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Functional Medicine

Gut Flora: You Should Be Very Afraid

By August 10, 2021August 30th, 2021No Comments

We think it’s so easy — just take that probiotic to make up for whatever damage that might have happened from the prescription antibiotic your doctor gave you, and you’ll be fine, right? And that antibiotic — you hear about antibiotic resistance, but you know you take it correctly, and you really needed it for that sinus infection, so it’s not that big of a deal either, right? You’re wrong in ways that you can’t possibly imagine and that should make you very, very nervous.

The World Health Organization has started to use the phrase “The Post-Antibiotic Era” to describe our current period of time. In September 2013, the Centers for Disease Control issued its first solid numbers regarding antibiotic resistance. It estimates at least two million Americans fall ill to antibiotic-resistant infections, and between 23,000 to 100,000 people die from them every year. There are 18 known bacteria that are COMPLETELY resistant to anything we throw at them, and that number is, of course, climbing.  This resistance has occurred for a couple of reasons: one is, the CDC says that 50% of the prescriptions written for antibiotics are unnecessary or inappropriate (for example, when a broad-spectrum antibiotic is given when a culture isn’t taken to determine a more targeted drug), and two, because 80% of available antibiotics are actually given to animals in confined feed lots (which might make you decide to buy grass-fed, or at least, antibiotic-free meat). Roundup (glyphosphate), found in conventionally raised farming, has been shown to have an inhibitory effect on food microorganisms [i] and suppress beneficial bacteria in the gut. [ii]

You probably have no idea how ineffective antibiotics are for the things they’re prescribed for most often. They’re not effective for bronchitis [iii], sinus infections [iv],[v], or ear infections [vi]. They are incorrectly prescribed in 80% of strep infections. [vii] And, of course, they are often given for the common cold or the flu, despite the fact that those are both viral, because either the patient demands a prescription, or because the doctor wants to prophylactically prevent a secondary bacterial infection. Think about all the times in your life you’ve taken an antibiotic — it’s most often for respiratory conditions and yet it’s there that they are the least effective. The person who says, one or two months after his sinus infection, that he’s gotten another one, probably has the same infection that wasn’t properly handled or was resistant to medication. When people feel better taking an antibiotic, it’s often just because of a reduction in the pathogenic bacteria, not because it’s actually killing them off, and it’s been shown time and time again that taking an antibiotic only reduces your illness time by a day or two. “But that’s a lot!” you cry! If you knew, though, that taking that antibiotic might PERMANENTLY damage your gut flora, or cause other bacteria to become resistant, you might pause, or possibly decline taking that medicine. And it’s now been found that bacteria “talk” to each other, and convey resistance to medications.[viii] Yes, that means bacteria are passing on antibiotic resistance to other bacteria.

The biggest problem is, our gut flora can’t take this abuse. Let’s start with some basics that will explain why this is potentially such a problem. You inherit your gut flora from your mother in a vaginal birth and continue to populate your gut with different strains from the air, food, soil, etc. until the age of two, when it’s “set”. Going back to your mother, how healthy was her gut flora? How many antibiotics did she take in her lifetime? How about your grandmother? We’ve had antibiotics for 80 years now and while there’s no doubt that they’ve saved a lot of lives, there’s no doubt they are less and less effective, and the collective damage to gut flora is irreparable. Add in the high Caesarian-section rate, and you can begin to get an idea that our gut flora is currently the weakest in human history. Studies are showing that babies born of C-sections have higher rates of celiac disease, autoimmune disorders like Type 1 diabetes, and obesity.

Our gut flora outnumbers our body cells by 10-to-1. Yes, we’re only 10% human! The Human Microbiome Project is attempting to distinguish all the different actions and functions of the gut flora, but to give you some idea on this:

