Key Takeaways
- A 2026 study found that oral and gut microbial diversity declined after prophylactic antibiotics and dental surgery, with the largest changes during the first 10 days.
- Microbial diversity moved close to baseline by day 90, but some antimicrobial-resistance genes increased in relative abundance.
- The study did not prove permanent microbiome damage or show that these microbial changes caused illness.
- Because the study lacked a comparable group that underwent surgery without antibiotics, researchers could not fully separate the effects of antibiotics from those of surgery and recovery.
- Antibiotics remain important when patients have a clear therapeutic or prophylactic indication.
- Dentists should consider the patient’s health, surgical complexity, antibiotic choice, dose, and duration instead of prescribing antibiotics routinely.
- Patients should discuss concerns with the prescribing clinician rather than stopping or refusing antibiotics independently.
Introduction
Antibiotics can prevent or treat serious infections, but they can also affect many bacteria beyond those responsible for an infection. A new study published in The Journal of the American Dental Association examined how prophylactic antibiotics prescribed for dental surgery changed microbial communities in both the mouth and the gut.
The researchers found the greatest reduction in microbial diversity during the first 10 days after surgery. By day 90, diversity had moved close to baseline in many samples. However, some antimicrobial-resistance genes increased in relative abundance over time (Littlejohn et al., 2026).
During my years in clinical dentistry, I saw how easily patients could interpret antibiotics as a routine precaution with few consequences. Yet every prescription involves a balance between potential benefit and potential harm. These findings do not prove that a dental antibiotic course causes permanent microbiome damage, nor do they mean that patients should refuse antibiotics when a valid clinical indication exists. Instead, the study reinforces the need to prescribe antibiotics selectively and explain clearly why the patient needs them.
Daria Buinevich, DDS, summarizes new research on changes to the oral and gut microbiome after prophylactic antibiotics for dental surgery. The study found the greatest changes during the first 10 days, with microbial diversity moving close to baseline by day 90.
What Did the New Study Examine?
Littlejohn and colleagues followed 64 patients who underwent dental surgery and received prophylactic antibiotics. The researchers collected saliva and stool before surgery and again 3, 10, 30, and 90 days afterward. They used 16S ribosomal RNA sequencing to assess bacterial diversity and composition. They also performed shotgun metagenomic sequencing on a subset of samples to examine antimicrobial-resistance genes (Littlejohn et al., 2026).
The study reported three central findings:
- Microbial diversity declined significantly in both oral and fecal samples, particularly on days 3 and 10.
- The oral microbiota showed greater disruption than the gut microbiota.
- Diversity approached its baseline level by day 90, but some resistance genes became relatively more abundant.
The researchers also found that antibiotic type and patient characteristics, including sex, race, and gastroesophageal reflux disease, correlated with differences in baseline diversity, disruption, or recovery. These associations suggest that patients may not respond to antibiotic exposure in exactly the same way. They do not yet provide a clinical formula for predicting an individual patient’s response.
What Does “Microbiome Disruption” Actually Mean?
The microbiota consists of the microorganisms living in a particular environment; the microbiome includes their collective genetic material and ecological interactions. In the mouth, these communities live on teeth, the tongue, mucosa, restorations, and dental implants. In the gut, they participate in digestion, metabolism, colonization resistance, and immune signaling.
Researchers often measure alpha diversity, which describes the variety and distribution of organisms within one sample. A decline shows that the microbial community changed and became less diverse. It does not, by itself, establish that the patient developed disease.
That distinction matters. Microbiome research can identify ecological changes long before researchers understand their clinical significance. A sequencing result is not the same as a diagnosis, and “different from baseline” does not automatically mean “permanently damaged.”
