The impact of antibiotics on the microbiome

In the UK, one of the highest rates of antibiotic prescriptions in the outpatient population comes from dentists and oral surgeons.(1, 2)

Systemic antibiotics are commonly prescribed before removal of the third molar (wisdom tooth), periodontal therapy, placement of dental implants, or other surgery in the oral cavity. Although the clinical benefits of these measures are highly debated, they still form a common practice.(3-5)

In this week’s blog practising dental surgeon and registered nutritional therapist, Keeley Nicholas, discusses prescribing antibiotics, the effect they have on our gut and how to protect our microbiome.

The impact of antibiotics on the microbiome

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Since their discovery (1920s) and commercialisation (1940s) antibiotics have been revolutionary in reducing morbidity and mortality rates in the treatment of infectious diseases.(6)  However, the inappropriate and overuse of antibiotics for minor infections, viral infections and prophylaxis in medicine; and the use of low doses to promote growth in agriculture has resulted in serious concerns with regards to antibiotic resistance.(7) This is now a worldwide issue and a major threat to public health. The emergence of ‘superbugs’ that are resistant to multiple antimicrobials has resulted in high mortality rates.(8)

Antibiotics and disease

Despite being used to ‘benefit health’ when a serious infection resides, antibiotics can also have a negative impact on overall health. This is because of the deleterious effect they can have on the delicate balance of the microflora that reside within and on the human body.(9) Antibiotics destroy supportive as well as causative bacteria throughout the whole body, leading to a loss of diversity and density, both of which are essential for a healthy microbiome.(10)

Disruption in the balance of the microbiome has been associated with numerous disorders including autoimmune and inflammatory conditions. Obesity, diabetes, atopic, allergic, and gastrointestinal diseases have all been associated with imbalanced or disordered gut microflora.(11,12)

Impact of antibiotics on the gut microbiome

Following antibiotics, some studies indicate that there may be some resolution of the gut flora to near normal levels within one to four weeks, but there is also evidence indicating that it may be many years before the gut microbiome returns to its pre-antibiotic state.(13,14)


Antibiotics taken at a younger age appear to have a more significant impact on the microbiome, increasing susceptibility to obesity, asthma and inflammatory bowel diseases. The younger the child is, the greater the damage appears to be. The type of antibiotic chosen also can impact considerably; macrolides antibiotics e.g. erythromycin and clarithromycin have a significant impact on the microbiomes of children, with long-term reduction in diversity and density, which does not appear to recover within a two year period.

Penicillin appears to have less of an impact, but recovery may still take over twelve months. Multiple doses or frequent use of antibiotics can lead to further damage, as the microbiota does not have time to recover and a less favourable microbiome may be established in the long-term.(15)

The full extent of antibiotics and their negative impact on the gut microbiome may never be realised. Irreversible loss of less abundant species has been reported(16), imparting irreparable damage as some species are eradicated completely. Even small perturbations may have a life-long effect on function, metabolite production, immune status and barrier protection, and this essentially increases the risk of disease.(17)

Probiotic Therapy

Probiotics are defined as ‘live micro-organisms which when administered in adequate amounts confer a health benefit to the host’.(18,19)   Many benefits have been attributed to probiotic administration, but their specific action is still not fully understood.(20)  Bifidobacteria and Lactobacillus are the main species used in probiotic formulations. Taking probiotics during antibiotic therapy appears to have a protective effect on the gut microbiome, minimising the damage, limiting the long-term health concerns that may result from a disrupted gut microbiome.(21)

Modifications occurring in both numbers and diversity of the gut microbiota as a result of antibiotics may not be totally prevented by probiotic consumption(22,23) and bacterial counts can recover to approximate baseline levels with time in the absence of probiotics; indicating resilience and certain recovery of the gut microbiota.

The use of probiotics, however, appears to increase the similarity to baseline levels, hence improving recovery.(24) Probiotics can help to minimise the negative impact from antibiotics(25) and have been associated with a reduction in the more obvious antibiotic-associated effects, such as diarrhoea and gastrointestinal complaints following antibiotic use.(26,27)

On a microscopic level Bifidobacteria spp. are particularly susceptible to antibiotics, and counts appear to decrease with most antibiotics. This may be of particular concern because Bifidobacteria are shown to enhance a healthy microbiome and ensure beneficial functions including butyrate production, chemotaxis, and adherence.(28-31)  Taking a probiotic supplement, rich in Bifidobacteria, can limit the overall decrease in counts and retain beneficial metabolic function. Taking the probiotic during the antibiotic regime, but with a two hour time difference, is shown to provide the most protection.(32) In order to restore levels, a probiotic may need to be taken over a relatively long period.(33)

How can we protect our microbiome?

Prescribing antibiotics (Dentists)

With such concerns, an antibiotic prescription should be thoroughly considered by the prescriber. The necessity of the prescription should be assessed, and prescribing guidelines adhered to, undertaking local treatment measures (draining of abscesses, or extirpation of pulp tissue), and only using antibiotics as an adjunct to this treatment when systemic infection is present.(34,35)

The choice of antibiotic should also be carefully considered, as the level of destruction on the gut microbiome can vary with different antibiotics.

Augmentin (amoxicillin combined with clavulanic acid), erythromycin and clarithromycin appear to impart considerable damage to the microbiome, whereas amoxicillin has a decreased effect. The microbiome of children can be severely affected by antibiotics and careful consideration should be given when antibiotics are being prescribed for children.(36)

Patient’s expectations may also need to be managed, as patients requesting antibiotics increases the likelihood of a prescription being given, even in the absence of systemic infection.(37)

The damage to the gut microbiome, the short and long-term effects of this damage, and the long-term risks that may result from this should ideally be outlined to the patient for informed consent to be obtained. Probiotic foods (sauerkraut, bio yoghurt) and probiotic supplements can also be suggested, as a way of possibly reducing the antibiotic impact on the gut microbiome.

