Even routine antibiotic prophylaxis leaves a mark on the microbiome

Prophylactic antibiotics are routine before many dental surgical procedures, yet how they actually reshape the oral and gut microbiome — and whether that disruption resolves — has been surprisingly under-studied. This prospective cohort followed 64 patients undergoing dental surgery with prophylactic antibiotics, collecting saliva and stool at baseline and again at 3, 10, 30 and 90 days post-op, using 16S rRNA sequencing for the full cohort and shotgun metagenomics on a subset to track antimicrobial resistance genes.

Both the oral and gut microbiomes showed significant drops in alpha diversity (p<.01), most pronounced at days 3 and 10, with near-complete recovery to baseline by day 90 — confirming the authors' hypothesis of disruption followed by recovery. Notably, the oral microbiome was more disrupted than the gut microbiome, suggesting it is more susceptible to postoperative antibiotic exposure than commonly assumed. Patient-level factors — sex, race, gastroesophageal reflux disease, and which antibiotic was used — all influenced baseline diversity as well as the degree of disruption and speed of recovery. Taxonomic analysis showed substantial shifts in key health-associated bacterial genera after surgery, and — the finding with the longest practical shadow — some antimicrobial resistance genes increased in relative abundance over time rather than reverting, a signal of possible lasting ecological consequences from a single prophylactic course.

The take-home for practice is not that prophylaxis should be abandoned, but that it is not microbiologically free: even a standard single-course antibiotic regimen measurably disturbs both oral and gut ecosystems, disruption and recovery vary by patient, and resistance gene enrichment can outlast the clinical recovery window. The authors frame this squarely as a stewardship argument — prophylaxis decisions should weigh patient-specific factors, not just procedure type.