Antibiotics: Take care of yourself (and your microbiome)

It’s easy to override what your body is telling you, especially when you have a calendar bursting with commitments. However, pushing through an illness—especially one that requires antibiotics—is not a good idea.

Prevention is always best (but not always possible)

During the approaching cold and flu season, you may expect to be keeping tissues and lozenges nearby for a week or two. It would be nice if we could count on prevention, but most of us have to be around other people (and their illnesses) on a daily basis. You know the basics: be sure to wash your hands and get a flu shot. But short of donning full-body protective gear, you’re probably going to be exposed to a number of bugs.

And unfortunately, some of those bugs will make you ill. And sometimes, seemingly minor symptoms hang on and/or turn out to be bigger problems. If you find that your “cold/flu” symptoms are lingering or worsening, check in with your doctor. Don’t put it off. You may be surprised to walk away from your appointment with a prescription for antibiotics to fight off what you thought was just a tenacious cold. 

At Ixcela, we frequently hear questions about antibiotics, and for good reason. Antibiotics pretty much wipe out your gut microbiome, and it can take some time to rebuild it again. It’s true that antibiotics aren’t great for the organisms residing in your gut, but these drugs exist to fight infections and keep us alive and well.

If you’re an Ixcela client, you’re familiar with a few of the metabolites that come from the gut and you know how important it is to maintain just the right balance to help you feel your best. So, what can you do when you have spent so much time making positive changes to improve your gut health, only to have to undo your progress with antibiotics? Don’t despair.


Feel better while taking antibiotics

Take the drug properly

First, get rid of the infection by taking your medications properly. I can’t stress this enough. Not all antibiotics are the same. Don’t just skim the instructions for your prescription. This information can be detailed and how you take the drug is a big deal—not a suggestion. Get answers to any questions you have and make sure to tell your doctor about every vitamin, supplement, and medication you take. Many supplements will interfere with how an antibiotic works in your body. 

There may be all sorts of specific guidance that wouldn’t occur to you. Take enough water with the pills. Take with food or on an empty stomach. Even standing up or reclining can be a factor in how certain antibiotics affect you. If you don’t follow the instructions, the drug won’t be fully effective and it may take a further toll on your body.

Ease side effects

The side effects of antibiotics include (but aren’t limited to) an array of unglamorous symptoms: diarrhea, nausea, bloating, stomach pain, and vomiting. They can leave you feeling pretty awful. 

Thankfully, there are a few simple things you can do to feel a bit better. 


  • Make good food choices to give your body the nutrients it needs for healing.

  • You may be able to take probiotics a few hours after your dose. Probiotics may prevent diarrhea and can help you repopulate your gut microbiome. Be sure to ask your doctor if this will affect the medication(s) you’re taking, and what they suggest for timing a probiotic.

  • Neglect your to-do list. Slow down. Plan for extra sleep. Go to bed earlier. Find time for a nap or two. Your body will be able to use these breaks to recover. Pushing yourself may slow your recovery.
  • Take time to care for yourself. Do something that makes you feel good. Adding a few drops of aromatherapy oil to your shower is one low-effort way to feel a little better while you’re recovering.

Rebuild your gut microbiome

So your prescription is gone and you’re ready to get back to your routine. Let’s build up your gut microbiome! If you’re on the Ixcela program, you already know this takes time and commitment, but it’s worth the effort. Make sure you’re nurturing your gut health with each choice you make. 


  • Pay close attention to what you put in your body and try not to deviate from your eating plan. When you’ve been sick and you’re lacking energy, it can be especially hard to resist easy-to-eat, no-prep, processed foods. Don’t give in to cravings for unhealthy foods. Now more than ever, you need to help your body by giving it plenty of whole foods. Take your vitamins. Enjoy some fermented foods with live, active cultures.

  • Drink up. Hydration is especially important if you’ve been experiencing diarrhea or vomiting due to antibiotics.

  • Avoid alcohol, which can be dehydrating and further irritate your gut.

  • Listen to your body—don’t overdo it the moment you start feeling better. Yes, you have a lot to catch up on, but you will get there when your energy levels return to normal. Doing too much too fast inhibits recovery.

  • Slowly work your way back into your exercise routine. Don’t start where you left off. Give yourself time to regain strength and energy.


It’s easy to override what your body is telling you, especially when you have a calendar bursting with commitments. However, pushing through an illness—especially one that requires antibiotics—is not a good idea. Instead of being stubborn, you need to give in to all the hints that tell you to slow down, whether they come from your doctor or your body. Making good decisions will help you (and your gut microbiome) bounce back faster.



erika_angleABOUT ERIKA 

Dr. Erika Ebbel Angle received her Ph.D. in Biochemistry in 2012 from Boston University School of Medicine. She holds a B.S. from the Massachusetts Institute of Technology. Erika is the Executive Director and Founder of Science from Scientists, an award-winning, National non-profit which sends real, charismatic scientists into classrooms to improve the attitudes and aptitudes of 3rd-8th-grade students in Science Technology Engineering and Math (STEM). She is also the CEO and co-founder of Ixcela, a biotechnology company aimed at developing tests and interventions to improve gut microbiome efficacy and health.