Receiving antibiotics

Patients often expect or may request antibiotics in the hope that their condition will be resolved sooner. The anticipation of receiving antibiotics can increase the likelihood of antibiotics being prescribed, even when the situation does not warrant antibiotics.(37)

Patients should take professional advice regarding the specific situation, and accept when antibiotics will not help. Alternative options e.g. analgesics, anti-inflammatories, natural anti-inflammatories e.g. turmeric, or allowing the body to fight the infection (in the short-term) can also be considered.

Listening to the professional advice given, regarding the long-term effects of antibiotics and the resultant long-term health risks, can help us to make informed decisions about our own treatment choices.

When antibiotics are essential, probiotic foods or probiotic supplements can be taken to help to minimise the damage to the microbiome.

Key Takeaways

Prescribing antibiotics (Dentists)

  1. Be judicious with prescribing guidelines – careful consideration of antibiotic requirement in line with prescribing guidelines.
  2. Assess requirement for antimicrobials and decide whether analgesics or anti-inflammatories (curcumin) may be more beneficial in the short term if treatment cannot be undertaken immediately due to time constraints.
  3. Consider carefully the type and dose of antibiotic being prescribed. Be aware of those antibiotics that have the biggest impact on the microbiome, and prescribe those that will be effective for the required pathogen and have minimal impact on the microbiome.
  4. Careful consideration should be given when prescribing antibiotics to children, as the impact on the microbiome and life-long health effects can be considerable.
  5. Manage patient’s expectations and/or requests for antibiotics, and ensure patient is fully informed regarding the damage to the microbiome and health impacts that can result in the long-term. Consider obtaining signed informed consent.
  6. Recommend probiotics, or probiotic foods to minimise effects of antibiotics on the gut microbiome (see below).

Receiving antibiotics (Patients)

  1. Do not request antibiotics. Your doctor or dentist will assess your situation and prescribe an antibiotic, only if it is essential.
  2. Accept antibiotics only when the situation warrants it.
  3. When an antibiotic is prescribed, question your specific situation. Will the antibiotic help? Is it essential?
  4. Be aware that in certain situations an antibiotic is not necessary or warranted, it may not even work, but there may be an impact on your long-term health.
  5. Antibiotics can have a long-term effect on the gut microbiome. This has been associated with numerous diseases, autoimmune conditions, gut disorders, diabetes and obesity.
  6. The microbiome of children can be more severely damaged by antibiotics.
  7. Certain types of antibiotics can cause greater destruction on the gut microbiota (including Augmentin, Clarithromycin, Clindamycin).
  8. Antibiotic resistance is a worldwide concern. Becoming infected with bacteria resistant to all current antibiotics may ultimately lead to death. It is the bacteria and not the individual that becomes resistant to an antibiotic, and so the responsibility resides with us all.
  9. Consider taking good quality probiotics during the antibiotic period and for several weeks (to months) following the completion of the antibiotic course to minimise damage and restore the gut microbiome.

Keeley Nicholas BDS. MFGDP(UK). MSc (nutritional therapy).
Keeley is a practising dental surgeon (with over twenty years clinical experience), and a registered nutritional therapist, with a Masters in Nutritional Therapy.
She is passionate about both specialities and works in dental clinics in South Birmingham and Hereford, and also runs a Nutritional Therapy practice in Worcestershire.
Her aim is to incorporate functional medicine principles into general dental practice to promote a more holistic care of individuals.

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With many thanks to Keeley for this blog; if you have any questions regarding the health topics that have been raised, please don’t hesitate to get in touch with Clare via phone; 01684 310099 or e-mail


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  2. European Centre for Disease Prevention and Control. (2014) Surveillance of antimicrobial consumption in Europe 2012. ECDC, European Centre for Disease Prevention and Control, Stockholm, Sweden.
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Last updated on 20th November 2020 by cytoffice


4 thoughts on “The impact of antibiotics on the microbiome

  1. I can fully justify what impact antibiotics have on your microbiomes . A few years ago I had some dental implants ,for which I took probiotics prior to the treatment and I was fine. However, I had a chest infection a few months ago and after taking antibiotics, guess what my system was shaken and I am now dealing with Candida. I would like to add this was encouraged because I read that honey was good for this condition, so some on a slice of fruit bread went down well. Of course this just fed the Candida. I am making a good recovery in cyto-plans supplements.

  2. Training as a microbiologist ’67-71, we were made aware of the known dangers of feeding antibiotics to livestock & indiscriminate use of antibiotics.
    Very saddening that the lesson was not learnt.

  3. Am now wondering why my husband, who has now returned from three days in hospital in a worse state than when he went in, was given Clarithromycin “as a precaution”.

  4. Couple of months ago I had a surgical tooth removal. I was prescribed an antibiotic, two types of painkillers and an antibacterial mouth wash. I wasn’t keen to take the antibiotics and discussed it with the dentist who recommended to take them anyway. I was told to take the first painkiller straight away (before the local anestethic wears out) and then every couple of hours for a week! Being trained in Nutritional Therapy and Herbalism I took my own decision (not that I would recommend it to everybody) not to take any of the prescribed medication. I was mindful of my diet before and after the procedure and I used a gargle of mixed antibacterial herbs as often as I could after the procedure.
    I was stunned myself over the outcome. Being in general sensitive to pain I had expected a certain degree of pain but to my amazement I only experienced a slight “sensation” on the day and then the healing and recovery was very smooth and quick.
    When I think I avoided unnecessary dose of antibiotics and heavy painkillers I am amazed what can be done with diet and herbs. A great job done by the dentist needs also be acknowledged.

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