A fundamental part of your health is the state of your immune system. A healthy immune system is necessary to fight off infections from bacteria, viruses, yeasts, and fungi. A well-functioning immune system means you are less likely to get sick, and are likely to recover quickly. Some disorders of the immune system can advance to an autoimmune state, where your immune system becomes overactive and begins to attack your own body. Keeping your immune system healthy requires you to avoid chronic states of inflammation, which are more likely to trigger the immune system to overreact.
How can you avoid chronic inflammation? For many people, chronic inflammation begins in the gut. Because we eat the wrong things; like too little fiber, too much fat or protein, foods we are allergic or sensitive to or consume alcohol and caffeine, or products containing nicotine, we are likely to irritate the gut and unbalance our microbiome. Think of the gut as an ecosystem that requires certain conditions to operate efficiently and beneficially. Too many toxins, or other stressors added to that environment causes it to weaken or even fail, just like an external ecosystem. This internal microbiome has evolved symbiotically with humans. There is a vast population of beneficial bacteria and other organisms that live in our gut, helping us break down foods and extract their nutrients, keeping the intestinal walls in good repair, and eliminating toxins and waste products from the body. There is a population of much less helpful bacteria as well, even ones that are dangerous, but these are generally kept in check- unless something goes wrong with the microbiome.
When a healthy microbiome alters, the population of beneficial bacteria plummets and the bad stuff can take over. When that happens, all kinds of effects can follow. To start with, your gut starts processing foods less efficiently. Your absorption of proteins, beneficial fats, and vitamins and minerals can be impaired. Your elimination of waste products can diminish, which allows toxins to build up and puts a strain on the liver and kidneys. The mucosa of your intestinal wall begins to thin, and the wall itself can become damaged and inflamed. This inflammation can cause cramping, loose stools, and general discomfort. As the inflammation persists, it can damage the tight cell junctions of the intestines, allowing bacteria into the bloodstream and causing inflammation elsewhere in the body that becomes chronic. This can cause symptoms ranging from achiness, being overly tired, brain fog, memory issues, lack of motivation, and feeling like you have no energy. It also sets you up for becoming more vulnerable to infection, and therefore prone to being sick more often, or more severely.
Not only is this a poor state of affairs to find yourself in, but it sets you up for a cycle of worsening health if you end up treating frequent infections with frequent antibiotic use. Sometimes antibiotics are necessary. There are serious infections that are life-threatening that absolutely call for a course of antibiotics. Unfortunately, antibiotics are also often over-prescribed (sometimes because of a patient’s demand), or even misprescribed- an antibiotic given for an infection that is likely viral or fungal, or a class of antibiotic that is too strong or not indicated for the type of infection that presents. This is deeply unfortunate for a number of reasons. To start with, if a patient takes the wrong antibiotic, or takes one when it isn’t needed, or even takes them too often, it allows bacteria to potentially become resistant. According to a survey by the Kaiser Family Foundation, nearly half of adults (45%) say they have personally not taken their antibiotics as prescribed by a doctor. This is one of the leading causes of antibiotic resistance. Antibiotic resistance means that the bacteria is not eliminated entirely and that surviving bacteria have evolved a resistance to that specific or class of antibiotic, which means that a stronger antibiotic will likely be needed in the future to combat that strain of bacteria. Not only that, some bacterial strains are evolving resistance so that NO antibiotic will work against them. This means that if you are unlucky enough to catch one of those strains, you may very well end up dead. Another reason to consider limiting your antibiotic use when possible (and ALWAYS take them correctly) is because of the devastating effect that antibiotics can have on your microbiome.
When you take an antibiotic to kill the bacteria that are at the root of an infection, that’s not the only bacteria it kills. It also kills the useful bacteria in your gut that populate your microbiome. The bacteria that has evolved, and that your body depends on, to make sure your gut (and therefore your immune system) functions smoothly. One course of antibiotics can be like a bomb going off in the microbiome. The percentage of beneficial bacteria in the gut that is killed by a single course of antibiotics can vary depending on the type of antibiotic used. For example, researchers found that tetracyclines and macrolides not only stopped good bacteria from growing, but they lead to the death of about half of the strains of microbes found in the gut that the researchers tested for. It’s important to note that even a short course of antibiotics can alter the makeup of the bacterial species in the gut. These community changes can be profound, with some people’s microbiomes taxonomically resembling those of critically ill ICU patients after taking the drugs. It can take months or even years to recover the original species’ composition.
