How antibiotics affect the microbiome

Antibiotics impact the gut microbiome by causing rapid reductions in microbial diversity and shifting the balance of bacterial populations in the gut away from health-promoting species. The longer the course of treatment, the more species are affected and the longer the microbiome takes to recover. Taking a combination of different antibiotics is also more disruptive to the gut microbiome, as is repeated course of antibiotics.

After antibiotic treatment, gut bacterial populations can recover within a few weeks. However, some studies show it can take months to rebuild and occasionally a course of antibiotics can lead to the extinction of certain species (Palleja et al 2018).

Antibiotics commonly reduce key beneficial bacteria such as Bifidobacterium and Faecalibacterium, while allowing populations of opportunistic, inflammatory species such as Escherichia and Klebsiella to expand. This is why some people experience diarrhoea, which is a common complaint when on antibiotics.

Microbiome recovery is highly individual, and your baseline composition strongly influences outcomes. Some people recover quickly, while others experience lingering digestive issues and other systemic symptoms.

Gut microbiome repair

As practitioners looking to support you to restore your microbiome, we focus on three things: diet, probiotics and prebiotics.

Diet

The most important factor in restoring the gut ecosystem and maintaining microbiome health in the long term, is ensuring your diet has plenty of plant foods. These are rich in fibre, including prebiotics, and contain different polyphenols that feed our beneficial bacteria.

Poor diets, lacking in prebiotics and polyphenols, can increase vulnerability to infection after antibiotic use, while conversely, plant-rich diets increase microbiome resilience to antibiotic treatment (Kennedy et al 2024).

Probiotics

Research has shown that using probiotics alongside antibiotic treatment leads to a faster recovery of beneficial species (John et al. 2024). Probiotics do not re-seed, rather they support and communicate with other organisms in the gut, influencing bacterial behaviour, gene expression and immune responses.

We refer to clinical trial data to see what probiotic strains would be most supportive, including whether the antibiotics are targeting a respiratory infection or a gut infection.  We commonly prescribe Saccharomyces boulardii CNCM I-745 (SB) and Lacticaseibacillus rhamnosus GG (LGG). Clinical trials have shown SB is very effective at reducing antibiotic-associated diarrhoea. SB is a yeast, so antibiotics (that only target bacteria) don’t decrease its efficacy. SB doesn’t decrease the effectiveness of antibiotics either. For safety reasons, there are some cases where we wouldn’t recommend SB, including where someone’s health is very frail or where there are deep puncture wounds or cannulas in use.

Clinical trials show LGG protects against antibiotic-induced changes in the microbiome, reduces inflammation markers and positively influences microbiome balance. However, LGG is also impacted by antibiotics, so this requires frequent, high doses and timing carefully within the antibiotic regimen. Depending on the nature of the infection and your health needs we may prescribe better-targeted probiotics.

Prebiotics

Prebiotic fibres selectively feed beneficial gut bacteria, helping support microbial regrowth after antibiotic exposure. Prebiotics have been shown in human studies to increase populations of beneficial bacteria and to promote the production of health-promoting short-chain fatty acids, particularly butyrate.

Prebiotics are found naturally in certain plant foods, but for protecting the gut microbiome from antibiotic-induced changes and for encouraging large-scale and long-term shifts in the gut ecosystem, we recommend prebiotic supplements (usually powders that can be mixed into drinks or food).

We most commonly recommend partially hydrolysed guar gum (PHGG), lactulose, galactooligosaccharides (GOS), or inulin/FOS. Each different prebiotic has different properties and targets different groups of beneficial bacteria. For example, PHGG is the most gentle on the stomach and can normalise stools and help prevent antibiotic-related diarrhea. Inulin/FOS feeds up a broader range of beneficial bacteria but can cause digestive symptoms especially if used in large quantities.

In our practice, we personalise all our treatment plans, and so we consider an individual’s microbiome profile, health history, diet, lifestyle, symptoms and other needs in order to choose which prebiotic to recommend and at what dose. It’s always helpful to have baseline microbiome data gathered prior to antibiotic use to guide our treatment plans. However, if someone hasn’t done a microbiome stool test before commencing treatment, we can still make recommendations for prebiotics to take alongside and immediately after antibiotic treatment to help protect microbiome health, but our recommendations may not be so well targeted.

