Analysis of Antibiotic triggered CFS Reader

Reader Notes

I’ve been debilitated with CFS since taking Levaquin in 2005. A few weeks ago I actually thought I was on the verge of some improvement but I found out how wrong I was. Last week I was given gentamicin ear drops for a minor ear infection caused by impacted wax. After just 3 doses I had to stop taking it because I started urinating extremely frequently. A day later I developed horrible intestinal burning sensations and, while in some ways I actually felt better, other symptoms became much more intense.

It seems that the ear drops likely caused something in my gut to bloom. I tried Miyarisan and VSL3 to see if they could mitigate the intestinal symptoms and both seem to help a bit, with the VSL3 working better, but the symptoms are only lessened for a few hours. I’ve also noticed round white spots, about a half inch in diamater, in my stools the last two days, which I’ve never seen before. I have a sample at ubiome now but I only sent it off two weeks ago and of course it was before I took the gentamicin so that sample may not provide insight, and I can’t wait six weeks or so for new sample results. Something is very, very wrong in my gut. Do you know of any other labs that have a quick turnaround that are trustworthy and provide a report that is actionable? The delay in getting results is so frustrating.

Anyway, it seems like my gut microbiome must have been very fragile to respond so horribly to just 3 doses of ear drops.

Standard Items:

  • Lactobacillus: 0.0x
  • Bifidobacterium: 0.36x
  • Akkermansia:  4.5x
  • Diversity:  13%ile
  • Firmicutes to Bacteroidetes: 1.2:1 (Normal 2.1:1) – shift probably caused by antibiotic

Uncommon Bacteria

Bacteria name Rank % of Samples
Dysgonomonas Genus 0.7%
Desulfuromonadales Order 1.2%

High Bacteria

Akkermansia:  3.22 X
Flavonifractor: 2.32 X
Bacteroides:  1.64 X


Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.


  • Bacillus subtilis
  • Bifidobacterium Animalis subsp. Lactis
  • Broad beans  and lupin seeds
  • Cranberry bean flour
  • Cranberry polyphenols
  • Daesiho-tang (DSHT)
  • Fasting
  • Fructo-oligosaccharides
  • Gallic acid
  • Grapes (table)
  • Green tea
  • gum arabic
  • Heme
  • High meat diet
  • High protein diet
  • Lactobacillus acidophilus
  • Lactobacillus plantarum
  • L-citrulline
  • Lingonberries
  • Low fat diets
  • Low processed foods diet
  • Melatonin
  • Metformin
  • Pomegranate ellagitannins
  • Resveratrol, Red wine, Grape Seed Extract
  • Rhubarb
  • Saccharin
  • Stevia
  • Tannic acid


  • Bacillus licheniformis
  • Bifidobacterium longum
  • Flaxseed
  • Garlic
  • High fat diet
  • Inulin
  • Lactobacillus kefiri LKF01
  • Lactobacilluscasei strain Shirota (Yakult brand only)
  • Omega 3 fatty acids
  • Polymannuronic acid
  • Sucralose (Splenda)
  • Walnuts
  • Whole-grain barley
  • β-Glucan

To the above, dairy should be added to increase the Firmicutes to Bacteroidetes ratio (see this post)

Comments on Antibiotics

The onset was due to Levofloxacin a member of the fluoroquinolones  family

  • “At the phylum level, both types of antibiotics (β-lactams and fluoroquinolones) tested caused a decrease of Firmicutes and increase of Bacteroidetes (p<0.001; FDR = 0.002) ” [2012] – agrees with the ratio above.
    • “Like all fluoroquinolones tested, levofloxacin did not cause a clear increase of the microbial load. However, it significantly affected 14 bacterial taxa, out of which 10 unknown Bacteroides and 1 unknown Coproccocus were 3 to 56-fold increased and 1 unknown Blautia was 2-fold decreased (p<0.01; FDR<0.09) “




  • “As for the gut microbiome, after the 4 days of antibiotics, total anaerobic bacterial count decreased from 8.5 log10CFU/g to 6.2 log10 CFU/g. Enterococci, coliforms and bifidobacteria decreased significantly as well. ” [2015]
  • “Gentamicin resistance, as assessed by the Stokes method, occurred in less than 2% of isolates of Escherichia coli, about 10–25% of most other enterobacteria, about 40% of Acinetobacter spp. and about 25% of Pseudomonas aeruginosa. This finding of relatively low rates of gentamicin in Enterobacteriaceae was surprising in view of the unregulated use of antibiotics until recent years.” [1989]
    • In other words, bye bye E.Coli, and many other families

You should insist on antibiotics that shifts your ratio closer to normal.,i.e. increase of Firmicutes and decrease of Bacteroidetes — your MD may need to do some research!

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.