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Back Story

I’m male, 5’ 10”, currently 145 lbs, 60 years old. I first became ill suddenly in 1987, with what at the time seemed to be food poisoning or a stomach bug. The nausea, stomach upset and loss of appetite lasted months after, I became bedridden. Dozens of tests, doctors, revealed nothing.

Gradually over time, the symptoms subsided and I began to eat and gain weight again. After about a year and a half, I became functional, but never recovered to my previous state. This has been the course of life since. The symptoms would reoccur, last several months, then subside. With no definitive cause for beginning, nor treatment for ending.

The ongoing fatigue over the years was relentless. I somehow managed to complete a 30 year carrier, and took retirement at first opportunity. Doctors speculated that my work was a stress factor responsible for my condition, and retirement would solve it. It didn’t.

For the past several years, I’m mostly housebound, able to go outside and do minor tasks on occasion. Currently, my worst of symptoms are LPR/ reflux related. Not in the traditional sense, mine is a gas/ aero, that I believe is being caused by severe dysbiosis/ imbalance.

I cite this study as an example,

Accompanied with voice loss, throat and chest pain, severe at times.

A recent endoscopy showed “mild gastritis”. Doctors offer me benzodiazepines and antidepressants, stating my symptoms do not correlate with their findings.

Previous endoscopes/ colonoscopies were unremarkable. Gastric empty test normal.

I have tested negative for SIBO several times. IBS Smart test, h pylori, celiac, mast cell (MCAS), all negative.

Numerous diets, eliminations, supplements, herbs, prescribed medications have brought no help or relief. Most have made symptoms worse.

I did manage to have a biopsy taken and sent to Dr John Chia, to test for entero virus. It came back highly positive, however, I am somewhat skeptical that it could be a red herring. My vague attempts with pre/ probiotics resulted with increased gas and/ or diarrhea.

One clue, on two occasions (1995, 2014) after having colonoscopy, I mysteriously had remissions afterwards, that lasted several months. The speculation, is that the prep somehow created a reset of bacteria/ flora. I recently tried to replicate, by doing a prep cleanse. However, despite drinking a full gallon plus, I ran out of solution before being completely cleared out. I felt a brief improvement, but have suffered with horrid lower gas/ flatulence since.

Not the result I was after.

Initial Comments on Back Story

For myself, stress was the trigger of each of my ME/CFS episode so the speculation by his MDs was reasonable. The 1987 event, and the resulting cascade of the microbiome is the root concern. The microbiome evolves, just like society evolves. In 1987, most homes had a VCR and a few lucky people had digital pagers. Today, very few have VCRs (in use) and almost every one has a smart cellular phone. In 2023, arguing whether the right choice should be BetaMax or VHS has become irrelevant. Similarly, focusing on the cause in 1987 is really irrelevant. It may have been a virus, Lyme disease or a dozen other culprits – it is very unlikely to be relevant to addressing today’s microbiome.

Analysis

Looking at the distribution by frequency, we see an over-population of bacteria with low levels.

The Bacteria over 90% and Bacteria under 10% are a simple statistic to understand. If you have 188 different genus and true randomness then you would expect around 19 in each group. We has 12 over 90%, close, but a whopping 61 under 10% — that 32% of all bacteria, not 10%!!! In other words, we have a massive number of different bacteria at low levels. It is not a problem of a few bacteria being too high.

Percentile	Genus	Species
0 – 9	61	76
10 – 19	20	16
20 – 29	14	16
30 – 39	9	8
40 – 49	15	20
50 – 59	14	14
60 – 69	16	20
70 – 79	10	22
80 – 89	17	22
90 – 100	12	21

Looking at Dr. Jason Hawrelak Recommendations for levels, he was at the 99.7%ile and the very few misses for being ideal.. they were border line.. (i.e. 15.1 versus 15; 0 versus 0.0001). In short, almost an ideal microbiome by that criteria.

