This is an interesting case which appears to illustrate well that microbiome-agnostic prescription of antibiotics can produce horrible results. Doing a yearly 16s microbiome test will allow you to potentially negotiate with your MD to pick antibiotics that both address the MD concerns and potentially improve your microbiome as a side effect. See this post: Negotiations with your Medical Professional
My backstory:
I have used FQ antibiotics many times in the last 15 years for Chronic bacterial prostatitis..
During the last few years I was diagnosed with diverticula and had an episode of diverticulitis 3 years ago which also required antibiotics.. In the last 2 years my bloating was so severe that I was like a pregnant woman.. I am a male 40 years old.. So last July I went to the beach and caught E.Coli once again from the water or the beach.. This gave me acute infection with fever the next day.. This is where the drama starts as I ended up going to 4 different labs giving me different results and switching antibiotics for 5 months.. My gut was so bad that I’ve spend one night at the WC and another day I was stuck in traffic and I didn’t come back in time.. So embarrassing..
So January I stopped the FQs since I got a severe reaction with a set of symptoms that almost took my life.. My calf tore while being in bed, not even walking, swollen joints with fluid, tinnitus, diarrhea for 1 month, stomach ache and spasms, neuropathy, brain fog, insomnia and more..
I was sure that everything started from my gut, something triggered auto-immune along with toxicity from the drugs.. 2 months in bed.. 4 months and I barely walk with many symptoms.. What saved me initially I think was homemade Kefir I had and making myself..
Then I did the test at Biomesight and understood why and what happened.. Now I know very well that life or death starts from the gut..
Current State
First, I like to get a feel for where the microbiome is at from a high level. Looking at the usual health measures:
- Dr. Jason Hawrelak Recommendations guidance puts the person at the 35%ile, definitely in the concerning space
- On the Potential Medical Conditions Detected, 14 items were flagged, again concerning
- In the Bacteria deemed Unhealthy list, the following stood out
| Name | Rank | Percentile | Count | Comment | More Info |
|---|---|---|---|---|---|
| [Ruminococcus] gnavus | species | 95.2 | 27410 | Not Healthy Predictor | Citation |
| Anaerotruncus colihominis | species | 97.9 | 5200 | Not Healthy Predictor | Citation |
| Bacteroides fragilis | species | 86.3 | 17220 | H02076 Bacteroides infection | Citation |
Looking at the distribution by frequency, nothing really stands out.
| Percentile | Genus | Species |
|---|---|---|
| 0 – 9 | 14 | 18 |
| 10 – 19 | 19 | 34 |
| 20 – 29 | 19 | 19 |
| 30 – 39 | 12 | 14 |
| 40 – 49 | 15 | 7 |
| 50 – 59 | 9 | 15 |
| 60 – 69 | 13 | 13 |
| 70 – 79 | 8 | 15 |
| 80 – 89 | 10 | 9 |
| 90 – 99 | 15 | 18 |
Looking at the antibiotics list taken, I went over to the Antibiotics List for MDs page for this sample. We are using this to see which antibiotics likely helped the dysbiosis of the gut to happen.
The following were the antibiotics that he had been prescribed. I put after each the positive and negative estimates from the above page. We see a -.266 for something taken for 84 days…
- IV Cipro 1 time in hospital
- Cipro oral cycles (21 days) : 5x – (0.194)
- Norfloxacin cycles (14 days) 6x (0.282)
- Levofloxacin : 10 days – no data
- Fosfomycin: 8 sachets – no impact
- Cefaclor cycle (14 days): 12x – negative impact (Take Estimate: 35.1, Avoid Estimate: 39) (0.079)
- Amoxicillin / Clavulanic Acid cycles (21 days): 4x ( – 0.266 )
- Cefixime cycle (24 days) : 1x ( – 0.114 )
- Trimethoprim / Sulfamethoxazole : 3 days (0.128) / ( – 0.604 )
- Doxycycline: 2 days ( – 0.173 )
In this case, it is clear from the data above that the antibiotics were a factor for his problems. if he must take antibiotics again (or can persuade his MD to do a trial), the best ones suggested by the Artificial Intelligence algorithms are:
- rifaximin (antibiotic)s (1)
- metronidazole (antibiotic)s (0.887)
- ampicillin trihydrate (antibiotic) (0.834)
Action Plan Going Forward
The KEGG AI Computed Probiotics had the HIGHEST VALUES that I have ever seen with the top items being, I would go for three of these (2 weeks of one, then rotate to the next, repeat): Something that lists bacillus subtilis as the first ingredient, miyarisan (jp) / miyarisan, something that is just lactobacillus plantarum (i.e. 299v)
For supplements, we have (even at 20%) a short list. Usually supplements can be taken consistently.
- beta-alanine – Percentile: 5.2
- Glycine – Percentile: 3
- L-Cysteine – Percentile: 10.4
- L-glutamine – Percentile: 15.5
- Magnesium – Percentile: 3.7
- Molybdenum – Percentile: 0.9
Building Consensus Suggestions
Remember, no one knows how to pick the best bacteria to target. We apply multiple criteria and then work from what is agreed upon with the different approaches (i.e. consensus).
- Use JasonH (15 Criteria) – 11 bacteria picked (and the same for the other ones at the top of this list)
- Standard Lab Ranges (+/- 2 Std Dev) – 24 bacteria picked
- Box Plot Whisker – 58 bacteria picked
- Kaltoft-Moltrup Normal Ranges – 89 bacteria picked
- Percentile in top or bottom 10 % – 101 bacteria picked
The consensus list is long with 534 items (typical). My main take away
- Eliminate/Avoid the following:
- high red meat / high-protein diet / high animal protein diet /high saturated milk fat diet/ milk-derived saturated,fat / animal-based diet / rare meat / fat
- Dairy related: Cottage Cheese / Kombucha (home-made) / enriched butter diet
- low energy diet/ calorie restriction / low carbohydrate diet / gluten-free diet
- stevia / saccharin / chitosan,(sugar) / high sugar diet
- broccoli / Sauerkraut
- alcoholic beverages
- high red meat / high-protein diet / high animal protein diet /high saturated milk fat diet/ milk-derived saturated,fat / animal-based diet / rare meat / fat
- Take or Increase:
- inulin (prebiotic) / chicory (prebiotic) / oligofructose (prebiotic)
- high fiber diet / fruit/legume fibre / brown rice / whole-grain barley /whole-grain wheat / barley,oat
- walnuts
- Cacao
- Vitamins and Supplements
- Vitamin B-12 (Cyanocobalamin)
- grape polyphenols / grapes (but no wine!) / polyphenols
- from above: magnesium (found in consensus too with positive value), molybdenum and from consensus: selenium and zinc. But no iron supplements.
- Probiotics
- All of the items cited above are on the to take list (and many more), but the ones above are IMHO, “double blessed”
- A reminder, the items are based on the term that various studies used. In some cases, there can appear to be contradictions. In some cases this could be due to what was measure or not measured in the study as well as sample size. We do not know what is “right” when this happens, it drops into a state called “indeterminate”. There are some of those here, but also some very clear items like high fat beef.
Bottom Line
Given the severity of this person, I suggest trying suggestions for 2-3 months and then gets retested. I expect significant changes — but that is likely just a course correction. We need to do more course corrections to get back to a safe harbor.
ALWAYS REVIEW WITH YOUR MEDICAL PROFESSIONAL BEFORE STARTING
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