Antibiotic Apocalypse on the Microbiome

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
NameRankPercentileCountCommentMore Info
[Ruminococcus] gnavusspecies95.227410Not Healthy PredictorCitation
Anaerotruncus colihominisspecies97.95200Not Healthy PredictorCitation
Bacteroides fragilisspecies86.317220H02076 Bacteroides infectionCitation

Looking at the distribution by frequency, nothing really stands out.

0 – 91418
10 – 191934
20 – 291919
30 – 391214
40 – 49157
50 – 59915
60 – 691313
70 – 79815
80 – 89109
90 – 991518

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:

  1. rifaximin (antibiotic)s   (1)
  2. metronidazole (antibiotic)s   (0.887)
  3. 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)

Bacteria NameWeight
BIO-BOTANICAL RESEARCH / Megacidin [bacillus coagulans, bacillus subtilis]4285.54
miyarisan (jp) / miyarisan [clostridium butyricum miyairi]4130.42
enviromedica terraflora sbo probiotic [bacillus clausii, bacillus coagulans,bacillus megaterium
bacillus pumilus, bacillus subtilis]
INVIVO THERAPEUTICS / Bio.Me IB + [bacillus subtilis, enterococcus faecium]3716.08 / L. Plantarum Probiotic Powder [lactobacillus plantarum]3324.66
Of the bacillus, bacillus subtilis seems to be the best

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).

The consensus list is long with 534 items (typical). My main take away

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.