From a reader. His prior microbiome analysis is here.
A short update…
- About two months ago I had a sinus infection and got a week long course of Amoxicillin for it. Almost all my symptoms went away during the antibiotic treatment.
- Each day I was just waiting to get to take my daily dose, the improvement was so substantial.
- After finishing the course, it took about 48 hours until I was pretty much back to where I started.
- After the treatment stopped, the symptoms came back. Nothing changed in the end.
- But while on the treatment I felt great. I slept fantastic. All my pain went away. All my tired and wired symptoms went away. But the improvement did not persist.
- Two weeks ago I went to see a doc that I know fairly well, and told him what happened. After hearing my story, he gave me a month long treatment of Doxycycline. I do not know his rationale for not giving me Amoxicillin.
- Many years ago I also had a lung infection and was treated with Ciprofloxacin. It also removed the symptoms during treatment.
- The Doxycycline does nothing for my symptoms. It only creates an upset stomach, when Amoxicillin gave me no side effects except curing my CFS and MCS.
- Why does Amoxicillin help, but Doxycycline not? But not Doxycycline..the one antibiotic I managed to get a lot of..but it does not help.
Are there any conclusions to be drawn from this information?
We have this person’s microbiome uploaded, so first step is to just run “Just Give Me Suggestions”
- amoxicillin (antibiotic)s[CFS] is 590
- ciprofloxacin (antibiotic)s[CFS] is 191
- doxycycline (antibiotic)s[CFS] is 362
I then using the available data for these three to see what the other two does not — i.e. the smoking gun
| Taxa Name | Taxa Rank |
| Enterobacteriaceae | family |
| Moraxellaceae | family |
| Enterococcaceae | family |
| Aeromonadaceae | family |
| Pseudomonadaceae | family |
| Verrucomicrobiaceae | family |
| Morganellaceae | family |
| Atlantibacter | genus |
| Metakosakonia | genus |
| Pseudescherichia | genus |
| Limnobaculum | genus |
| Lelliottia | genus |
| Pluralibacter | genus |
| Kosakonia | genus |
| Shimwellia | genus |
| Roseimicrobium | genus |
| Rosenbergiella | genus |
| Brevifollis | genus |
| Pseudocitrobacter | genus |
| Franconibacter | genus |
| Siccibacter | genus |
| Gibbsiella | genus |
| Candidatus Moranella | genus |
| Candidatus Schneideria | genus |
| Candidatus Profftia | genus |
| Candidatus Riesia | genus |
| Candidatus Ishikawaella | genus |
| Cronobacter | genus |
| Phytobacter | genus |
| Mangrovibacter | genus |
| Biostraticola | genus |
| Luteolibacter | genus |
| Persicirhabdus | genus |
| Candidatus Regiella | genus |
| Haloferula | genus |
| Buttiauxella | genus |
| Leclercia | genus |
| Cedecea | genus |
| Trabulsiella | genus |
| Yokenella | genus |
| Raoultella | genus |
| Fucophilus | genus |
| Acinetobacter | genus |
| Pseudomonas | genus |
| Prosthecobacter | genus |
| Candidatus Phlomobacter | genus |
| Citrobacter | genus |
| Enterobacter | genus |
| Klebsiella | genus |
| Kluyvera | genus |
| Morganella | genus |
| Proteus | genus |
| Salmonella | genus |
| Shigella | genus |
| Aeromonas | genus |
| Plesiomonas | genus |
| Enterococcus | genus |
| Verrucomicrobium | genus |
| Scandinavium | genus |
| Jejubacter | genus |
| Sulfuriroseicoccus | genus |
| Entomohabitans | genus |
Next, we look at his last sample for these and found:
| Taxa Name | Tax Rank | Percentile |
| Enterobacter | genus | 73.64152 |
| Enterococcus | genus | 69.35996 |
| Lelliottia | genus | 68.33713 |
| Enterococcaceae | family | 62.73872 |
| Enterobacteriaceae | family | 60.38241 |
| Enterobacterales | order | 59.50287 |
| Klebsiella | genus | 54.63183 |
| Klebsiella/Raoultella group | no rank | 54.63183 |
| Pseudomonadaceae | family | 41.17647 |
| Pseudomonas | genus | 41.0804 |
| Verrucomicrobiaceae | family | 21.69038 |
| Verrucomicrobiales | order | 19.43128 |
| Aeromonadaceae | family | 17.55486 |
| Moraxellaceae | family | 14.05018 |
Next step is to look at the combinations of these top 3 bacteria to see how they rank (percentile) in combination
- Enterobacter,Enterococcus – 72%ile
- Enterococcus, Lelliottia – 75%ile
- Enterobacter, Lelliottia – 74%ile
- Enterobacter, Enterococcus, Lelliottia – 79%ile
The presence of Lelliottia makes things marginally more significant.