It used to be that many doctors ignored this effect, but now, even somewhat conservative doctors recommend taking a probiotic along with an antibiotic. Indeed, it’s about time! The functional and integrative medical community has been arguing this for decades!
Rebuilding your microbiome through the use of pre, pro, and post-biotic supplements is essential with any antibiotic use, but also for those with any sort of gut issues or chronic inflammation. Limiting or replacing antibiotic use, where possible, is also a good strategy. Beyond those two strategies, a patient should also have their food allergies and sensitivities assessed. Food allergies and sensitivities can cause chronic inflammation and can damage the microbiome, in addition to making you feel terrible. The gold standard of functional testing for food allergies is the P88 Dietary Antigen Test. This test combines 4 different tests (IgE, IgG, IgG4, and C3d) on 88 foods to determine not only allergy and sensitivity but the degree of inflammation potential for each particular food by measuring complement. Having this test done is warranted if a patient has any of the symptoms of food sensitivities or has any gut issues.
There is another reason to check for food allergies and sensitivities after a patient has had several occasions to use antibiotics, or is having gut symptoms from their use. This is because the continuing erosion of the gut lining that can accompany imbalances in the microbiome can make food allergies and sensitivities more likely, leading to even further erosion of the gut lining and perpetuating more allergies in a downward spiral. “Any change to the mucosal immune system could lead to changes in the composition of the symbiotic bacteria, which in turn may affect the response of the mucosal immune system to other immune stimuli. Hence, multi-use of antibiotics might thus increase the risk of immune dysfunction and allergic diseases.” (Chen, et al, Therapeutics and Clinical Risk Management, 2019). Studies have generally concluded that this is especially true for those under 18 who have used multiple different antibiotics but can be true for adults as well, and food sensitivities may well be implicated in addition to allergies. What’s more, most of us have been exposed to a variety of antibiotics because of their heavy use in animals raised for consumption or dairy uses and by contamination of water sources from feedlot runoff.
Patients who have been prescribed antibiotics for bacterial gut infections like those sometimes found in “food poisoning” have a double risk to the microbiome and the possible development of food allergies and sensitivities- from the antibiotic use, and from the infection itself. “Viral and bacterial infections can, however, interfere with tolerance to dietary antigens, thereby perturbing intestinal homeostasis” (Aguilera-Lizarraga et al, Nature, Feb 1, 2021). What’s more, those same bouts of gastroenteritis have a chance to cause IBS in the patient. “An infectious gastroenteritis is a significant risk factor to develop IBS, defined as a constellation of abdominal pain and altered bowel patterns. Between 3 and 36% of enteric infections lead to new onset IBS5, while up to 17% of IBS patients report that their symptoms started upon gastrointestinal infection. Over 10% of the general population experience IBS symptoms, of which food ingestion is one of the most common triggers”. Keep in mind that when a patient complains of gastroenteritis (particularly if it is severe) they are often given a broad-spectrum antibiotic as a precaution since whether the infection is bacterial or viral is not known unless culturing is done- which it often isn’t. This means that those who have viral gut infections may suffer both the effects of the infection and of the unneeded antibiotic on the microbiome, and provoke an inflammatory response that triggers food allergies, sensitivities, and even IBS.
So what should this mean for the standard of care? It means that any patients who have had bouts of gastroenteritis, have used multiple antibiotics, or have been given broad-spectrum antibiotics (particularly in childhood), or those who have other gut symptoms, should be given a comprehensive food dietary antigen test like the Precision Point P88. In addition, if there are gut symptoms and possible reasons to suspect IBS, then the patient should also be given an Advanced Intestinal Barrier Assessment test to determine the degree of damage to the intestinal wall and the concurrent risk of systemic inflammation.