  • It is estimated that 70-90% of your immune system resides in your gut. Autoimmune diseases have been directly linked to imbalances in gut flora [ix],[x] and celiac disease has been directly linked to dysbiosis. [xi] We had a patient in her 60’s who got debilitating celiac disease after a single round of antibiotics, and another who improved his ulcerative colitis 80% by not washing the vegetables from his garden.
  • Gut bacteria are responsible for B vitamins, vitamin K, and the production of amino acids and fatty acids.
  • It is now being thought that gut microbes, along with some of the inflammatory foods we’re eating, like junk food and bad fats, make endotoxins which are one of the root causes of inflammation. Rats with no gut microbes can eat any amount of “bad” foods and not gain weight or have inflammation, but when given gut flora, immediately develop high levels of endotoxins, and the resulting inflammation.[xii] And those endotoxins? Huge contributors to leaky gut syndrome.
  • Your gut has the same number of neurons as your spinal cord, and about 95% of your body’s serotonin is produced in the gut, as well as many other neurotransmitters. It almost seems odd, then, to have prescriptions for SSRI medications and never actually deal with what might be happening in the gut.
  • Your gut flora individuality is like a fingerprint, in that it’s different for everyone. That being said, diversity is the key to health, in regards to microbes, and if you don’t have diversity, or you don’t have the right type of bacteria, it leaves you open to a host of diseases, including obesity. [xiii] It’s this diversity of your gut, not just the number of bacteria, which seems to be key to staying healthy. First world children have less diversity than third world children, with corresponding levels of asthma and allergies, and even though rural third-world countries have greater exposure to infectious diseases and lower life expectancies, they also have much lower rates of overall degenerative and chronic diseases.

The use of antibiotics is what’s frightening — they doesn’t just deplete gut bacteria, but can actually permanently wipe out whole strains. Scientists are now going into remote areas of the Amazon and collecting gut bacteria from tribes that have never been exposed to Westerners, antibiotics or modern foods, and are finding that a pristine microbiome not only has huge diversity, including species never before sequenced.

Of course, how we have tended to look at bacteria is a “good” versus “bad” scenario, but it is much more complicated than that. First, everyone has pathogenic bacteria in their gut, but they are often kept under control by adequate amounts of beneficial bacteria. Take an antibiotic, however, wiping down or out our good guys, and the bad guys can flourish, leading to deadly Clostridium difficile infections, for example. Or take Helicobacter pylori, which we’ve been trying to exterminate since 1983, when it was linked to peptic ulcers. But it’s also been shown that H. pylori regulates acid in the stomach — when people eliminate their H. pylori, they have less peptic ulcers, but higher rates of acid reflux, Barrett’s esophagus, and esophageal cancer, rates of which have soared since we’ve been eliminating H. pylori. It also calms the immune system (populations with higher H. pylori have lower rates of allergy and asthma), and regulates ghrelin and correspondingly, metabolism — obesity related to low H. pylori levels is currently being investigated.

Additionally, it’s being thought now that the rising incidence of celiac disease and gluten intolerance is being driven by our gut dysbiosis or pre-existing gut infections (more common than you think). This dysbiosis “primes” the gut to incorrectly react to gluten protein. While the structure of gluten has changed into a molecule that is more reactive to the human body [xiv] (and not in a good way), it is our poor gut flora that is already inflamed, causing an over-reaction with particular proteins.

What happens if you wipe out your home team so badly it can’t recover? The symptoms can range from chronic, debilitating diarrhea, to malnutrition, anemia, systemic infections, and death. When faced with a pathogenic infection as a result of taking antibiotics, most doctors employ the very method that got the patient in trouble in the first place — antibiotics — but what is becoming a quickly developing (and more effective) treatment are fecal transplants. A fecal transplant takes the gut bacteria from a healthy person and introduces it to the sick person, often with shockingly dramatic improvements. In a study done with patients who had had a C. difficile infection and never properly recovered (most had had over 150 days of incapacitating diarrhea), a fecal transplant reversed their symptoms in 24 hours, on average, with a total cure rate of over 90%. In fact, they halted the study because it became unethical to withhold such a successful treatment to the control group. [xv]

The problem is, you can’t actually replace what you’ve lost. We’re under the mistaken impression that you can simply take an antibiotic, and then follow with a probiotic and your gut will be completely back to normal, but that’s not what being seen in research. Even fecal transplants, with their dramatic impacts, simply buy time for the home team to recover. Probiotics, as well, help to keep the “bad guys” in check, but don’t replace lost strains. If my system got “flushed out” with some food-poisoning diarrhea, for example, I might use a probiotic pill to help my gut out while it repopulates, but when someone has to rely on probiotic pills for their digestion to be “normal”, that’s an indication that there’s some dysbiosis/dysfunction in their gut. Taking higher and higher amounts of probiotics isn’t great either — buying one with insane amounts of Colony Forming Units (CFU’s) can cause dysbiosis as well. And, of course, there’s no probiotic that is specific for your individual microorganism makeup.

