Ask Eirik: How Can I Rebuild My Microbiome After a Course of Antibiotics?

All of the antibiotic substances that we humans have infused into our bodies and our environment over the most recent centuries have dramatically altered our relationship with microbes. We’re now in the midst of a pandemic of inflammation-related, chronic illness. Our reckless, widespread use of antibiotics has most certainly contributed to causing this dire situation. We made a huge mistake in thinking that antibiotics are harmless drugs. This mistake has come back to bite us – hard.

With that being said, antibiotics can save lives. They are obviously useful in some medical situations. Moreover, it’s certainly possible to recover following a course of antibiotics. If it wasn’t, pretty much everyone would be sick. 

I’m frequently contacted by individuals who have a less than friendly relationship with antibiotics. Many complain about gut and immune-related problems that developed after they’d been on a course of tetracycline, doxycycline, or other similar pharmaceutical agents. Others again have read about the dangers of antimicrobial drugs and are concerned about what will happen if they go on a course of antibiotics. What all of these people have in common is that they want to know if I have any tips as to what one can do to rebuild one’s microbiome following a course of antibiotics.

That’s what I intend to get into in this edition of Ask Eirik. The following e-mail, which I received today, will form the basis of the post…

Hello, Eirik! I’ve been a reader and promoter of your work for years now.

I’m about to begin oral treatment with an antibiotic called ciprofloxacin.

Do you have a special protocol that one can use after the treatment is done?

Or just your general recommendations, which I’ve applied for two years now.

My health is better than ever and in great part it’s thanks to you. So THANK YOU for your work!

Have a great day.
Greetings from Argentina
Matias

My reply:

Hi Matias,

I greatly appreciate that you’ve been promoting my work for so long. I obviously recognize your name (first name+surname), and I’ve noticed that you’ve been commenting on some of the posts I’ve put up on the site and on Facebook. If I’m not mistaken, we chatted a bit about meat in the comment section a while back. I very much value you and the other people I’ve recognized have been consistently following and promoting the site for many years.

It’s great that you’re well-prepared and are already thinking about how you can combat some of the microbiome-related problems that the antibiotic treatment you’re about to undertake may cause. You’re right to be concerned. That said, ciprofloxacin obviously won’t completely annihilate your microbiome. Also, it’s important to be aware of the fact that it doesn’t take billions of bacteria to make a difference. The antibiotic may wipe out the majority of the members of certain species of bacteria; however, if some cells remain, they may quickly grow and divide when antibiotics are no longer introduced into the system. Also, it’s important to remember that microbes are quick to evolve and swap genetic material between themselves. The use of an antibiotic drug initiates a Darwinian selection event in which those life forms that do best under the altered environmental conditions thrive, whereas those that are susceptible to the antibiotic agent face a rough time.

If I were you, I would focus on bringing new microbes into your system following the antibiotic treatment. I’d suggest that you temporarily consume small-moderate quantities of a diversity of fermented vegetables (preferably homemade) and eat some raw cabbage and other vegetables that have a lot of friendly bacteria clinging to them. Also, you should obviously make sure that you’re eating a species-appropriate, fiber-rich diet. Additionally, it’s great if you’re able to expose yourself to microbes harbored by healthy pets and/or humans, for example through hissing, cuddling, etc.

Chances are this is all that you need to do to get your microbiome back in shape. It may even be that you’ll find that you don’t really need to do anything special following the antibiotic treatment, in the sense that your microbiome may naturally rebalance itself as long as you adhere to a healthy diet and lifestyle. The chances of this happening will depend on the duration and strength of the antibiotic course and the status of your microbiome prior to the antibiotic treatment, among other things.

The worst case scenario is that you experience moderate-severe health problems (e.g., recurrent gastrointestinal distress, fatigue) as a result of the antibiotic treatment. If you experience diarrhea or other similar gut issues, you may want to consider consuming moderate-large quantities of fermented vegetables or kefir for a short period of time, so as to potentially decrease the pathogen load in the gut. If the problems persist over time you may want to consider performing one or more microbiota transplants or see if you can get a hand of capsules containing a diversity of organisms that were originally derived from a healthy human. But chances are it won’t come to that.

I hope that helps.

– Eirik