteria encouraged the settlement of other bacteria (the model of this one bacteria being out of control and being the sole source is naive – there is a shift across dozens of bacteria, some reduced, some increased).

Which bacteria could it be? I haven’t a clue, and likely no amount of testings will currently reveal it:

Cultural studies indicate that more than 500 distinct microbial species can be found in dental plaque. However, molecular methods of 16S rDNA amplification reveal an even more diverse view of the subgingival bacterial flora and suggest that a large proportion of even this well-studied and familiar microbial environment remains uncharacterised.” [2005]

There is a criteria that can be tested for and which branches the route taken:

  • If you have low or no E.Coli, then the “classic” CFS path is likely the best – it avoids all herbs that adversely impact E.Coli
  • If you have high E.Coli, then the path that I suggest for Crohn’s and other IBD is likely best. The suggestions below are for high E.Coli people,

Unless you take an extremely aggressive healthy probiotic (if one exists), it is unlikely that will dislodge the evil bacteria. The most probable path is to “nuke” the bacteria and then aggressively resettle afterwards. My usual path of encouraging the good and discouraging the bad may need to be abandoned for severe cases.

So, the suggestion for a game plan is to hit the infection hard first; perhaps seeing a Jarisch Herxheimer reaction (herx).  If a herx occurs, then wait until it weakens, switch to another anti-pathogen agent  and repeat. This was the path that I did with my 2nd round of CFS – I was in a state of herx for 6 out of 8 hours after each antibiotic (which was taken every 8 hours..). When the antibiotics did not produced it, I used potenators-fibrinolytic (see below) and biofilm breakers to increase the herx. Once a herx cannot be produced by any herb/splice/antibiotic then it is time for the probiotics.

Patient Experience Prior

Patient  “M” does not recall herxing from anything, Nystatin, Erythromycin, Mutaflor- with the possible exception of Allicin (from garlic)

Supplements that causes worst problems that persisted

  • Flaxseed and Linseed mixture


  • Linseed can cause severe problems have been reported back to 1903 in the Lancet [1903] [2013]
  • Appears to impact gut bacteria in sheep and cattle, no human studies [1961][2003] [2009]
  • Linseed and Flaxseed has antibiotic properties [2014]

The pattern appears to be that natural antibiotics did not impacted the evil bacteria but may have reduced some of those that kept them in check.

Battle Plan

The first goal is to try for a herx — simple as that, alternatively, because we have a visible symptom, a fuzzy tongue, would be improvement of that symptoms. In general, 4 days on an anti-pathogen is sufficient to produce a herx, if one is likely to happen.


Getting long term antibiotics, especially different ones in rotation, is getting harder and harder to have prescribed. I have known desperate people in the US who have exploited animal antibiotics (especially for dogs and cats) which do not always require prescriptions if done mail order[sample site that requires a prescription]  out of frustrations with MDs. It is not a recommended approach.

  • Often dentists will prescribe low dosage long-term antibiotics(from the tetracycline family) for gum disease –

My preference would be using the Jadin/Pasteur Institute schema of rotating antibiotics as a starting point.

Doxycycline (Tetracycline)
Ciprofloxacin (Quinolones)
Minocycline (Tetracycline)
Azithromycin (Macrolides)
Zithromax (Macrolides)
Clarithromycin (Macrolides)
Biaxin (Macrolides)

A uBiome report on the mouth bacteria may provide guidance for further antibiotics, but as stated above — the bacteria could in the uncharacterized biosphere.

Mouth infections – treatments

Since the origin is assumed to be the mouth, extra focus needs to be on this, in terms of conventional medical treatment (see below for teas/rinses)

  • A 0.2% chlorhexidine solution for two minutes daily [1995]

“Limited data exist regarding the effect of antibiotic use alone in treating periodontitis” (mouth bacteria) [2005]


At this point we have a decision point: is this the classic CFS Dysfunction with the typical shifts in certain families or is it “bacteria gone wild!”

