antibiotics: how to heal while you're healing

Hi everyone, sorry I didn't have a mid-week post for you all last week but I was busy finishing up my first clinical rotation (and seeing an open heart surgery). Just because I didn't post doesn't mean I was not thinking about you all...

This week I posted a question to my Facebook friends: "What piece of nutrition advice do you find most confusing? This can be confusion over the healthfulness of a certain food or food component (carbs, fat, protein), timing, counting, literally ANYTHING! I want to know what YOU want to know...Ready....GO!"

I got a lot of great questions, and I really appreciate all of the responses! I am going to make an effort to address most of the questions I received over the next few weeks.

The topic of today's blog post was intended to be a quick, easy, Facebook response. But, before I knew it I had written over a page, so I abandoned that idea. So here you go (thanks to Jen Miani for asking about this) :

The question:

"After long-term antibiotic regimens, what do you think is nutritionally beneficial for gut recovery? Other than the probiotic regimens recommended with these antibiotics."

The explanation:

There are up to 1,000 different species and subspecies of bacteria that live in your intestines, termed the gut microbiota. Your gut microbiota, the "good" bacteria, are like a diverse community that lives in your intestines.  This community of bacteria helps you to break down food, synthesize vitamins, keep harmful substances from entering your body, and strengthens your immune system (1). When the community is disrupted it can quickly become unbalanced, putting you (the host) at a greater risk for disease and inflammation.

Antibiotics are given to kill bacteria that are causing an infection or to prevent an infection from occurring, such as after a surgery. What many do not realize, and what most doctors do not mention, is that antibiotics can do quite a bit of harm too. Antibiotics, which are largely overprescribed, kill the “bad” bacteria as well as the “good" bacteria that live in the gut. By killing the good guys, antibiotics undo the balanced relationship that exists between you and your gut bacteria (2). Antiobiotics decrease the diversity and quantity of bacteria strains in the intestines. When important members of the bacteria community are killed off, those that remain have a hard time carrying out all of the important functions because they don't have the support from the rest of the community. Resistant members of the community, meaning bad bacteria that are extra strong, are able to survive in the face of an antibiotic. Increases in these resistant members makes you more prone to further infection and development of antibiotic resistant disease (not good). The extent of the changes to your gut microbiota will depend on the strength of the antibiotic and the length of time it is taken. However, regardless of type and time there are things you can do to protect yourself and your gut community... 

how to heal while healing: 

First, select a good quality, pharmacy grade PROBIOTIC. When it comes to probiotics, buying one at the grocery store may be cheaper, but those are not always best. The antibiotics have wiped out your good gut bacteria so you want a probiotic with a variety of strains since you want to replenish as much of the bacteria as you can. You also want a high CFU (colony forming units) count, which are the amount of live cells capable of forming new colonies. Images below depict extremes, a probiotic with far too little and a probiotic offering a lot...

One strain, 5 billion CFUs... not going to be very helpful during or following antibiotic treatment...


10 strains, 200 billion CFUs...good variety here but so many CFUs may not be tolerated well...


 Generally, looking for 25-50 billion CFUs and the greatest number of strains is going to be most helpful.

Here are some companies that make great high quality supplements: Klaire labs (Therbiotic probiotic), Designs for Health, NOW Foods, and Jarrow formula supplement company. You can find these on Amazon,, or individual company websites.

Second, Support your gut with glutamine. Glutamine is an amino acid that improves gut function, intestinal development, and immunity. It repairs and replenishes the cells that line your intestines thereby keeping your intestinal barrier strong and keeping harmful things from being absorbed. Although we can get glutamine from our food, after a period of stress, disease, or infection, extra glutamine support in the form of L-glutamine will help your gut repair and stay balanced (3).

Third, try fermented foods! Fermented foods naturally contain probiotics! A probiotic supplement will help replenish your gut bacteria, but the more sources and variety you can get the better! Fermented foods include kefir, sauerkrautkimchi, and kombucha. You can also try Kevita, a slightly carbonated drink with probiotics added. 

(Fun fact: kefir is the highest naturally containing probiotic food, it is like a drinkable yogurt. Get the plain because it is unsweetened. Blend it to make a smoothie or drink a glass before bed.)

Notice, I did not include yogurt on my list of fermented foods. Although it contains some probiotics, they are not as active or in as high of a quantity as the above mentioned fermented foods. 

Fourth, eat real food.

Diet has a MAJOR effect on your gut microbiota (4). The typical American diet, also known as the Standard American Diet (SAD) or a "Western" diet, is high in omega-6 fats, low in omega-3 fats, high in processed foods and added sugar. Switching mice to a diet that mirrored the SAD diet, rich in sugar and omega-6 fats, showed changes in the microbiome in just one day. At two weeks the mice showed increased fat tissue (5). A SAD diet causes negative changes to many strains of gut bacteria (1). Excess sugar will decrease helpful strains and feed the bad bacteria. When your gut is already taking a hit from the antibiotics, you definitely do not want to add the consequences of a poor diet into the mix. Avoid a SAD diet and eat real food.

Thanks again for the question, Jen! I hope this helps!

real food wins








  1. Brown K, DeCoffe D, Molcan E, & Gibson DL. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients. 2012;4:1095-1119.
  2. Modi SR, Collins JJ, & Relman DA. Antibiotics and the gut microbiota. J Clin Invest. 2014;124(10):4212-18.
  3. Wang B, Wu G, & Zhou Z, et al. Glutamine and intestinal barrier function. Amino Acids. 2014; doi: 10.1007/s00726-014-1773-4 .
  4. Maslowski KM, & Mackay CR. Diet, gut microbiota and immune responses. Nat Immunol. 2011;12(1):5-9.
  5. Turnbaugh PJ, Ridaura VK, & Faith JJ, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):1-10.