The widespread adoption of antibiotics has led to countless improvements in medical care. Unfortunately, the evolution of antibiotic use has gone from applications in life-saving situations to today, where even dermatologists will prescribe anybody and everybody a ‘low-dose’ antibiotic for a plethora of cosmetic ‘conditions’.
Regardless of the application, there is a new realization in the research community surrounding the systemic impact of antibiotic use. Specifically, more and more findings are suggesting that the use of antibiotics, often including those used to treat minor infections, removes the overwhelming majority of bacteria composing the human gut microbiome. 
Interestingly, research has also emerged showing that exercise can improve the same gut biome that can be permanently damaged by antibiotics. 
How long is the microbiome affected after antibiotics?
The exact answer to the above question depends largely on the details of each different antibiotic.
In one of the most impactful studies on antibiotic use, researchers gave participants a 3-antibiotic ‘cocktail’ over the course of 4 days. Nearly immediately, the gut became a breeding ground for pathogenic bacteria and was increasingly uninhabitable for beneficial bacteria. The altered state was not transient but lasted for weeks or did not recover at all.
After 6 weeks, participants’ gut flora had largely returned to pre-treatment levels. However, some of the most common gut bacteria remained completely undetectable at 180 days. 
How is exercise one of the many tools you can use to repair your microbiome?
Exercise has been shown to improve physiological processes throughout the body. Study upon study has shown that exercise modulates the immune system and supports the growth of cells in the innate immune system.
Recently, researchers have compiled evidence showing how drastically exercise affects the underlying factors behind gut health.
One study evaluated the bacterial composition of high-level competitive rugby players. In these athletes, exercise enriched the athletes’ microbiome and was correlated with improved creatine kinase and protein intake. 
If you are not familiar with creatine kinase, read our article on the phosphagen energy system. Improving creatine kinase means improving your ability to produce anaerobic work like heavy squats or sprints.
In another study, researchers found a connection between cardiorespiratory fitness and gut diversity. In the athletes with elite cardiorespiratory fitness, the microbiome almost specialized in producing butyrate, a measure of gut health. 
Reduced microbiome diversity is associated with inflammatory bowel diseases (IBDs) and obesity-related inflammatory characteristics. Consistent exercise has been shown to improve microbiome diversity, and therefore the use of exercise is now believed to be a powerful tool to prevent gastrointestinal disease states. [2-4]
Steps to improve your gut health with exercise:
As we discussed above, consistent exercise can improve several measures of gut health. On a basic level, take advantage of these findings by moving every day. The findings are not limited to one training modality, so you can benefit from cardio-based training or resistance exercises. [2-4]
- Palleja et al. Recovery of gut microbiota of health adults following antibiotic exposure. Nature Microbiology. 2018
- Monda et al. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxidative Medicine and Cellular Longevity. 2017.
- S. F. Clarke, E. F. Murphy, O. O’Sullivan et al., “Exercise and associated dietary extremes impact on gut microbial diversity,” Gut, vol. 63, no. 12, pp. 1913–1920, 2014.
- M. Estaki, J. Pither, P. Baumeister et al., “Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions,” The FASEB Journal, vol. 30, no. 1, pp. 1027–1035, 2016.