Previous human research has shown both resilience and incomplete recovery after antibiotic exposure. In one study of healthy adults exposed to commonly used antibiotic regimens, species richness generally returned toward baseline within two months, but taxonomy, metabolic output, and the resistome remained altered in some participants at six months (Anthony et al., 2022). Another study found near-baseline gut composition after approximately six weeks, although several common species remained undetectable after 180 days (Palleja et al., 2018). The drug, dose, duration, baseline microbiome, diet, health status, and previous antibiotic exposure can all influence the response.
The new dental study therefore fits a broader pattern: microbiomes often recover substantially, but recovery does not always reproduce the original community precisely.
Why Do Resistance Genes Matter?
Bacteria can carry genes that help them survive antibiotic exposure. Together, these genes form the resistome. When an antibiotic removes susceptible organisms, bacteria carrying relevant resistance mechanisms may gain an ecological advantage. Some bacteria can also exchange genetic material.
An increase in the relative abundance of resistance genes does not mean that the patient currently has a resistant infection. It means that the microbial community may contain a larger proportion of genetic material associated with resistance. If a future infection develops, resistance can reduce treatment options or make therapy more complicated.
Research outside dentistry has also detected persistent enrichment of antibiotic-specific resistance genes after treatment in healthy adults (Kang et al., 2021). This is one reason antimicrobial resistance cannot remain solely an issue for hospitals or infectious-disease specialists. Dental prescribing contributes to antibiotic exposure in the community, so dentists have a meaningful role in stewardship.
Why Do Dentists Prescribe Antibiotics Around Surgery?
Dentists may use antibiotics for two different purposes. Therapeutic antibiotics treat an established or spreading bacterial infection. Prophylactic antibiotics aim to prevent an infection before it occurs.
Some patients face enough risk to justify prophylaxis. Current guidance supports antibiotic prophylaxis before certain invasive dental procedures for a small group of patients with cardiac conditions that place them at the highest risk of a severe outcome from infective endocarditis. These procedures include those that manipulate gingival tissue or the periapical region of a tooth or perforate oral mucosa (Wilson et al., 2021).
By contrast, the American Dental Association does not generally recommend routine prophylaxis solely because a patient has a prosthetic joint. It advises clinicians to consider antibiotics only in selected situations and, when appropriate, coordinate with the orthopedic surgeon (American Dental Association, n.d.-a).
The evidence surrounding implant surgery remains less uniform. A 2022 multicenter, double-blind randomized trial found no statistically significant reduction in early implant failure or postoperative infection after a single preoperative dose of amoxicillin in healthy or relatively healthy patients (Momand et al., 2022). A 2024 systematic review similarly concluded that routine prophylaxis did not substantially reduce early implant failure and estimated that 143 patients would need treatment to prevent one early failure, although estimates vary across reviews and surgical settings (Momand et al., 2024).
These findings do not show that antibiotics never help in implant dentistry. A clinician may reasonably reach a different decision for extensive grafting, prolonged surgery, significant immune compromise, or other higher-risk circumstances. An active infection may require therapeutic antibiotics rather than prophylaxis.
What the Study Cannot Tell Us
The new research offers valuable longitudinal data, but several limitations should shape its interpretation.
First, the study followed patients who received antibiotics but did not include a comparable group undergoing similar surgery without antibiotics. Surgery itself can change diet, oral hygiene, inflammation, and medication use. Without a non-antibiotic control group, researchers cannot separate every effect of the antibiotic from every effect of the operation and recovery period.
Second, the cohort included only 64 patients, and the researchers evaluated resistance genes in a subset. That limits the precision of subgroup findings and the ability to generalize them to every patient, dental procedure, and antibiotic regimen.
Third, 16S sequencing describes bacterial community structure but usually cannot establish detailed functional activity or consistently resolve organisms at the species or strain level. Shotgun metagenomics provides richer genetic information, but the presence of a gene does not prove that bacteria expressed it or that it caused a clinical outcome.
Fourth, the study followed participants for 90 days. That period captures early recovery but cannot determine whether every remaining difference later resolves, persists, or affects health.
