The in’s and out’s that even your doctor or pharmacist might not know


Antibiotics can be good, yet bad. When you get a bacterial infection, antibiotics can be a miracle. They can save lives. However, like all things in this dualistic world, they have two sides: the “light” side that can save your life, and the “shadow” side that can disrupt your health. You should take antibiotics when you need them, but you must know how to protect yourself and your loved ones, especially your children, from potential shadow-side fallout down the road. So how do you stay well after taking antibiotics? That’s why I put together this booklet as part of my new online certification course and book: Nutritional Gastroenterology.

The microbiome

While antibiotics may be effective in the elimination of pathogenic organisms, a common, unintended side effect is the killing off or blocking of beneficial microbes that are also susceptible to the antibiotic.

A healthy gut has a healthy microbiome—an “organ” of microorganisms that lives inside your gut. It cross talks with your immune system to keep it healthy. Seventy to 80 percent of your immune system lives in your gut. Part of your gut’s ability to keep you well is through constant conversations between a healthy gut microbiome and your immune system.

The microbiome is the genetic material of all microbes—bacteria, fungi, protozoa, and viruses—that live on or in the human body. Most microbes live in the gut, particularly in the large intestine. Some live in the small intestine. A healthy gut microbiome is a diverse one, meaning you have lots more good gut bugs in there than bad ones. The ratio of a healthy microbiome is about 75-80% good gut bugs to 15-20% of not-so-healthy ones.

Changes in the microbiome can alter your health. The biggest reduction in microbiome ecological diversity, and the cause of other adverse side effects, stems from the use of antibiotics. For example, your child needs antibiotics to get rid of pneumonia, but then develops diarrhea. The diarrhea is a secondary effect of the antibiotics making the gut flora less diverse and therefore less healthy. Or after taking antibiotics once or twice a year, your healthy child suddenly becomes allergic to environmentals like mold or to foods like dairy. Since your immune system resides mostly in your gut, if your gut gets disrupted, its ability to deal with “foreign” molecules, from pollens to foods, can become disrupted unless you rebuild the gut microbiome.

The antibiotic problems

Antibiotic Paradox. One of the many functions of normal microbiota is the ability to resist infection. After taking antibiotics to fight off one type of infection, there is a period of time during which you actually become more vulnerable to new and diverse infections.This is now being referred to as the Antibiotic Paradox. Antibiotics are prescribed to help you. Yet, “fallout” from taking them leaves your microbiome more monotone, your gut bacteria somewhat paralyzed and your immune system, for a while, less robust.  Even your nutritional status can be affected. So you are, for a while, until your gut microbiome is restored back to health, less able to fight off new pathogens you may be exposed to.

Digestive Ding. Gut bacteria help you digest and they even produce helpful nutrients. The microbiome’s digestive capability and nutrient status can be adversely altered for a while after taking antibiotics. Even though you needed to take the antibiotic to clear one infection, it left you open to other infections and other health problems. Important note. Your immune system works less efficiently and is more vulnerable to disease for two to six weeks after you take antibiotics.


Antibiotics damage your good bacteria, which damages the majority of your immune system. So after taking a round of antibiotics, you are more prone to “catching” a virus or a bug. You need to be aware of this so you can decrease your potential exposure and replace your gut good bacteria to reboot your immune system. Big pharma is aware of this problem and is madly trying to design antibiotics that kill unwanted pathogens without harming the healthy microbiome.

Post-Antibiotic Dysbiosis. When you have more bad gut bugs in relation to the good ones in your gut, this imbalance is termed dysbiosis. It is common to have a period of transient of “post-antibiotic dysbiosis” after taking antibiotics.


While the antibiotics were fighting off your infection, they were also killing off some of the good gut bugs. Post-antibiotic dysbiosis is especially a threat to your health if you had to take a number of rounds of antibiotics or several different types of antibiotics at the same time or in close proximity to each other.

