In January 2014, young and talented Romanian engineer Fabian Popa was feeling fine when pneumonia struck from nowhere. He remembers coming home from work and feeling a burning sensation in his chest. After a short time coping with the coughing, severe fatigue set in and Fabian found himself unable to work.

Having heard about the potential for unwanted effects caused by antibiotics, Fabian held out hoping the coughing would subside. After ten days he relented, and upon listening to his lungs, the doctor said: "Well, you have pneumonia. Take this antibiotic." And that's what he did.

Fabian took Bayer brand Avelox, a fluoroquinolone antibiotic. In the United States, similar drugs Ciprofloxacin ("Cipro") and Levofloxacin are more commonly prescribed. Everything was fine for a month, but then things started to go wrong in mysterious ways. The biggest signs that something was wrong were neurological in nature, and he experienced muscle weakness and twitching. Chronic diarrhoea set in and Fabian began to gain weight.

After exhausting his options in Romania, Fabian moved on to to Germany where he eventually got a diagnosis of an autoimmune disease called Hashimoto's thyroiditis.

In this interview, Fabian speaks candidly about his recovery from "iatrogenic" injury. Iatrogenesis (from the Greek for "brought forth by the healer"), doesn't necessarily imply an error, but rather an unintended outcome. Had he not taken the medicine, Fabian might not have been here to talk about his recovery. But still, the unwanted effects of the antibiotics were severe.

Fabian's story of recovery is incomplete but still inspiring. As an engineer, he applied his analytical and problem solving skills to blood chemistry, urinary organic acids, and stool culturomics to design a solution that consisted of diet and lifestyle modification and nutritional supplements. At the end of this interview, I asked Fabian: "Let me just check, you are feeling better than before aren't you?" to which he replied: "Yes, of course [...] Maybe next time we talk, I can report that there's autoimmune no more."

Here's the outline of this interview with Fabian Popa:

0:05:07 Fluoroquinolone antibiotics.

0:07:47 Hashimoto's thyroiditis.

0:18:43 Dr. Grace Liu, PharmD.

0:18:46 Dr. Tommy Wood, MD is the CMO at Nourish Balance Thrive.

0:19:33 Haptoglobin.

0:22:32 Diamine oxidase is one of the two enzymes that break down histamine, the other being Histamine N-methyltransferase.

0:23:06 Complement component 3 blood test.

0:23:59 Tumor necrosis factor alpha blood test.

0:25:37 Fabian used the autoimmune Paleo diet, my favourite guide is called A Simple Guide to the Paleo Autoimmune Protocol.

0:29:58 The Marshall Protocol (please don't do this!)

0:30:48 Tim Ferriss podcast.

0:33:58 Faecal microbiota transplantation (FMT) at the Taymount clinic.

0:37:03 Justin Sonnenburg presentation at the UCSF Paleo Symposium.

0:37:04 Diet-induced extinctions in the gut microbiota compound over generations.

0:38:54 Stool culturomics can be superior to metagenomics [1, 2, 3, 4, 5, 6, 7, 8]

0:39:46 uBiome and my report tool.

0:40:32 Iatrogenic injury.