I am inclined towards the latter and thus would advocate trying the Crohn’s herbs described in a prior post

  • Wormwood (Artemisia absinthium) [2014] – as effective as rifaximin 1200 mg daily
  • Rheum officinale: Rhubarb Root
  • Chitosan
  • Zingiber officinale: Ginger Root (Inji root)
  • Epilobium angustifolium: Fireweed or Willow Herb
  • Rosmarinus officinalis: Rosemary
  • Chrysanthemum lavandulifolium: Daisy
  • Scutellaria baicalensis: Chinese/Baikal Skullcap
  • Terminalia chebula: Haritaki
  • Cuminum cyminum: Cumin
  • Punica granatum: Pomegranate
  • Hibiscus sabdariffa L: Roselle or Sorrel
  • Withania somnifera: Ashwagandha
  • Salvia Plebeia
  • Trianthema decandra: Gadabani
  • Quercus infectoria: Oak Gall Tree
  • Allium hirtifolium Boiss: Persian shallot

To the above add the CFS herbs

  • Neem
  • Tulsi

The suggested flow is shown below:


The best starting point may be those that are easily available as teas — because there is likely a reserve in the mouth. Assuming the fuzzy tongue is a symptom of the main infection, you would want a few days drinking a lot of one tea to see if it makes any difference (visual on the tongue or otherwise). Teas are effectively water based extracts. This should be done as a systematic trial and error — recording results. Do not try everything at once — it is slow and systematic, taking notes constantly.

  • If you react strongly — make notes oh how and then make a call to continue or not. The notes can become a detective game to identify what may be involved.
  • If you do not continue, we will try with lower dosages later.
  • If it works for the good and you continue, wait until it’s impact stabilizes and then try the next tea (while continuing this one). Alternatively, you could stop it, and move on to the next — there can be arguments favoring both approaches.

I know for myself, we have found many as teas in Indian, Chinese or Russian Groceries at very reasonable prices (assuming you don’t mind the packaging being in Polish, Russian or Hindi). Eastern European suppliers often have much lower costs that is reflected on shelf prices when being sold to immigrants from those countries.

Mouth infections – treatments

  • Honey(any type!) has had positive result in PubMed [2014][2014][2013]
  • Teas (see above)

The Reinforcements

The reinforcements are items that increase the effectiveness of anti-pathogen agents.

” Bacterial biofilms cause chronic infections because they show increased tolerance to antibiotics, desinfective  chemicals and resist phagocytosis and other components of the defense system of the  body” [2009]

A few human bacteria that uses biofilms [2005] include:

  • Acidogenic Gram-positive cocci (Streptococc us sp.)
  • Gram-negative anaerobic bacteria
  • Non-typeable Haemophilus influenzae
  • Pseudomonas aeruginosa, Burkholderia cepacia Endocarditis
  • Viridans group streptococci, staphylococci
  • Group A streptococci
  • Gram-positive cocci
  • Enteric bacteria
  • Gram-negative rods Bacterial prostatitis Escherichia coli and other Gram-negative bacteria

In short, you should assume that biofilms is a major defense mechanism and make sure you are taking supplements to break them down.


Where do I go from here… Part #1

A new reader emailed me and provided a very detailed medical history and asked for suggestions. The reader knows that the issue is in the gut very well, is well educated in health issues and have seen several of the leading medical authorities. Almost all treatments failed to have any positive results.

Reader Beware

Before I go through my analysis of the information and make proposals to discuss with their health professionals. I should clarify that I am not a MD, nor a health professional. My current job title is Principal Software Engineer for a rapidly growing company that has received over $140 million in venture capital over the last year or so. In the past I have held Senior software positions for both Amazon and Microsoft; I get regular ongoing contact from Google HR to join their team (which would be a trifecta for my curriculum vitae). I was in a gifted child program and started to read medical journals at 14 yo, My Master of Science in Commerce topic was actually analysis of treatment effectiveness for different conditions by emergency service My particular strengths are:

  • Modelling systems, especially reduction of complexities to get to a reduced core model. I need to do this often when triaging problems with software systems, I have recycled that skill looking at auto-immune issues.
  • Not getting overwhelmed by complexities – if anything, I like to work with “rich-complex issues”
  • A systematic logical, disciplined mind — expected from doing a Honors Mathematics undergrad program. Nit-picking is a trait, which can be good or bad (depending on the people that you are working with).

And yes, I have had Chronic Fatigue Syndrome three times and recovered each time. I know and remember the helplessness of having a condition with no known effective treatment. Today, I have a working model that appears to be effective for me, I am in remission and believe that I can stay there by minimizing the risk of relapse be selected probiotics, herbs and prioritizing the appropriate lifestyle and life-decisions.  It is not a matter of what I want to do, but what is good for me.