This means that you will want to be a bit careful after taking antibiotics, as your ability to fight off other infections is somewhat hampered. For instance, if your child has been on these meds, be careful of taking them to the airport and on a plane. If you have been on antibiotics, think twice about going to that huge convention. If you do take your child on a plane, or if you do go to that convention, be armed with probiotics and, if possible, consume a bit of fermented food each day (more on that later).

Shift happens. Gut bacteria can “shift” from antibiotics. Until you “shift” it more healthward, you are at an immune disadvantage. (And it is not just antibiotics that have this potential affect. Other medications, poor diet, stress, too much alcohol, inadequate sleep, and even sustained negative emotions, like anger or fear, can put your gut flora at risk.)

What can happen when your microbiome is not healthy after taking antibiotics and you haven’t “reseeded” it back to health with probiotics?

  • Low-grade inflammation, which can cause fatigue and pain.
  • You can develop allergic reactions to foods you weren’t allergic to previously.
  • You can develop allergies to environmentals (like grasses, weeds, and molds) that you weren’t allergic to previously.
  • Your allergic responses may be more exaggerated.
  • You can develop gut issues, from pain to changes in bowel habits.
  • If you had a history of inflammatory bowel issues such as severe diverticulitis, you may have a period of pain and inflammation in that same area.
  • It may even be that post-antibiotic dysbiotic syndrome sets the scene for antibiotic resistance down the road.

What about probiotics?

When your gut is dysbiotic, out of balance, you’ll want to rebuild or restore your microbiome. You must rebuild a transient dysbiotic state caused by antibiotics or your disrupted gut bacteria (and thus your gut wall and gut immune system) can suffer for years afterward. This is especially important for kids. Antibiotic use in children, especially before the age of two, has now been associated with juvenile arthritis, psoriasis, and susceptibility to repeated infections. It has been proven in large pediatric population studies that antibiotics can alter your child’s microbiome.

That’s why you need to protect your gut by taking probiotics while on antibiotics, and for a while afterwards.

Today we can directly test the gut microbiome and know what is growing in there. Lynne V. McFarland, from the Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, published an in-depth article on the use of probiotics to heal what I have termed the “post-antibiotic dysbiotic shift.” McFarland looked at studies that showed the genes of the bacteria that grow in the gut, what disrupts them, and what heals them. She reviewed 352 articles from 1985–2013 that dealt with probiotic treatments and their potential effect on normal microbiota, and she finally included 63 studies that met all her strict requirements.

McFarland’s analysis found only two probiotic products with more than one randomized controlled trial. So understand that when you buy probiotics, there is only a little research on which bugs are the best to purchase. The probiotic mix of L. acidophilus and B. bifidum showed a complete restoration of the gut flora in one study, but only partial recovery in the other study. The probiotic mix of L. acidophilus (2 strains) with B. bifidum and B. animalis showed complete restoration in one study, but only a partial recovery in the other.

Five other probiotic products had only one supporting clinical trial showing effective gut microbiome rebuilding: B. longum; Clost. Butyricum; L. acidophilus; mix of L. acidophilus with L. paracasei and B. lactis; and the mix of L. acidophilus with L. paracasei and B. bifidum and two strains of B. lactis. Three probiotic products with one supporting clinical trial showed partial restoration—S. boulardii, L. rhamnosus GG, and a mix of L. rhamnosus with L. bifidus and L. acidophilus. Two probiotics products showed no improvement of the microbiota—B. breve and a mix of L. acidophilus and B. longum. Different strains had different benefits for specific problems.

In summary, most strains of probiotics had only single scientific trial. The functional claim to restore gut microbiomes is not as robustly supported as we might like, at least not yet. However, 10 or 12 of the probiotic products showed complete or partial restoration of the normal microbiota in at least one study. This says that to rebuild healthy diversity in your gut, you should take a product with at least 10 bugs that are normally found in the human healthy microbiota. Doing so works effectively and rapidly.

