Why and how antibiotics destroy your healthy digestive bacteria?

There’s almost no place in the earth without bacteria. Our skin, the food we eat, the water we drink, and even the mouse you’re using to scroll down this page has bacteria on it. The only way we can get rid of bacterial organisms would be to sterilize everything we touch, which is something surgeons need to do in the operating room. But even so, what about your skin? What about your gut? They have plenty of healthy bacteria, and if they fail to colonize those areas, harmful microorganisms would easily cause severe health problems. The problem arises when we try to get rid of pathogenic bacteria and sweep our healthy microbiota in the process. Antibiotic use has saved millions of lives and still does. Some of these molecules were discovered by accident, others through complex chemical engineering. As new antibiotic products reach the market, our capacity to kill bacteria is enhanced hundred-fold. However, sometimes patients, and even some physicians, abuse  antibiotics or misuse them. Some preventative therapies require long-term antibiotic use to avoid the risk of relapses, as in the case of tuberculosis; and to prevent complication to existing health conditions, as in the case of cystic fibrosis. All of these approaches of antibiotic use can affect our healthy digestive bacteria along with disease-causing microorganisms. But is it really concerning?


What happens in your gut after taking antibiotics?
Antibiotic therapy, even when correctly applied, causes changes in the quantity and diversity of digestive bacteria. In recent years, more and more researchers have been interested in understanding how these changes affect our gut microbiome. They have realized that when there are subsequent rounds of antibiotic therapy, the diversity of gut microbiota is reduced, and the recovery is usually incomplete. In other words, antibiotics sweep clean our gut from good guys and bad guys, and when it’s finished, we may even have problems recovering what we lost.


For example, many studies have reported that, even after short-term antibiotic use, the gut microbiota experiences an increase in Enterococcus species and decrease in other healthy bacteria such as Bifidobacteria. The Enterococcus bacteria do not usually cause gastrointestinal disease, but when the patient is an older adult, a hospitalized patient, or has a weak immune system, it can cause serious infections and even spread through the bloodstream. These changes can be reverted in 2 days when we are healthy, but in some cases, the effects take up to 6 weeks and more to get back to normal.


However, we all have different strains of healthy bacteria in our gut, and there’s no one single truth for us all. There are variations in the gut microbiota for each person, variations in antibiotic use, dose, and whether they are taken in pills, injected or inhaled. The interaction between antibiotics and our healthy bacteria depends on all of those factors, but also our genetics, our diet and health problems. That’s why many patients may experience diarrhea after taking antibiotics while others are more resilient and do not have any adverse effect.


Every single antibiotic has a different target group of bacteria, and differences in their mode of action. That’s why each group of antibiotics modulates our gut bacteria in different ways. Sometimes, doctors detect the bacteria causing disease are resistant to multiple drugs, and they need to use more than one antibiotic, or broad-spectrum antibiotics. This type of therapy is even more aggressive and takes out the disease-causing bacteria, but affects your gut more deeply than simple antibiotic treatment for a short time.


As you can see, there are many factors involved in antibiotic therapy and how it modulates our digestive bacteria. Some of these factors can’t be easily controlled or haven’t been studied thoroughly in this context, for example, stress, genetics, and diet. This is the reason why it is challenging for researchers to investigate precisely all of the effects of antibiotics in our microbiota. They have made many advances, though, especially with the most commonly used antibiotic groups, for example, macrolides and beta-lactams.


Macrolides and gut microbiota
They are, for example, azithromycin and erythromycin. However, azithromycin is used more frequently because it has less adverse effects on our gastrointestinal system. Clarithromycin is also widely used, but according to a study performed in three adults with gastrointestinal ulcers, it suppresses the species Bifidobacterium, Lactobacillus, and Clostridium. Clarithromycin also increases the rate of Enterococcus, Klebsiella, and even Pseudomonas species, which can cause many diseases in hospitalized patients.


However, as we may expect for the reasons we mentioned before, there are studies with different results. For example, a study performed in 2011 with healthy adults showed that macrolides caused an increase in the rate of Streptococcus species. According to this study, antibiotic treatment with macrolides does not cause a very dramatic effect on the gut microbiota. Interpreting this data can be quite challenging, and physicians always compare them to the signs and symptoms experienced by their patient, their health status, age, and other relevant data.


Beta-lactams and gut microbiota

They are the most widely known and used group of antibiotics and include all types of penicillin, cephalosporin, and other subgroups. They are used to control infections in the respiratory system, skin, and many other systems because they have very broad activity against various types of bacteria. When the normal microbiota is altered with a beta-lactam, other species start to increase, for example, Bacteroides, Faecalibacterium, and Enterococcus. Bacteroides species and Enterococcus are both opportunistic pathogens, which means that in certain conditions they can cause severe disease, especially in immuno-compromised patients, after surgery or trauma to the intestinal mucosa.


Antibiotic treatment is useful and saves lives every day, but they should be used with caution. No wonder why they are prescription drugs and should be used following the advice of your doctor. These molecules can change our gut microbiota dramatically, with many consequences if we are susceptible to them.


References:
Blaser, M. (2011). Antibiotic overuse: stop the killing of beneficial bacteria. Nature, 476(7361), 393.
Iapichino, G., Callegari, M. L., Marzorati, S., Cigada, M., Corbella, D., Ferrari, S., & Morelli, L. (2008). Impact of antibiotics on the gut microbiota of critically ill patients. Journal of Medical Microbiology, 57(8), 1007-1014.
O'sullivan, O., Coakley, M., Lakshminarayanan, B., Conde, S., Claesson, M. J., Cusack, S., ... & Ross, R. P. (2012). Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy. Journal of Antimicrobial Chemotherapy, 68(1), 214-221.
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PloS one, 5(3), e9836.
Pérez-Cobas, A. E., Artacho, A., Knecht, H., Ferrús, M. L., Friedrichs, A., Ott, S. J., ... & Gosalbes, M. J. (2013). Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PloS one, 8(11), e80201.
Morotomi, N., Fukuda, K., Nakano, M., Ichihara, S., Oono, T., Yamazaki, T., ... & Taniguchi, H. (2011). Evaluation of intestinal microbiotas of healthy Japanese adults and effect of antibiotics using the 16S ribosomal RNA gene based clone library method. Biological and Pharmaceutical Bulletin, 34(7), 1011-1020.
Monreal, M. T. F. D., Pereira, P. C. M., & Lopes, C. A. D. M. (2005). Intestinal microbiota of patients with bacterial infection of the respiratory tract treated with amoxicillin. Brazilian Journal of Infectious Diseases, 9(4), 292-300.