A special class of CFS Patients

With the model of CFS being rooted in a gut bacteria dysfunction, there are thee main paths that could result:

  • The dysfunction auto-corrects (about 5% of patients at 6 months, 4% of the reminder in the next 6 months, with decreasing odds onward)
  • The dysfunction become stable and the patient stays in a stable pattern that waxes and wanes
  • The dysfunction increases, perhaps ending with a diagnosis of Crohn’s or other inflammatory bowel diseases. Typically once those diagnosis are made, the patient no longer qualifies for a CFS diagnosis.

This reader is in this latter class that has seen continuous deterioration over the years. It is dealing with these out of control microbiome that this and subsequent posts are looking at. These suggests are unproven, they are suggestions arising out of my model that I am look at.

Short Summary of Significant Factors for Patient “M”(IMHO)

Skipping over the common symptoms and focusing on the more unusual ones:

  • Three Stool/Fecal Transplants — first one “worked” but only for a few weeks, subsequent transplants did not
  • Distinguished list of world-class CFS specialists seen, and recommendations followed
  • Have gone to the most severe form of CFS, effectively bed-ridden
  • “furry tongue” – “was very much a feature of my symptoms when i had fairly severe gut problems aged 16-19″

The classic starting point is always the simplest model that explains most of the history.

Preliminary Analysis

What appears to bubble up as a model from my analysis is that there is a reserve of the bad bacteria is in the mouth, or between the mouth and the stomach.  This is consistent with re-population of evil-bacteria after a fecal transplant, and the logical flow: bacteria move from the mouth to the gut and not the reverse.

There could be two things happening : the mouth bacteria issue may be independent and simply thrive on the chemicals that the gut bacteria pumps into the system. Keeping to the simplest model, we will assume the mouth bacteria has repeatedly recolonized the gut [Reference]

Furry Tongue is associated with constipation according to WebMd. High numbers of staphylococcus and streptococcus was found on “M” before the first fecal transplant and different analysis at different time produced different results. Recent studies have found a high variability of populations of a person microbiome according to the time of day — the assumption of the population being stable over days may be incorrect.

Logical Course

Postulate: The root cause is bacteria in the mouth, with staphylococcus and streptococcus being significant contributors/support for other evil bacteria. The reader may have to address both gut bacteria and mouth bacteria. In an earlier post, I raised the issue that for some people there may be a significant reserve of evil bacteria in the mouth and/or sinus region. This should be assumed here.

Attacking the reserves

There are two ways of fighting the evil bacteria:

  • killing them off by herbs, antibiotics, etc
  • displacing them with healthy bacteria

The preferred sequence appears to be kill and then re-settle with healthy bacteria when dealing with major dysfunctions of gut bacteria. The evil bacteria should be assumed to be “thugs” and the good bacteria being very polite and civilized. A heavy hand seems like the best course.

Reducing the Reserve

The ideal situation would be herbs, spices, teas that can be kept in the mouth for a while. There are a number of them that are known to be effective, including (listed according to my preference):

  • Tulsi
  • Haritaki
  • Neem
  • Tumeric [2013]
  • Ashwangandha

There are some 60+ articles available on Pub Med for herbs and staphylococcus,  and just 19 articles for herbs and streptococcus. Many of the herbs are used in traditional Asian medicine and may be easy to obtain in locations with large Asian populations (and a challenge elsewhere).

Making teas or heated drinks of the above may take a little creativity. If the source is coarse enough, teas may be easy to make (or ready as tea bags – unfortunately, often at a much higher cost), or by boiling (effectively making a water extract) and then pouring thru a paper coffee filter.

An old “medicine” Licorice

As I am writing this, I am dealing with a sore throat and sucking away of Spezzata, a form of licorice. It seems to be a natural suggestion here, as this early post describes its action.This form is slowly dissolved in the mouth and thus saturates it.

Another old “medicine” Altoids

Altoids second ingredient is acacia gum a.k.a  gum arabic (right after the sugar :-( ). This is very much in agreement with it’s intent in 1780, by Smith Kendon, founder of Smith & Co., developed an exceptionally strong lozenge known as Altoids® mints, originally marketed to relieve intestinal discomfort, let alone a remedy for bad breath. Almost none of the newer equivalent products have gum arabic in it.

  • “The action of acacia gum against suspected periodontal pathogens and their enzymes suggests that it may be of clinical value.”[1993]
  • “Ten grams of gum arabic may produce a prebiotic effect in humans by boosting gut populations of specific bacteria”[2008]

On the down side, the EU Study group deem any impact has not been proven sufficiently[2002]. For a more recent review see this [2009] review.

