Antibiotics and Gut Health : The Effects of Antibiotics on your Digestion

Key Takeaways: 

  • Antibiotics not only act on bacteria that cause infections but also affect the resident microbiota
  • Resident microbia play crucial roles in digestion, immunity, metabolism, and mental health. They maintain the integrity of the gut mucosa and protect us from pathogens.
  • Supplementing with Butyrate during and after antibiotic treatment creates an environment where good bacteria can flourish at which time probiotics can be introduced*
  • Not all probiotics are created equal. A gut test like Viome can help identify optimal strains for your body

When you’re feeling ill and looking to get better, how often do you take the time to ask your doctor about the side effects of the medication they prescribed? And if you do ask, you’re most likely looking at understanding the big side effects of the medication, you know, the ones you hear listed in rapid succession at the end of drug commercials. The truth is, the one medication that we rely on, that has saved millions of lives since its discovery by Alexander Fleming in 1929, can devastate the one part of your body you don’t often think about, the gut. We’re talking about antibiotics.

Antibiotics can devastate, destroy, reduce, lay waste to and ravage the gut microbiome. It is estimated that in our gut we carry a hundred trillion microbes from more than a thousand species and more than seven thousand strains. Debatable or not, that’s a tremendous number. These microbes play crucial roles in digestion, immunity, metabolism, and mental health. They maintain the integrity of the gut mucosa and protect us from pathogens. Supporting the proper balance of bacteria and other microorganisms in your gut are imperative to your digestion as well as to your overall health and wellbeing.

The Gut and Antibiotics

When the doctor prescribes an antibiotic for a diagnosed need, the gut microbiome is affected either directly or indirectly. The job of antibiotics is to deplete/neutralize pathogenic bacteria. Because their character is broad-spectrum, many/most antibiotics will indiscriminately kill subsets of commensal (meaning co-existing without harming us)  bacteria. That action will change the microbiome. This is the point where the prescriber needs to weigh the benefit of the drug against the possible side effects, even those that might appear down the road. But physicians lack the time to investigate every adverse effect of every drug they prescribe. Some antibiotics reduce the activity of gut-friendly bacteria while others might reduce their numbers. 

Beyond a direct effect, antibiotics can impair the microbiome indirectly by upsetting its homeostasis. Some microbiota species might play a role in the development of butyrate as a secondary characteristic, while metabolizing other nutrients as the primary. Others might protect their comrades from attack by something we eat. Depletion of commensal bacteria by antibiotics can lead to a decrease in the butyrate that is manufactured by bacterial fermentation of resistant starch. Concurrently, that may introduce gut inflammation and reduce not only the volume of butyrate, but also its capacity to clear unwanted bacterial invaders (Bhaskaran, 2018)*.  Look out for dysbiosis, that microbial imbalance that now features the unwanted bacterial strains on the marquee (Lakhan, 2010)*. It’s important to find and to take measures to restrict the overuse of antibiotics, despite that some have the potential to act positively on gut biota by increasing the abundance of beneficial strains (Ianiro, 2016).   

What does NSAIDS do to the Gut?

Bacterial infections are not the only reason we swallow pills. Believe it or not, over-the-counter medicines are still drugs. NSAIDS (Nonsteroidal anti-inflammatory drugs) are widely used to control pain, but may induce adverse events in various body systems, most occurring in the GI tracts. NSAIDS , such as ibuprofen, aspirin and naproxen, shut off pro-inflammatory chemicals called cyclo-oxygenases (COX-1 and COX-2). The job of COX-1 is to protect gastric mucus layers and to maintain normal kidney function.  COX-2 synthesizes prostaglandins that produce pain and inflammation. NSAIDS can shut down COX-1 as well as COX-2 and allow gastric distress to follow, including the stomach bleeds that affect some aspirin users. 

What we especially like to learn about is the development of new COX inhibitors that deal with inflammation but do not interfere with the protection of anti-inflammatory prostaglandins. Some of these new NSAIDS contain phosphatidylcholine (PC). There are nitric-oxide-NSAIDS in the pipeline, too. These two types spare the cardiovascular system from the insults that plagued the “coxibs” that were pulled from the market for causing cardiac episodes, including heart attacks (Garcia-Tayado, 2018). As gastric insults, the NSAIDS available now harass specific strains of gut bacteria. Not only NSAIDS but also proton-pump inhibitors (Prevacid, Prilosec) modify intestinal microbiota, affecting sensory and nerve functions. Overzealous supplementation with potassium chloride may cause small bowel ulcerations and stenosis, while contraceptives are associated with intestinal ischemia (Scarpignato, 2019). Unfortunately, not many are aware of these other drug “personalities”. 

Reducing levels of native microbes jeopardizes their ability to prevent invasion by harmful ones, such as C. diff and some salmonella. And if carbohydrates are not adequately broken down by indigenous strains, too much water may be absorbed and cause diarrhea, a lack of butyrate, and a misstep in the metabolism of bile acids.   Additionally, tight junctions suffer adversity and allow undigested food particles to invade the bloodstream. 

Restoring your gut after taking antibiotics and other medications

Before we think of gut restoration with probiotics, we need to consider providing them a nice place to reside. That is the work of butyrate, an endogenous short-chain fatty acid of myriad talents, but famous for being the main source of energy for colonocytes, the cells that line the colon and give biota a happy place to live*. Butyrate closes tight junctions, supports a healthy inflammation response, sequesters ammonia from faulty protein metabolism and protects the gut from attack by malformed DNA*. The mucus layer is the place where the bacteria live, and more than seventy percent of it is made from PC. Once we get past thirty years of age, our capacity to make enough endogenous PC to serve our trillions of cells is limited, leaving PC supplementation a good idea*. Now that the biota campground is refurbished, the probiotics can be introduced. Not all probiotics are created equal - what works for you might not work for your twin. We can’t say which strains are best for you without identifying which occupy your gut.  Here, your physician can help by guiding a stool test or perhaps try a test like Viome. And remember, always be sure to get the fiber you need, too. 

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