Coiling for Lyme

Trying to cure one case of Lyme Disease

Microbes and Me

I’ve been mulling over my gut microbiology for the last month. It is amazing what a difference it has made to eat a variety of live cultures in fermented foods. My favorite, so far, is fermented cabbage (aka sauerkraut).

The reason I started on the fermented cabbage is that I want to get rid of my food allergies. I’d like to be able to eat the full variety of vegetables and grains that I love. I long believed that getting rid of Bartonella was all I needed to do to get rid of the food allergies. Then, after reading a few recent articles about the intestinal microbiome, I realized that I somehow needed to reseed my intestines with microbes that break down these foods to be able to digest them again. Mind you, I’ve been consuming vast quantities of probiotic pills for the past 7 years, but they have not been enough to get rid of the food allergies.

Anyway, this is part 2 of my personal history with microbes, both the malignant kind, like the tick-borne infections, and the beneficial kind that I’m doing my best to cultivate in my intestines. I’m doing this because as I ponder my own history, I’m finding my path to recovery.

Part 1, Learning about Host Microbiology, includes links to the articles that inspired my review of my medical history from the point of view of my microbiome. It also covers my relationship to antibiotics prior to contracting Lyme Disease as well as the effects of the first six years of harboring the infection.

Food Poisoning

Back in autumn 2006, my health was on a downward spiral. Without knowing it, I’d had Lyme Disease, Bartonella and Babesia, for over 5 years. My body was running out of the reserves that we all rely on to deal with stressful situations. I was having odd symptoms, mostly neurological, like mistyping and having difficulty making decisions. I was gaining weight (a key indicator of PCOS, which may have something to do with how our intestinal flora interact with our insulin regulation), slowly but surely, and my periods were getting more and  more disabling.

In December, I went on a vacation, to China, to, literally, get away from it all. I thought I was having trouble with too much stress. I guess I was, but partly it was because I couldn’t handle as much stress as I’d been able to before. In China, I had a fantastic adventure. Many of my symptoms seemed to be gone after the first few days.

Towards the end of the trip, the first week of January 2007, I ate dinner at a restaurant in a major city with my traveling companion and a handful of his relatives who we had stopped to visit. To me, the rice tasted a little funny. So after two spoonsful, I didn’t eat any more of it. However, all the people I was with ate lots of it. I got food poisoning, most likely Bacillus cereus, given that it came from rice and that my primary symptom was explosive diarrhea and extreme cramps that started the following morning.

Since then, I’ve wondered why I was the only person to get sick, especially since we all ate out of the same serving bowl. I wondered if because they served me first, as the guest, I got a contaminated portion that restaurant piled on top from an older batch of rice.

After reading Some of my Best Friends are Germs, by Michael Pollan, I have a new theory. Pollan explains that when there are E. coli outbreaks, many more people ingest the bacteria than the number that get sick, and the number that become mortally ill is an even smaller portion. The theory used to be that certain people were healthier, which didn’t quite match what health professionals saw on the ground. The newer explanation is that the make up of some people’s intestinal flora provides a stronger barrier and protects better against a given kind illness-producing bacteria. It could be that my friend, who in the 15+ years I knew him never took antibiotics, and his relatives, had guts that were in better condition than my own. So I got sick. And they didn’t.

To make matters worse, whatever the food poisoning did to my intestines and intestinal microbes, I had diarrhea for a long time afterwards — 18 months. I was also vomiting daily for several months. I somehow imagine that I got rid of the food-borne infection within a day or two, the normal course for B. cereus, but that it messed up my immune system so much that all the tick-borne infections went wild.

Between daily vomiting and diarrhea, I was pretty weak. I collapsed at work. I went home and took a few days to rest, doctor’s orders. I was back at work for two weeks before collapsing and getting sent home for three more weeks. When I tried to work again for a few days, I knew my number was up.

I was having problems with standing and walking, concentrating, headaches, nerve pain in my arms and hands. My tricuspid valve was making noise again, along with heart palpitations. I was weak. I still had diarrhea. I was a mess.

First Round of Antibiotics

I went to a gastroenterologist who did a colonoscopy and an endoscopy to figure out what was going on in my digestive tract. She informed me it wasn’t normal to have diarrhea and vomiting for so long or to be as weak as I was.

She didn’t find anything too abnormal. Although I had some E. coli, it didn’t seem like enough to be causing the problems I was having. She didn’t find evidence of any parasites or parasite eggs (though I imagine that the plastic liquid I had to drink before the procedure would have washed out anything macroscopic as demonstrated by the expulsion of a single flax seed that I consumed more than six months prior) or of anything other than non-specific irritation, whatever that is. Still, she thought there could be a problem that wasn’t obvious and gave me a course of Flagyl.

Flagyl, I later learned, is a great way to activate Lyme spores so that they can be killed by other antibiotics. So it sort of makes sense that my neurological symptoms got a lot worse while I was taking it. Of course, the reason for taking it was “empirical treatment,” as in, sometimes Flagyl makes diarrhea go away. Well, mine got worse. I took a pretty high dose for five days. Looking back, I wonder if this made the weakened colonies of beneficial bacteria even more weak. Or if it contributed to what later started to look like leaky gut syndrome.