Prebiotics, like the oligosaccharides found in vegetables and whole grains, as well as in breast milk (to encourage gut flora growth in a baby) are like food and housing for your home team — they encourage your native flora to grow. Focusing on good prebiotics, as well as severely reducing foods like sugar and bad fats (which cause that inflammatory reaction with the gut flora and can encourage dysbiosis) would be a better plan of action. “What if I take my home team and cultivate them in a Petri dish for sometime in the future?” I sometimes get asked. That doesn’t work either — when implanted back into the gut, your original “home team” bacteria don’t survive long enough to reinoculate.

This is where the impact starts to hit people — when we begin to realize that we’re destroying the biggest and most complicated “organ” we have from sheer lack of understanding. In labeling bacteria “good” and “bad”, we’ve sanitized our houses, our skin, our bodies, and our kids, and the result is a confused and weakened immune system, obesity, neurological dysfunction, chronic diseases, and more modern, deadly diseases.

It was after all this research that I began to see that I would literally have to be dying to take another antibiotic. It makes more sense to keep my immune system strong, and use herbs and nutrition to fight infections if necessary, while in the meantime to regularly eat the traditional foods that gave us a little probiotic help — fermented foods like sauerkraut, kimchi, kombucha, lacto-fermented vegetables, etc. It’s not just the specter of antibiotic resistance that should scare people silly, it’s also the depletion of their own gut flora and the resulting physiological damage for following generations that might make you choose differently the next time you’re in the doctor’s office.


[i] Clair, Emilie, et al. “Effects of Roundup® and Glyphosate on Three Food Microorganisms: Geotrichum candidum, Lactococcus lactis subsp. cremoris and Lactobacillus delbrueckii subsp. bulgaricus.” Current microbiology 64.5 (2012): 486-491.

[ii] Krüger, Monika, et al. “Glyphosate suppresses the antagonistic effect of Enterococcus spp on Clostridium botulinum.” Anaerobe (2013).

[iii] Smith SM, Fahey T, Smucny J, Becker LA. Antibiotics for acute bronchitis. Cochrane Database of Systematic Reviews 2004, Issue 4. Art. No.: CD000245.

[iv] Lemiengre, Marieke B., et al. “Antibiotics for clinically diagnosed acute rhinosinusitis in adults.” Cochrane Database Syst Rev 10 (2012).

[v] Ahovuo-Saloranta, Anneli, et al. “Antibiotics for acute maxillary sinusitis.” Cochrane Database Syst Rev 2.2 (2008).

[vi] Glasziou, Paul P., et al. “Antibiotics for acute otitis media in children.” The Cochrane Library (2000).

[vii] Nakhoul, Georges N. “Management of Adults with Acute Streptococcal Pharyngitis: Minimal Value for Backup Strep Testing and Overuse of Antibiotics.” Journal of general internal medicine (2013): 1-5.

[viii] Omar M. El-Halfawy, Miguel A. Valvano. Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial Cells. PLoS ONE, 2013; 8 (7): e68874

[ix] Brown, Kirsty, et al. “Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease.” Nutrients 4.8 (2012): 1095-1119.

[x] Cani, Patrice D., and Nathalie M. Delzenne. “The role of the gut microbiota in energy metabolism and metabolic disease.” Current pharmaceutical design 15.13 (2009): 1546-1558.

[xi] Sjöberg, Veronika, et al. “Intestinal T-cell Responses in Celiac Disease–Impact of Celiac Disease Associated Bacteria.” PloS one 8.1 (2013): e53414.

[xii] Bäckhed, Fredrik, et al. “The gut microbiota as an environmental factor that regulates fat storage.” Proceedings of the National Academy of Sciences of the United States of America 101.44 (2004): 15718-15723.

[xiii] Ley, Ruth E., et al. “Microbial ecology: human gut microbes associated with obesity.” Nature 444.7122 (2006): 1022-1023.

[xiv] Kuraishi C, Yamazaki K, Susa Y.  Transglutaminase: Its Utilization in the Food Industry.  Food Rev Int. 2001;17(2):221-46.

[xv] van Nood, Els, et al. “Duodenal infusion of donor feces for recurrent Clostridium difficile.” New England Journal of Medicine 368.5 (2013): 407-415.

Published online and in print in Acupuncture Today and other publications, January 2014

Author Dr. Marlene Merritt, DOM, MS, CNS

• Doctor of Oriental Medicine • Certified Nutrition Specialist • Institute for Functional Medicine Certified Practitioner • Bredesen Certified in Cognitive Decline • Shoemaker Proficient in Treating Mold Illness

More posts by Dr. Marlene Merritt, DOM, MS, CNS