Antibiotic effects on the microbiome may last longer than we thought
Review by Prof. Eamonn Quigley (USA)
Study Summary
While the short-term effects of antibiotics on the microbiome are well known and are illustrated by the consequences of superinfection with C. difficile when the resident microbiome is suppressed, it has been assumed that the intrinsic resiliency of the microbiome ensured its timely and complete recovery. While hints that some taxa may suffer longer-term damage have been extant for some time, now comes compelling evidence of a more generalized and long-lasting effect. Using the Swedish Prescribed Drug Register, these investigators examined the impact of oral antibiotic use over the previous eight years on gut microbiome composition using metagenomics in just under 15,000 adults. While antibiotic use within the past year had the greatest impact on the microbiome (as indicated by reductions in species diversity and richness as well as changes in composition), effects were seen for even one course of antibiotics over the previous eight years. The most striking effects were observed in relation to the use of clindamycin, fluoroquinolones, and flucloxacillin. For example, each course of clindamycin within the prior year was associated with the detection of 47 fewer species. These three antibiotics also led to a relative increase in abundance of species linked to diseases such as obesity and diabetes. They also noted that the magnitude of microbiome disruption immediately after antibiotic treatment predicted the duration of its effect in the long term.
Commentary
The introduction of antibiotics in the 1940s changed medical practice and saved many lives. We are now, however, in a crisis of our own making. The indiscriminate use of antibiotics has resulted in the emergence of resistant strains involved in important illnesses such as tuberculosis, sepsis, and sexually transmitted diseases. Antibiotic abuse extends well beyond inappropriate prescribing (for viral infections, for example) to their availability on the open market to the general public and their widespread use in animal husbandry – scenarios which individually and collectively promote antibiotic resistance and set the stage for opportunistic infections. The research in this manuscript magnifies these concerns by demonstrating, first, that antibiotics exert much longer term impacts on the microbiome than previously believed and, second, that antibiotic-related changes in the microbiome feature, not just reductions in diversity and commensal taxa, but the emergence of taxa that have been linked to obesity, diabetes, and risk for cardiovascular disease. These findings are eerily reminiscent of findings, in an animal model, of the metabolic effects of exposure to minute levels of antibiotics reflective of those that could be transferred to humans through the food chain from animals in which they had been used to promote growth.1 Not all antibiotics were culpable. Though its conclusions are bolstered by the sheer size of the population studied and its close representation of the general population, this was not a prospective study and deserves repeating in a prospective manner with longitudinal sampling of the microbiome and meticulous documentation of disease occurrence and/or the development of risk thereof.
Citation
Baldanzi G, Larsson A, Sayols-Baixeras S, Dekkers KF, Hammar U, Nguyen D, Graells T, Ahmad S, Gazolla Volpiano C, Meric G, Järhult JD, Tängdén T, Ludvigsson JF, Lind L, Sundström J, Michaëlsson K, Ärnlöv J, Kennedy B, Orho-Melander M, Fall T. Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals. Nat Med. 2026 [epub ahead of print}.
Reference
- Blaser MJ, Domingue-Bello MG. The Invisible Extinction. Ann Rev Microbiol 2025;79:311-34.
View past News You Can Use commentaries