A study out of the National Cancer Institute, Rockville, MD, looked at multiple studies on the risk of children getting antibiotic-associated diarrhea after taking a round of these meds. They concluded that there was quality evidence showing a protective effect of probiotics in preventing diarrhea in children after taking antibiotics. Lactobacillus rhamnosus or Saccharomyces boulardii (at 5-40 billion colony-forming units/day) seemed to give the best protection, especially in children. So try to get these bugs in the probiotics you take to rebuild your gut.

How To Take Probiotics Wisely To Re-Seed Your Gut Microbiome Back To Health

Without rebuilding the gut microbiome, antibiotics can disrupt gut flora for up to two years and you want to avoid that. The following information comes from my recommending and using probiotics for many decades on thousands of people and having written one of the first gut/nutrition/mind/body books (Healthy Digestion the Natural Way 2000 Wiley & Co.) and have a new one launching in 2017 (Nutritional Gastroenterology – digestive freedom for practitioners and smart patients).

When you have to take a round (or more) of antibiotics, you need to re-shift your microbiome back to a healthier state. 

The three main steps to shift your microbiome are simple:

(1) probiotics;

(2) “good” food in; and

(3) “bad” food out.

While you are rebuilding your gut microbiome, it is not only about probiotics.

It is also about food.

Getting the unhealthy foods out and the healthier foods in. Avoid refined sugars, excessive alcohol, junk food, and consume a healthy rainbow plant-based diet, fish, nuts, seeds and all the goodies to help your gut heal. Avoiding dairy products while on antibiotics and for a month afterward helps the gut heal even better especially in people with a history of gut disorders or multiple food reactivity’s.


  • Take probiotics twice a day while on antibiotics and for six weeks afterwards. Probiotics and antibiotics should be taken at least two hours apart. Most probiotics need to be refrigerated, but not all. You might find it easiest to keep the probiotic near your toothbrush to remember to take it twice a day, AM and PM, away from food and antibiotics. Many are dairy-based, some are not, so be careful if you are lactose intolerant or if you tend to feel better without dairy.
  • After you have stopped taking the antibiotics, continue the probiotics twice  daily for six weeks unless you have any ongoing adverse intestinal symptoms. If you do, continue taking them twice a day until the gut symptoms (pain, change of bowel habits, change of smell and look of stool, how you feel after you eat food).
  • Probiotics are best taken on an empty stomach.
  • Probiotics work best with diversity, so use one brand one month and another the next or rotate the entire time. I like many probiotics products, especially EndoMune, a blend of over 20 billion CFU, Orthomolecular, Designs for Health, and Thorne Products. Doctor’s lines are more accountable.
  • Units count. Use products with at least 10 unique strains of bacteria with over 10 billion CFU count. Or higher. The effectiveness of a probiotic depends on how many “live” cells it contains. Many manufacturers label their probiotics based on how many bacteria were present before pasteurizing, so use well-known brands, not just less expensive ones. You can call a company and ask what the live cell number of their product is after pasteurizing.
  • Inexpensive brands have been pulled off shelves from reputable pharmacies and discount houses because they were shown to not have what they claimed on the label. They also might be contaminated with bacteria you do not want. That is why I stick with doctor’s lines and reputable brands, although higher cost does not always guarantee better efficacy.
  • Probiotics with multiple strains are best unless you are accomplishing a specific task, such as single bacterial strain such as L. rueteri for vaginal protection.
  • If you have a chronic intestinal disease, taking probiotics at least twice a day on an ongoing basis is optimal. Once you reach remission, you may try going on them once a day and see how you do, or take them from Monday through Friday and give yourself the weekend off. Continue to consume one fermented food item a day.
  • How to know when you no longer don’t need probiotics twice a day: Monitor your tongue. When starting on probiotics and healthier eating, you may need some digestive support to help clear up a coated tongue and get that middle crevice of the tongue looking less menacing. Your breath should be sweeter. You might notice less plaque on the inside of your bottom front teeth.  You should be eliminating at least once a day, if not twice, and your stools should smell sweet (like hay, not stinky). When you start to notice improvement in these things and/or your gut issues, you can then reduce your probiotic dosage from twice to once a day.
  • VSL#3 High Potency Probiotic has been shown to work well against colitis. If you have a history of inflammatory gut issues (recurrent diverticulitis, Crohn’s disease, ulcerative colitis, and microscopic colitis, I like to use one month of VSL#3 and the next month Pro*Biotic 225 (an Ortho Molecular product). I have found this mixture very beneficial. I have no conflict of interest here.
  • Probiotic downside. Adults and children who are severely immuno-compromised should avoid the use of probiotics and even fermented foods. They must work with a medical nutritionist like myself ( or with a practitioner that is very educated in this arena.