Oral Probiotics

There are now available an increasing number of oral probiotics

  • Now Foods OralBiotic on Amazon (60 capsule for $14) – Streptococcus salivarius BLIS K12
  • Oragenics Evora Plus Probiotic on Amazon (30 mints for $16) – Streptococcus oralis, Streptococcus uberis, and Streptococcus rattus
  • Swanson Oral Probiotic: Blis K12® S. salivarius, L. rhamnosus, L. plantarum, L. reuteri, L. paracasei, L. salivarius
    • This one was a delight to find because it contains L.Reuteri which is hard to find in a probiotic. This one looks the most promising of all of the Oral Probiotics.

In terms of species available in these, they include:

  • Streptococcus salivarius BLIS K12
  • Streptococcus oralis
  • Streptococcus uberis
  • Streptococcus rattus
  • Streptococcus salivarius
  • Lactobacilus. rhamnosus,
  • Lactobacilus plantarum,
  • Lactobacilus reuteri,
  • Lactobacilus paracasei,
  • Lactobacilus salivarius

Taking the Herbs

The longer that the spices are in the mouth, the more bacteria should be reduced. There is a gotcha, the bacteria defends itself with biofilms so doing an oral mouth rinse of biofilm breakers such as EDTA and NAC should be part of the treatment(See this earlier post). Since these are both consumable, they could be added to teas described below (assuming the taste is not too bad!). Some teas are know to be effective (Ginger and Tulsi teas I like,  Garlic tea would be an experience!)

  • Ginger tea and Garlic tea – based on [2015] results for mouth bacteria.
  • Tulsi tea – demonstrated as an effective mouth wash [2014], and appear very effective [2014] [2011]

The above is intended to reduce the reserves, the items below can/should also be taken as capsules to address the gut bacteria.

Cost Savings

I usually advocate buying herbs such as Tulsi, Neem, Haritaki, Turmeric in bulk (typically $10-$20/lb) and making your own capsules. It is one way you can get certified organic supplements :-) at a very reasonable cost . The cost difference per capsule can be as high as 20x — which makes a huge difference for the budget.

In the above case, one could follow a similar pattern (instead of buying tea bags):

  • If the grind/herb is coarse enough, make tea in the old, pre-tea-bag method.
  • If the grind is too fine – consider getting coffee filters or reusable tea bags [Example, Amazon.Uk]

Is it working?

This is always the greatest challenge with any supplement — how to determine if it is effective, especially when it has a slow mechanism of action. For example, Vitamin D supplements may have no noticeable effects for months. We could hope to see a change of the fuzzy tongue. perhaps by taking “selfies” of the tongue daily (ideally with the same light conditions).

Bottom Line

Whether the mouth is really the reserve or not is immaterial with the targeting of the mouth above — whatever goes into the mouth, ends up in the gut! In my next post, I will explore a much more aggressive approach — taking off the boxing gloves of assuming only a CFS style of bacteria shift.

Zing — when a probiotic is TOO good!

Last week my wife tried Yakult with excellent results for reducing histamines, but the Lactobacillus casei Shirota also was too too much for her. All bacteria, including Lactobacillus produce antibiotics against selective other bacteria.  If you get too lucky, you can effectively get in a die-off / Jarisch–Herxheimer reaction that is out of control. With antibiotics, the substance will wash out of your systems in hours. With probiotic, the bacteria may take hold and keep pumping out it’s antibiotic endlessly! Not quite endlessly, but easily for 1-2 weeks of non-stop herx or longer.

Today I got pinged by a reader who had this type of reaction to Lactobacillus reuteri NCIMB 30242 (it is still going on weeks after stopping), a different friend also reacted similar with a different L. Reuteri species.

As a point of reference, L.Reuteri produces the following antibiotics:

So what kills Lactobacillus? The answer appears to be Penicillin, clindamycin and gentamicin, the antibiotics generally not recommended for CFS (because it kills Lactobacillus!)

The second path was taken by my wife, “Probiotic vs Probiotic”, she loaded up on other probiotics that she knew was safe and effectively starved out this species by over-populating her gut with other probiotics fighting for food.

Bottom Line:

There is a risk of a herx with any probiotic, and the duration may be much longer than that of an antibiotic, and the intensity may increase over time until it has finished it’s job.

Above I have described why it happens and why it is different than regular prescription stuff — you are using a living organism that may become resident.



Get every new post delivered to your Inbox.

Join 351 other followers

%d bloggers like this: