While our world thinks it is controlled by our minds it is interesting that our first indicator of things being out of true come from that ‘gut feeling’ and anyone who has suffered short or long term digestive problems has felt the impact on their mood and sense of wellbeing.

Maintaining proper gut flora is a crucial but still largely misunderstood component of human health. While antibiotics have lengthened our lifespan, our excessive use of these drugs may cause serious long-term consequences. Our newspaper headlines are full of stories about antibiotic resistant infections (particularly in the health care system) and it is becoming more and more apparent that antibiotics have been not only overprescribed and overused, but too often ill-used. This potential catastrophe can be attributed to a combination of healthcare providers giving antibiotics out like candy, overzealous patients demanding them as a cure all and people failing to take the full dosage as prescribed. It is extremely important, if not critical, that we as a species avoid unnecessary antibiotic use and take them responsibly.

While more people, especially those committed to a holistic lifestyle, are opting to avoid taking antibiotics, there still are times when we have no other option, but in our reluctance we must not make another mistake. In our wish to limit our use we may be tempted to take just enough of our prescription to begin feeling better, but not complete the course. While we hope to get by with using less thereby limiting the number of good bacteria we kill off, we do not realize that it is also failing to completely kill off the infection which laid us low. This is then allowed to simmer in the background, growing and potentially adapting before reemerging, when it may not respond to the same medication.

Lesson: Despite reservations, unless you have a negative response to the medication, finish the course! 


Can you repair your microbiome?

Yes, and the good news is you can start to rebuild your gut flora even while you are taking antibiotics. You can begin to heal, support and repopulate your system in a number of ways.


To some, taking probiotics during a course of antibiotics might seem to be a contradiction of ideas. Won’t the antibiotics just kill all of the probiotics? No, and even if they do it is okay. According to several case studies, probiotics don’t need to actually colonize the gut to be beneficial; even transient strains can provide powerful therapeutic effects.

One study of 135 hospital patients taking antibiotics found that 12% of the group receiving probiotics developed antibiotic-associated diarrhea, compared with 34% of the placebo group. While 17% of the placebo group developed diarrhea specifically from C. difficile, none of the group receiving probiotics did. Another study tracked changes in gut bacteria in three different groups receiving antibiotics, with one group receiving placebos, one group receiving probiotics beginning after the antibiotic treatment ended, and the third group receiving probiotics both during and after antibiotic use. The group receiving placebos had significantly higher levels of facultative anaerobes* 20 days after finishing antibiotics compared with baseline, while the two groups receiving probiotics showed no significant difference.

Even though both of the probiotic groups ended up at baseline levels, only the group taking probiotics during and after antibiotic treatment maintained stable levels of facultative anaerobes* throughout the experiment. In the group receiving probiotics only after completion of antibiotic treatment, facultative anaerobes* increased significantly during antibiotic treatment, and decreased after beginning probiotic supplementation demonstrating the importance of taking probiotics during antibiotic treatment, as well as after.

* marker for gut dysbiosis.  

Caring for your Flora and Fauna

Good vs Bad Gut Flora bacteria IBD , Crohns, Crohns Disease, IBS, Diverticulitis, Keto, GAPS,

It Is very important to feed and fortify the good bacteria you have. While this might seem a little late it can be an effective way to lessen the impact of medications on your gut lining. Adopting a diet using prebiotic foods is an effective way to promote the growth of beneficial bacteria in the gut and an incredibly important part of any regimen to protect or rebuild a healthy microbiome.

During and after antibiotic use, it can be hard to eat (Note: your mum was right - a nice bowl of soup is just the thing). Skip the Gatorade and the urge to snack on empty, but bland calories. We need to feed and nourish our system. Try to focus on getting plenty of soluble fiber this can be found in starchy tubers, squash and peeled fruit and vegetables like carrots, beets, parsnip, turnips, rutabagas, plantain, taro, and yucca, and insoluble fiber found in beans, peas, wholegrain rice, soy, rye, wheat, oat in the form of resistant starch, (something cooked, cooled and reheated – especially when butter or coconut oil has been used in the initial process) that can feed you and your beneficial bacteria.

Repopulate Your Inner Garden and Support Biome Diversity

The main hurdle after a course of antibiotics isn’t just recovering the number of flora but recovering the diversity. It is important to get find a probiotic option which offers as many cultures as possible (PureBiotics™ Maxima) to prevent antibiotic-associated diarrhea and lower the risk of a gut infection. As your system recovers you should also consider looking for opportunities to compound the diversity of your microbiome by exposing your system to as much different beneficial bacteria as possible. This can be done by consuming fermented foods like kefir, beet kvass, sauerkraut, kombucha, kimchi, and other fermented vegetables or fruits. Every culture has similar products and considering your ancestral biome came from them it is not a bad idea to return to your roots – although culinary exploration is good too!

Healthy Gut Immune

Do not, however, be tempted by the TV ad claims for probiotic yogurt or other mass produced products. Keep in mind that these products are often full of more sugar than you need, plus, as they have normally been pasteurized, the ‘live’ content is zero to minimal. This along with the biome die-off from the antibiotics may be enough to cause or exacerbate a Candida albicans event (yeast overgrowth).

Did you know that your ancestral biome can vary greatly from those around you as it is literally passed down through the generations (mother to child)? There is current research on how differences might be linked to allergies, dietary intolerance and digestive problems. Another option to help diversify the bacteria you’re exposed to is by growing your own fruit, vegetables and herbs. Not only is the produce you grow less likely to be drowned in pesticides but the process of growing it exposes you to soil, a rich biome in its own right. Gardening and getting out into nature is good for your gut and soul.

While you are rebuilding your gut, remember this: your body is a holistic system and what affects one area affects others.


Liver and Adrenal Health

Antibiotics and medication in general take a toll on your liver, especially when you are on them for extended periods. Your adrenal system is your bodies cleaning system. The liver is responsible for processing and detoxifying your body, and your kidneys help to flush them out. This is intensified when you are sick or taking meds; you not only have to recover from the illness but recover from the cure. Your liver also deals with extra circulating lipopolysaccharides from increased bacterial death and intestinal permeability. Consider giving your liver and kidneys some love and support while they are working overtime.


In Conclusion

Our gut is sometimes referred to as our other brain. As I mentioned at the beginning of this article, we talk of our instincts as being a gut feeling. Therefore, it would seem at odds to our survival if we ignore and abuse it. Although this article is about our gut flora being under assault from antibiotic medication, it is important to be aware that it is not just antibiotics you take which causes issues, but also those which arrive in our water and food! When a herd of animals is treated with preemptive antibiotics (or hormones), a common action in animal husbandry, so inadvertently are we. Our water is also under assault, as waste water returning into the system includes antibiotics – too yucky to think about.

If all of that isn’t sad enough our gut biome also has its own lifecycle dying off as we age so it is imperative that we do everything we can to maintain, support and replenish what we have.

A Healthy, Happy Gut Equals a Happier Person.

Leave a comment

Please note: comments must be approved before they are published.