Good food in, bad food out

The human microbiome is overly exposed to antibiotics, not only by their medical use, but also by their utilization in farm animals and crops, so we get exposed from some foods, too. Especially dairy and meat. Thus, taking probiotics at least once a day or several times a week on an ongoing basis, as well as eating as sanely as you can, make a lot of gut health sense.

Probiotics work best with a healthy diet and the addition of fermented foods. Diversity is the emphasis here. Rotate your probiotic supplements and the forms you consume them in. Fermented foods and beverages are some of the best sources of probiotics as they have many enhancing, synergistic factors that are very healing (science has not yet identified all of them).

  • Try to consume fermented foods at least once a day, such as miso soup, organic gluten-free soy sauce, or umeboshi plum paste. You can take ½ tsp. of dairy-free yogurt or kefir, or eat fermented veggies, which are great in sandwiches (on gluten-free bread) and salads, or just a Tbsp. by themselves.
  • Consume food probiotics and prebiotics. Two Tbsp. of broccoli sprouts daily are very helpful in rebalancing the gut microbiome, and even help eradicate unhealthy gut bugs that may have started to grow when the antibiotics reduced your gut diversity. Prebiotics help “feed” the probiotics and are a special form of healthy fiber found in garlic, jicama, and onions, as well as Jerusalem artichokes and dandelion greens.
  • Avoid sugars and refined carbs as much as possible for at least one to two weeks, as these paralyze the gut microbiome.
  • Consume fewer dairy products for a while. A less healthy gut microbiome does not love dairy products. They can “slow down” the re-shifting of the gut microbiome back to a healthier state.

There is no one perfect probiotic. But choosing your probiotic carefully and rotating sources and bugs, plus eating well and including fermented foods in your diet, will take you a long way to establishing and maintaining a healthy gut, even when you have to take antibiotics. The gut is the “mother of your health” so all these efforts are well worth it.


 J Dig Dis. 2016 Oct 15. doi: 10.1111/1751-2980.12422

 J Dig Dis. 2016 Oct 15. doi: 10.1111/1751-2980.12422

 Dig Liver Dis. 2016 Sep 21. pii: S1590-8658(16)30734-4

 Toxicol Sci. 2016 Aug 7. pii: kfw150, Front Microbiol. 2016 Jan 12;6:1543

 Pediatrics. 2015 Aug;136(2):e333-43. doi: 10.1542/peds.2015-0036, JAMA Dermatol. 2015 Nov 11:1-9. doi: 10.1001/jamadermatol.2015.3650, J Rheumatol. 2015 Mar;42(3):521-6. doi: 10.3899/jrheum.140348

 BMJ Open. 2014; 4(8): e005047

 Explore (NY). 2016 Aug 26. pii: S1550-8307(16)30120-3

 Journal of Biological Regularion and Homeostatic Agents, October 2013, Inflammatory Bowel Disease, January 2014

 Front Microbiol. 2016 Jan 12;6:1543