A recent large-scale study conducted in Sweden has revealed that even a single course of antibiotics can have a long-lasting impact on the diversity of bacteria residing in the human gut. Published in the journal Nature Medicine, the research examined nearly 15,000 adults and analyzed the relationship between their antibiotic use over the prior eight years and the composition of their gut microbiome, revealing important insights into how different antibiotics affect microbial diversity and potentially influence health.
Antibiotics are powerful medicines designed to eliminate harmful bacteria that cause infections, but they do not discriminate between harmful and beneficial bacteria. The gut microbiome, a complex community of trillions of microorganisms living in the digestive tract, plays a vital role in human health, influencing digestion, immunity, and even metabolic and inflammatory processes. Disruptions to this microbial ecosystem, particularly reductions in bacterial diversity, have been associated with various health problems, including obesity, type 2 diabetes, and inflammatory bowel disease.
In this study, researchers from Uppsala University in Sweden cross-referenced stool sample data with national prescription records to compare the gut microbiomes of individuals who had taken antibiotics at different times within the past eight years against those who had not taken any antibiotics during that period. On average, individuals without recent antibiotic exposure harbored approximately 350 unique bacterial species in their gut. In contrast, those who had taken antibiotics showed a reduction in this microbial diversity, though the extent of the reduction varied significantly depending on the specific antibiotic used.
Among the antibiotics studied, clindamycin emerged as the most disruptive to gut microbial diversity. Clindamycin is commonly prescribed for skin and dental infections. The study found that each course of clindamycin taken within the year before stool sampling was associated with an average loss of 47 bacterial species. Furthermore, it altered the abundance of almost 300 bacterial species out of the 1,340 species analyzed. This represents a substantial reshaping of the gut microbiome following clindamycin use.
Other antibiotics also showed notable effects but to a lesser degree. Fluoroquinolones, often prescribed for urinary tract and respiratory infections, and flucloxacillin, mainly used for Staphylococcus aureus infections (though not available in the United States), each corresponded to an average loss of about 20 bacterial species. They also caused significant shifts in the abundance of 172 and 203 bacterial species, respectively. The study observed that most antibiotics led to decreases in bacterial abundance, but some were linked to increases in certain bacteria associated with poor cardiometabolic health, indicating that antibiotic use might not only reduce diversity but also encourage the growth of potentially harmful microbes.
While lower gut microbiome diversity has been correlated with various chronic illnesses, the exact relationship between diversity and health remains complex. Some experts suggest that the presence or absence of specific bacterial species might be more critical than overall diversity. Jotham Suez, a microbiome researcher at Johns Hopkins Bloomberg School of Public Health who was not involved in the study, commented that although higher diversity is generally considered better, there is not yet strong evidence to definitively link diversity alone to health outcomes.
The timing of antibiotic use also played a significant role in the extent of microbiome disruption. The effects were most pronounced when antibiotics were taken within the year before the stool samples were collected. Generally, the more courses of antibiotics an individual had taken, the greater the reduction in microbial diversity. However, even a single course of clindamycin, fluoroquinolones, or flucloxacillin taken up to eight years prior still showed measurable effects on the gut microbiome.
Interestingly, the study found that bacterial diversity tended to recover most rapidly during the first two years following antibiotic use. After this initial recovery period, the rate of microbial restoration slowed considerably, and individuals did not appear to regain their original microbial diversity fully. This finding aligns with results from smaller and shorter-term studies, suggesting that the impact of antibiotics on the gut microbiome can be both profound and long-lasting.
The researchers offered potential explanations for why certain antibiotics had stronger effects. Both clindamycin and fluoroquinolones are broad-spectrum antibiotics, meaning they target a wide range of bacterial species. They also reach high concentrations in the colon, the primary site of the gut microbiome, which may explain their greater disruptive potential. Flucloxacillin, on the other hand, is a narrow-spectrum penicillin, so its strong effect was unexpected. This might be due to its pharmacok