Going Forward

Doing the usual 3 suggestions sets, we

•  Standard Lab Ranges (+/- 2 Std Dev) – 9 bacteria
•  Box Plot Whisker – 43 bacteria
•  Kaltoft-Moltrup Normal Ranges – 85 bacteria

The list of top suggestions look very close to what I was taking for my own remission (pre-microbiome analysis days).

• rosmarinus officinalis (rosemary)
• thyme (thymol, thyme oil)
• peppermint (spice, oil)
• lactobacillus paracasei (probiotics)
• lemongrass oil
• Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
• neem
• syzygium aromaticum (clove)
• Sumac(Rhus coriaria)
• cinnamon (oil. spice)
• Ajwain (trachyspermum ammi)
• Curcumin
• lactobacillus casei (probiotics)
• thiamine hydrochloride (vitamin B1)
• aloe vera
• ashwagandha (withania somnifera)
• garlic (allium sativum)
• olea europaea (olive leaf)

Looking at the to-avoid

• vsl#3 (probiotics)
• walnuts
• lactulose
• amaranth
• barley, oat
• arabinoxylan oligosaccharides (prebiotic)
• fish oil
• saccharomyces cerevisiae (probiotics)
• low protein diet : typically seen when B-vitamins are wanted.

The full details are below

Going over to the Food Site we see:

• Chicken and Turkey Liver being at the top of the list

mg per 100 grams	Significant amount	Nutrient
25800	Significant	Protein
13.925	Significant	Niacin
12.9	Significant	Iron, Fe
4.293	Significant	Retinol
2.313	Significant	Riboflavin
0.84	Significant	Pyridoxine (Vitamin B6
0.56	Significant	Folic acid
0.02113	Significant	Vitamin B-12

Pass 2 — Looking at Prescription items

One non-prescription showed up near the top, an item that I have used with good effect: monolaurin. The top antibiotics list include:

• piperacillin-tazobactam (antibiotic)s [Penicillin]
• benzylpenicillin sodium (antibiotic) [Penicillin G]
• hyoscyamine (l),(prescription) – “It can treat muscle cramps in the bowels or bladder. it can treat symptoms of irritable bowel syndrome (IBS), colitis, and other digestive problems.” [Src]
• minocycline (antibiotic)s [Tetracycline] – used by many ME/CFS physician, and also by me. It has many good characteristics (neuroprotective, cross body-brain barrier, etc)
• tobramycin (antibiotic)s – usually only used for eye infections
• ampicillin (antibiotic)s [Penicillin]

The above have various risks, and should be review carefully. My own preferences would be minocycline first, then hyoscyamine [because IBS is a factor for this patient]. I should note that using a different algorithm without consensus (Special Reports for your MDs) reports contrary results.

Feedback on Antibiotics

Another freak incident that resulted in a five month remission. In 2011, I had one tonsil that became huge. The other remained completely normal. Doctors were suspect of cancer, and both were removed. Thankfully, it was not cancer. So they didn’t look any further to determine the cause.

But at 49 year old, this was no picnic. Rough surgery and recovery, but it followed with probably the most significant remission of all. It was an amazing turn around, all symptoms backed off, energy returned to nearly normal. After 5 months though, symptoms began to return, and within the year I was back to my previous state

I was on amoxicillin for several weeks after the surgery. When the symptoms began to return, we became suspect that it was the amoxicillin that had done something. My doctor put me back on it, but there was no improvement. Whatever had taken place, was a random-chance occurrence. Maybe the amoxicillin was responsible, by creating a shift in bacteria balance.

I found that Cecil Jadin’s protocol is what I tend to advocate. One of the key reason is that it was it was tuned from many years of clinical experience at the Pasteur Institute for Tropical Medicine for what they termed as an “Occult Rickettsia” infection. The basis of it is rotating different families of antibiotics. The mathematics are simple — first round may eliminate 90% of the issues with 10% being resistant. A different antibiotic usually require a different type of resistance, so 90% of the remaining 10% is eliminated.. leaving just 1%. Doing a third round, takes us down to 0.1%

I speculate that the few survivors from your first round of amoxicillin slowly rebuild . Because these bacteria were the survivors, those with resistance genes. The repopulated gut was largely resistant, hence no effect from this antibiotic later. Think of it as a boxing match. You landed a good punch — but instead of landing more punches, the opponent was able to recover and block the same punch later.

