Five Things you NEED to do when Prescribed Antibiotics

Therese Martinez

Five things you NEED to do when Prescribed Antibiotics

We are in a season of colds, flus, and nasty viruses. Being sick is awful. It takes you away from work, the gym, social outings, and can be downright miserable. Sometimes it only lasts 24 hours, and other times it lasts weeks. Sometimes we are hit with pathogens that can be fought with our own immune system, and other times we are hit with stronger bugs that force us to consider other treatment options. While I don’t think many of us get excited at the recommendation of antibiotics, sometimes it is the option that gets us back to work, the gym, and feeling better the quickest. Unfortunately, antibiotics not only take out the harmful pathogens in the body, but they also take out the good. And you know how I feel about those good bacteria! Wiping out the beautiful microbiome in your body means possible short and long-term significant repercussions given the MAJOR role those bacteria play in your overall health.


The effects can vary depending on duration, frequency, and dosage, but some antibiotic courses can affect someone for life, especially if taken at an early age. Damaging the gut microbiome with antibiotics can lead to allergies, asthma, weight gain and obesity (1). It can make a person more prone to illnesses as they age, compromise one’s immune system, lead to leaky gut which has LOADS of other problems, as well as susceptibility to increased inflammation long-term which also has LOADS of other problems associated with it (1, 2).


Basically, even though they may be an option, it is still important to try to avoid taking them whenever possible. Especially considering that of the 154 MILLION prescriptions for antibiotics written in doctor’s offices and emergency departments each year, THIRY PERCENT are unnecessary (1). The Centers for Disease Control found that many of these were written for respiratory conditions caused by viruses like common colds, viral sore throats, bronchitis, and sinus and ear infections- all of which DO NOT respond to antibiotics (1). Please make sure your condition requires the treatment. When in doubt, explore other options and ask around.


So, what should you do if you are forced to give in and go through a treatment of antibiotics?


  1. Supplement with Probiotics

Weird, right? Why would you put bacteria in when you are taking a medication to wipe them out? Well, it turns out that those bacteria can still benefit you even if they do not colonize (2). Studies show that probiotic use during a course of antibiotics can reduce side effects like diarrhea, gut dysbiosis, and prevent gut infection (2). Strains like Lactobacilli, Bifidobacterium, or Saccharomyces boulardii are the ones studied in most of these trials and can be found in many probiotic supplements at your local health food store. S. boulardii is of particular interest because it is a yeast, not bacteria, which means it won’t be taken out by your antibiotics (1,2). Sometimes supplementing with a separate dose of S. boulardii can be beneficial if you can’t find a probiotic with it in it. Also, try taking the probiotics as far away from your antibiotic dose as possible (2). Continue taking the probiotics after you are done with treatment for at least three weeks to help in the rebuilding phase. Try to find a probiotic with many different species/strains that include the ones mentioned above.


  1. Up Your Prebiotic Intake

Prebiotics help to feed and promote growth of the good bacteria in the gut. Therefore, optimizing intake over the course of treatment and after will be highly beneficial for catalyzing recovery. Make sure you eat plenty of prebiotics as soluble fiber found in:

  • Brussel sprouts
  • Carrots
  • Turnips
  • Beets
  • Plantains
  • Lentils
  • Broccoli
  • Starchy tubers
  • Squash
  • Peeled fruits

Insoluble fiber can be a little harder on the gut lining, and since your gut may already be compromised, you don’t want to stress it any further. Try waiting to reintroduce most foods with IF until after your course of treatment. Insoluble fiber is found in (3):

  • Greens (spinach, lettuce, kale, collards, arugula, watercress, etc.)
  • Whole peas, snow peas, snap peas, pea pods
  • Green beans
  • Kernel corn
  • Bell peppers
  • Eggplant
  • Celery
  • Onions, shallots, leeks, scallions, garlic
  • Cabbage, bok choy, Brussels sprouts
  • Broccoli
  • Cauliflower

Resistant starch is one exception when avoiding insoluble fiber (2). You have a pretty solid “go-ahead” when it comes to eating this kind of fiber during and after treatment. You can find it in cooked and cooled rice, raw potato starch, cooked/cooled potatoes, and green bananas. Remember that the cooling phase is essential for the resistant starch to form!

NOTE Try out some of these prebiotics prior to starting your course of treatment so your body can get used to them in order to avoid any side effects that may happen in addition to the effects of the antibiotics.


  1. Eat Fermented Foods

Experiment with some fermented foods after your course of treatment to encourage setting up new diversity among your bacteria. Continuing with a probiotic just doesn’t cut it when it comes to rebuilding the diversity in your gut that you want. Eat things like

  • Sauerkraut
  • kefir,
  • kombucha
  • kimchi
  • other fermented fruits and veggies

Watch the sugar content in the store-bought products, and note that they may only have a handful of strains so home-made is best (2).


  1. Give your Immune System some TLC

If 80% of your immune system is in your gut and you are wiping out loads of bacteria in there, you are going to want to do some damage control. Drink up bone broth and glycine-rich foods during and after treatment to promote healing of the gut lining (2, 4).


  1. Don’t tax the body!

The best way to get better quick and prevent future problems is to work on your diet and lifestyle post-treatment. Ramp up your veggie intake (gut-allowing) and other nutrient dense foods (grass-fed meats, pastured poultry, healthy fats-avocado, coconut, nuts), supplement where needed (find a professional to assess this) keep stress levels down, get proper/adequate sleep, and move every day.




Before treatment:

  • Try out prebiotics to see which may positively or negatively affect you

During and After:

  • Probiotic supplement (5 billion CFU/day for children, 10 billion CFU/day for adults; up to 40 billion CFU/day may be optimal in some cases) (4)
  • Yeast supplement- S. boulardii (250-1000mg/day)
  • Prebiotic food intake
  • Bone broth, glycine rich foods
  • Don’t tax your body with wheat, dairy, sugar, unhealthy fats and fried foods


  • Fermented foods
  • Minimal taxing foods mentioned before
  • Heal with nourishing, nutrient dense foods; revisit some of the prebiotic foods you may have discounted before now that you have a sturdier gut
  • Reintroduce insoluble fiber foods
  • Stay active, keep stress low, focus on good quality sleep


As always, PLEASE contact a professional to get a true prescription of a proper protocol for YOUR body. Everyone is different, these are just general recommendations. Stay healthy out there folks!

-Therese Martinez, MS, RD, CPT



Therese Martinez, MS, RD, CPT

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