Finally, the study did not establish that microbiome changes caused symptoms, infection, gastrointestinal disease, or another patient-centered outcome. Its results should generate better clinical questions, not alarmist conclusions.
What Antibiotic Stewardship Looks Like in Dentistry
Antibiotic stewardship does not mean withholding antibiotics from patients who need them. It means matching the prescription to the clinical problem and choosing the right drug, dose, and duration when treatment is necessary (American Dental Association, n.d.-b).
Before prescribing, a dentist should ask:
- Does this patient have an established infection, a guideline-supported indication for prophylaxis, or a procedure-specific risk that justifies antibiotics?
- Can local treatment, such as drainage, debridement, root canal treatment, extraction, or surgical management, address the source?
- Which drug provides the most appropriate spectrum?
- What dose and duration will achieve the goal with the least unnecessary exposure?
- Does the patient have allergies, recent antibiotic use, a history of Clostridioides difficile infection, medication interactions, immune compromise, or other relevant risk factors?
For most pulpal and periapical dental pain in immunocompetent adults, the ADA recommends definitive dental treatment rather than systemic antibiotics. Fever, malaise, spreading infection, or other evidence of systemic involvement changes that decision (Lockhart et al., 2019).
Duration also matters. More antibiotic is not automatically more protective. Extending prophylaxis after surgery can increase exposure without improving outcomes in every setting. In a randomized implant study, adding a two-day postoperative course to a preoperative dose did not improve implant or prosthetic outcomes; adverse events occurred only in the extended-course group, including one severe allergic reaction that required hospital care (Arduino et al., 2015).
What Should Patients Ask Before Dental Surgery?
Patients should not stop, shorten, or decline a prescribed antibiotic without discussing the decision with the prescribing clinician. They can, however, ask reasonable questions:
- What specific infection or complication is this antibiotic intended to treat or prevent?
- Does a guideline support prophylaxis for my medical condition or planned procedure?
- Do factors in my case make the surgery higher risk than a routine procedure?
- Why did you choose this antibiotic, dose, and duration?
- What side effects should prompt me to contact you or seek urgent care?
- If I recently took antibiotics, does that change the plan?
Patients should also give the dental team an accurate medication list and report antibiotic allergies, previous severe reactions, and any history of C. difficile infection. They should take a necessary antibiotic exactly as prescribed unless the clinician advises a change.
The study does not support routine microbiome testing before or after dental surgery. It also does not establish that every patient should take probiotics. Products differ substantially, and evidence for preventing antibiotic-related complications remains inconsistent. Patients with significant symptoms should seek clinical advice instead of trying to “repair” the microbiome with unverified supplements.
A More Precise Conversation About Risk
The easiest message would be that antibiotics are either harmless protection or indiscriminate damage. Neither claim reflects the evidence.
When a patient faces a meaningful risk of serious bacterial infection, an appropriate antibiotic can provide an important benefit. When the expected benefit is small or unsupported, the same prescription creates avoidable exposure for the patient and additional selection pressure for antimicrobial resistance.
Littlejohn and colleagues add a useful biological dimension to that calculation. Even a short perioperative course can temporarily reshape microbial communities in both the mouth and gut, and diversity alone may recover more fully than every genetic or functional feature. Future studies should compare similar surgical patients with and without antibiotics, distinguish among drugs and durations, follow participants longer, and connect microbial findings with clinical outcomes.
Until then, the most responsible approach is neither automatic prescribing nor automatic refusal. It is an individualized decision based on the patient’s health, the procedure, the quality of evidence, and the consequences of both treating and not treating.
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Final Thoughts
The new study provides important evidence that antibiotics prescribed around dental surgery can affect microbial communities beyond the surgical site. The largest changes appeared during the first 10 days, and microbial diversity moved toward baseline by day 90. However, the increase in some resistance genes shows that the recovery of diversity does not necessarily mean that every ecological effect has disappeared (Littlejohn et al., 2026).