Later, discussion of this story with a well-meaning gastrologist, he had me do a week of xifaxan. He felt certain, based on my story, it would get me back to the previous gains. It made me horrid sick, lasting for weeks after stopping it. There was no improvement.

My preference is not to pick antibiotics by symptoms (or what worked for the prior patient), but from the bacteria results that are desired. Results are not guaranteed — rather, IMHO this approach has higher probability of being successful.

Looking at Probiotics

First, using KEGG data: as is typical for most ME/CFS people (and consistent with the ME/CFS conference reports from 1998): Escherichia coli (Symbioflor-2 or Mutaflor). The next common one is Bacillus subtilis (natto), Clostridium butyricum, Lacticaseibacillus casei, Enterococcus faecalis.

From the consensus list we see a good overlap and have in order:

• lactobacillus paracasei (probiotics)
• lactobacillus casei (probiotics)
• lactobacillus casei shirota (probiotics) – Yakult
• bacillus subtilis natto (probiotics)
• symbioflor 2 e.coli probiotics

bacillus subtilis natto is the source for a supplement called nattokinase, which dissolves fibrin deposits and also an anti-inflammatory [2021]. It is also available not as a probiotic, but in a Japanese Dessert Food called Natto. Natto is an acquired taste.

My probiotic suggestions would be the following (at sufficient dosage, see this page):

• 2 weeks of Bacillus subtilis (perhaps 10 BCFU daily)
• 2 weeks of lactobacillus casei (perhaps 48 BCFU daily)
• 2 weeks of one of the E.Coli probiotics (Mutaflor: 4 capsules per day, starting at 1 and slowly increasing)

Then repeat. Note that some probiotics are strong avoid, for example: saccharomyces cerevisiae / saccharomyces boulardii.

Taking Herbs

There are a large number of herbs cited above. In keeping with my philosophy of avoiding resistance, take some of herbs for 2 weeks and then change to others herbs for the next two weeks. The question is how to take it? I know that some will claim that tinctures are more effective; IMHO, tinctures are very effective for reducing back accounts!

My personal practice is to take herbs in one of two ways:

• Buying them in bulk, organic and making our own 000 capsules. Most store purchased herb capsules do not appear to be organic, often with additional ingredients “to make them better” – which is often marketing hype.
  • We take them immediately prior to meals so that the stomach acid produced to handle the meal, also dissolves the active ingredients from the herbs.
• Taking them as a hot tea. Some herbs are horrible tasting… those tend to end up as capsules.

Many, but not all, herbs have documented dosages with links to studies (which can be informative for how to take). For example: Neem: 120 mg/day, Olive Leaf: 700 mg/day, Curcumin: 3 gm/day. My general rule of thumb is one 000 capsule with each meal.

Questions

Q: Curious to know, do you think there may be an advantage of using this method with probiotics, to deliver past the stomach, farther down the gut?

A: I know this common belief, but have not seen any clinical studies demonstrating it. What I have seen is probiotics delivered as a liquid in water, are documented to persist for weeks after a single dose. That is, the specific strain delivered was not detected before but was detected in subsequent weeks. This indicates that this belief is very questionable. Personally, I tend to use single documented strains of probiotics from Custom Probiotics and follow their directions. I do keep food at least a hour away from taking probiotics so stomach acid production will be quiet.

On a related issue, remember that the gut is downstream from the mouth and nasal passages. The source of bad bacteria may be there and may account for repopulation over time. One probiotic that has been shown effective for the nasal passages etc is Symbioflor-1. There are a few hard tablet probiotics out there (for example, Miyarisan — Clostridium butyricum). I have often just put them in my mouth and let them dissolve there.

NOTE: I will be doing a follow up post on The oral microbiome, coming soon!