The Flagyl made the vomiting go away, for which I was grateful.

Second Round of Antibiotics

A very smart friend who had picked up a parasite while traveling in a third world country suggested that I see an infectious disease specialist who focused on HIV, because they frequently see illnesses that regular doctors only run across once or twice in a career. She recommended a particular person who was no longer taking new patients. So I found someone else who fit the description.

Once again, the range of diagnostic tools gave no definitive answer. I was pretty bummed out. But the doctor gave me ten days of Cipro + Flagyl, suggesting that it would kill anything that didn’t belong in my body. Since I’d had some success with Flagyl, it seemed worth a try.

Cipro, I later learned, is an effective way to treat some strains of Bartonella. I also learned that a small but significant number of people develop long term digestive problems (diarrhea, undigested food, malabsorption) after taking Cipro. I even heard, by word of mouth, not from the results of any double-blind studies, that some people suddenly develop food sensitivities after taking Cipro, not from the antibiotic itself, but because it kills off so much of the intestinal microbiota.

A week or so after I stopped the Flagyl + Cipro combination, which made my diarrhea worse, the diarrhea stopped for a few days. My bowel movements weren’t normal, but at least they weren’t liquid. Then it came back.

Somewhere around this time, I developed an aversion to eggs. I had been eating them occasionally until the first dose of Flagyl. Then at some point, not sure of exactly the date, they didn’t look appetizing. In fact, the thought of eating them made me feel nauseated. (Of course, under those conditions, I was nauseated multiple times a day anyway.)

Also during the course of these drugs, I started having other problems, including low blood pressure, increased neurological pain, hypersensitivity in the skin on my legs (my pant legs caused excruciating pain), light sensitivity, extreme fatigue that caused me to sleep 14 hours a day, and night sweats. With antibiotics, I was feeling worse not better.An interesting thing I learned in Michael Pollan’s article is that repeated courses of antibiotics have a cumulative effect on intestinal microbes. When the antibiotics are taken close to each other, the microbial colonies grow weaker and weaker and take longer to reestablish themselves. Some species may die out, forcing the ones that are left to adjust, or leaving openings for not-so-beneficial bacteria to establish themselves or grow unchecked. The microbes that are left may be less able to serve their functions for the host person’s immune and endocrine systems.

Changing Course

The next thing I tried was Traditional Chinese Medicine. I saw an acupuncturist who thought every system and every organ and every life force (blood, chi, yin and yang) was depleted. She took me to an herbalist in Chinatown in NYC, where I lived at the time. It was summer 2007.

The herbs gave me a huge herx, only I’d never read about herxes at the time, so I was convinced there was some kind of toxic contaminant in the herbal concoction that was poisoning me. I managed to take the herbs for three weeks. It gave my intestines a rest.

The herbalist was not specifically treating me for Lyme or any other tick-borne illness. Her goal was to tonify my entire system. Some of the ingredients had antimicrobial properties, but these were incidental.

After I stopped the Chinese herbs, I started to feel a little better. Things were looking up, despite the persistent diarrhea. I thought maybe I would be able to go back to work in a month or so.


On Labor Day, I discovered that my intestines were severely damaged. I didn’t know that was what I was learning that at the time.

I had a few pancakes. I had been craving them for quite some time. An hour or so later, I started having serious neurological problems. The pain in my arms and legs was beyond anything I had experienced up to that point in time. I was dizzy. My peripheral vision was fuzzy. I was suddenly extremely weak and extremely sleepy.

I woke up the next morning with joint pain. Once it arrived, joint pain was a consistent companion for several years. The first few weeks, it was every joint. Eventually, it started to subside from some joints, sometimes, only to return again later.

Along with the joint pain, I started having abdominal swelling. It only lasted a week that first time. I’m not sure what caused it, whether it was swelling inside my intestines, swelling of my intestinal tissue, fluid retention or what. But my abdomen was big and hard. I was otherwise emaciated after months of diarrhea, but my abdomen made me look pregnant.

I don’t really know if the eggs interacted with the microbes in my intestines to cause this. Or if the eggs were poorly digested and “leaked” out of my intestinal tract, causing all sorts of inflammation. The eggs seem to have triggered an autoimmune response from my body, which went on to attack my nerves and joints, and maybe even my intestines. Possibly that attack made my body less resistant to the tick-borne infections which went on to cause more symptoms in my nerves and my joints. The latter were new symptoms that I hadn’t experienced since I got infected by the tick.

I sometimes wonder if the eggs inflamed my intestines so much that I started to become sensitive to other foods, the list of which I wouldn’t discover for several months. These foods may not have been digested fully by my intestinal microbes. Or, maybe the inflamed intestinal walls became permeable to other food substances.

Either way, the intermittent abdominal swelling that started in September became a chronic daily occurrence by November. My intestines were in bad shape. So were the rest of my internal organs. I can’t imagine that my intestinal microbes were thriving either.

End of Part 2


Categories: healing process

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