Patients should not interpret these findings as a reason to fear or refuse all antibiotics. When a patient faces a meaningful risk of infection, an appropriate antibiotic may provide an important benefit. The more responsible approach is to avoid routine or prolonged exposure when the expected benefit remains unclear while preserving antibiotics for situations in which the likely benefit outweighs the risks.
For dentists, the study reinforces an increasingly important responsibility: identify the indication, consider the patient’s individual risk, select the appropriate drug, dose, and duration, and explain the reasoning clearly. For patients, it supports asking informed questions rather than accepting or rejecting antibiotics automatically.
Frequently Asked Questions
Do Antibiotics Permanently Damage the Oral or Gut Microbiome?
The study did not demonstrate permanent microbiome damage. Microbial diversity moved close to baseline by day 90, although some resistance genes increased in relative abundance. Other studies also show that recovery varies among patients and that some compositional or functional changes may persist after microbial diversity improves (Anthony et al., 2022; Littlejohn et al., 2026; Palleja et al., 2018).
Should Patients Refuse Antibiotics Before Dental Surgery?
No. Patients should discuss the indication with the prescribing clinician rather than refusing, shortening, or stopping an antibiotic independently. Prophylaxis remains appropriate for selected high-risk patients, while certain complex surgical situations may require an individualized decision (Momand et al., 2024; Wilson et al., 2021).
Does Every Dental Implant Procedure Require Antibiotics?
Current evidence does not support routine prophylaxis for every healthy patient undergoing straightforward implant placement. The decision may differ when surgery involves extensive grafting, significant immune compromise, or other factors that increase the risk of infection (Momand et al., 2024).
Should Patients Take Probiotics After Dental Antibiotics?
The new study did not examine probiotics and does not establish that every patient needs them. Probiotic products differ considerably, and evidence supporting their routine use after antibiotics remains inconsistent (American Dental Association, n.d.-b). Patients should discuss supplements with a qualified clinician, especially if they have immune compromise or significant medical conditions.
References
American Dental Association. (n.d.-a). Antibiotic prophylaxis prior to dental procedures. Retrieved August 25, 2026, from https://www.ada.org/resources/ada-library/oral-health-topics/antibiotic-prophylaxis
American Dental Association. (n.d.-b). Antibiotic stewardship. Retrieved August 25, 2026, from https://www.ada.org/resources/ada-library/oral-health-topics/antibiotic-stewardship
Anthony, W. E., Wang, B., Sukhum, K. V., D’Souza, A. W., Hink, T., Cass, C., Seiler, S., Reske, K. A., Coon, C., Dubberke, E. R., Burnham, C.-A. D., Dantas, G., & Kwon, J. H. (2022). Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Reports, 39(2), 110649. https://doi.org/10.1016/j.celrep.2022.110649
Arduino, P. G., Tirone, F., Schiorlin, E., & Esposito, M. (2015). Single preoperative dose of prophylactic amoxicillin versus a 2-day postoperative course in dental implant surgery: A two-centre randomised controlled trial. European Journal of Oral Implantology, 8(2), 143–149.
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Momand, P., Becktor, J. P., Naimi-Akbar, A., Tobin, G., & Götrick, B. (2022). Effect of antibiotic prophylaxis in dental implant surgery: A multicenter placebo-controlled double-blinded randomized clinical trial. Clinical Implant Dentistry and Related Research, 24(1), 116–124. https://doi.org/10.1111/cid.13068
Momand, P., Naimi-Akbar, A., Hultin, M., Lund, B., & Götrick, B. (2024). Is routine antibiotic prophylaxis warranted in dental implant surgery to prevent early implant failure? A systematic review. BMC Oral Health, 24, 842. https://doi.org/10.1186/s12903-024-04611-0
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Conflict of Interest
The author declares no conflict of interest relevant to this article.
Funding
No external funding was received for this article.