Looking at the Taxa Tree
One possibility is that the cause of not a genus that is reported with 16s tests. Looking at the tree we can determine the “unknowns” The Family is 910 from which we remove (150,70,230,40,10) ending with 410 unclassified i.e. almost half of the bacteria in Enterobacterales are not identified. Any smoking gun may be hidden in the deficiencies of 16s testing.
Where we are
We do not know precisely the bacteria involved with ME/CFS and MCS. For this person, the antibiotic history does allow us to identify possible candidates. The next question is obvious, which antibiotics should we suggest to the MD? We have the consensus list and we want to reduce it to those that impact these three bacteria as the most likely to help.
For all three bacteria, we have the following list (Note that the [CFS] indicates that it is often used by ME/CFS Specialists)
| Weight | Antibiotic |
| 769.5 | tobramycin (antibiotic)s |
| 608.2 | amikacin (antibiotic)s |
| 590.4 | amoxicillin (antibiotic)s[CFS] |
| 563.5 | gentamicin (antibiotic)s |
| 441.6 | imipenem (antibiotic)s |
| 388.6 | streptomycin (antibiotic)s |
| 380.1 | erythromycin (antibiotic)s[CFS] |
| 326.5 | azithromycin,(antibiotic)s[CFS] |
| 301.6 | intesti-bacteriophage |
| 261.3 | vancomycin (antibiotic)[CFS] |
| 191.2 | ciprofloxacin (antibiotic)s[CFS] |
| 178.7 | clarithromycin (antibiotic)s[CFS] |
| 86.5 | rifaximin (antibiotic)s |
| 81.2 | carbapenem (antibiotic)s |
The challenge is now persuading the MD to prescribe these based on the microbiome sample and this analysis. Next we look at alternatives.
Non Prescription Approaches
As above, we restrict to those items that reduces all three of the above bacteria
- ALL probiotics were negative
- Nothing for Amino Acid and similar
- Nothing for Prebiotics and similar
- Nothing for Food or Diet Style
- Nothing for Vitamins and Minerals (Vitamin B2 was just a 2)
- Hesperidin (polyphenol) – was over 800 and the only Flavonoids, polyphenols with a positive value
- N-Acetyl Cysteine (NAC) – was over 700 and the sole common supplement
- chitosan,(sugar) – was 200’s and the sole sugar
Herbs and Spices
I have also been trying multiple different herbs. The one which so far has given the best effect is an alcoholic tincture of Artemisia Annua.
From reader
Wormwood(artemisia) is a 21 (minor positive impact predicted). It reduces some genus of Enterobacteriaceae but nothing reported for Enterococcus, Lelliottia or Enterobacter.
| Priority | Modifier |
| 329.4 | foeniculum vulgare,fennel |
| 294.4 | laser trilobum l.,kefe cumin |
| 289.6 | hypericin, St. John’s Wort |
| 213.1 | neem |
| 164.6 | tulsi |
| 118.7 | garlic (allium sativum) |
| 105.9 | Curcumin |
| 23.6 | triphala |
| -20.5 | cinnamon (oil. spice) |
| -49.6 | oregano (origanum vulgare, oil) | |
| -87.4 | persimmon tannin |
| -143.2 | Dangshen |
| -313.3 | berberine |
Suggestions to discuss with MD
If antibiotics are not viable then the following seems to be the best choices
- Hesperidin (polyphenol)
- N-Acetyl Cysteine (NAC)
- Foeniculum Vulgare, Fennel
- laser trilobum l.,kefe cumin
- Hypericin, St. John’s Wort
- Neem
Hesperidin..very interesting herb. It says to assist with blood flow and blood vessel health, exactly the type of issues I am dealing with. I will try it.
Feedback from person on draft
Bottom Line
This was a very interesting post because we seem to be able to identify the family of bacteria involved with this person’s symptoms Enterobacteriaceae. This agrees with the literature.
- “The prevalence and median values for serum IgA against the LPS of enterobacteria were significantly greater in patients with CFS than in normal volunteers and patients with partial CFS.” [2010]
- “Often, a lower Bacteroides/Firmicutes ratio can be accompanied by an increase in Enterobacteriaceae, therefore suggesting a complete reshuffling of the gut microbiota composition” [2021]
- “Increased Serum IgA and IgM against LPS of Enterobacteria in Chronic Fatigue Syndrome (CFS): Indication for the Involvement of Gram-Negative Enterobacteria in the Etiology of CFS and for the Presence of an Increased Gut-Intestinal Permeability” [2007]
I do have a concern that almost 50% of the genus in Enterobacteriaceae were not identified in the sample. We are in a bit of fog — which we will address by assuming it will also be sensitive to it sibling genus.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
CFS Remission 