Tracking progress

Gut bacterial populations can fluctuate rapidly for several weeks after the course of antibiotics is completed. We usually advise stool testing after a few weeks of microbiome support to check the impact of treatment, ensure the most accurate advice and inform any treatment plans going forward.

If you are about to take a course of antibiotics, or have recently completed a course, please get in contact for microbiome support.

REFERENCES

Elvers KT, et al. (2020) Antibiotic induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review. BMJ Open. 10.1136/bmjopen-2019-035677

John D, et al. (2024). A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome. Frontiers in Microbiomes, 3.

https://doi.org/10.3389/frmbi.2024.1359580

Kennedy, M.S. et al. (2025) Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature.

https://doi.org/10.1038/s41586-025-08937-9

Palleja, A. et al. (2018) Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 3.

https://doi.org/10.1038/s41564-018-0257-9

Reflux, or Gastroesophageal reflux disease (GORD) is a chronic condition where stomach acid frequently flows back into the oesophagus, leading to mucosal damage and symptoms such as heartburn, regurgitation of food or acid, chest pain, chronic cough, difficulty swallowing and dental erosion.

There are many factors that contribute to the onset of GORD, the most common being reduced tone in the lower oesophageal sphincter (LOS). This can be caused by certain medications, such as NSAIDs, calcium channel blockers, barbiturates, and anticholinergics. Decreased saliva production and delayed stomach emptying are also contributing factors, as are lifestyle factors such as smoking, obesity, a diet high in fatty and processed foods, and alcohol consumption.

Gut dysbiosis contributes to both reflux and GORD symptoms and slow transit time and methane overgrowth can increase symptoms. Gut dysbiosis occurs when there is an imbalance between beneficial bacteria and harmful bacteria in the gut microbiome. Certain species of Proteobacteria and Fusobacteria produce lipopolysaccharides (LPS) which contribute to systemic inflammation and are thought to promote reflux by oesophageal sphincter relaxation. Research shows that high levels of Proteobacteria and Fusobacteria are more evident in people with GORD.

Conventional medicine includes proton pump inhibitors (PPI), H2 Receptor Antagonists (H2RAs) and other antacids which reduce stomach acid and can help with symptom management. However, they fail to address the cause of the reflux and are associated with many side effects such as diarrhoea, nausea, and abdominal pain. They also increase the risk of Small Intestine Bacteria Overgrowth (SIBO), Colonic Methane Overgrowth (CMO), nutrient malabsorption, and gut dysbiosis.

We use Microbiome testing to identify and treat any underlying drivers of reflux. We develop individual treatment plans based on your unique microbiome profile and your symptoms. Our holistic approach includes dietary and lifestyle recommendations and targeted supplements where necessary.

Here are a few of my recommendations.

Dietary modifications:

1. Eat a fibre-rich, plant-based, Mediterranean style diet.
2. Avoid trigger foods such as chocolate, fatty foods, and processed foods.
3. Avoid alcohol, sugar, and minimise coffee.
4. Have a 3-hour window between dinner and bedtime.
5. Do not consume fluid with meals or immediately after meals.

Lifestyle changes:

1. Elevating the head of the bed by 20-30 cm can reduce night-time reflux.
2. Stop smoking or vaping.
3. Reducing weight can alleviate symptoms.
4. Managing stress through breathing and nervous system support.

If you want to know more, please make an appointment or book in a discovery call.

REFERENCES:

De Bastiani et al. (2023) Assessment of small intestinal bacterial overgrowth and methane production in patients on chronic proton-pump inhibitor treatment: prevalence and role of rifaximin in its management in primary care. Minerva Gastroenterol 2023;69:523-8.
DOI: 10.23736/S2724-5985.21.03118-1

Baumeister et al. (2019) Gut microbiota and oesophageal disease – an update Microbiota Health Dis 1: e207 1 II.
DOI: 10.26355/mhd_20201_207

Cinnamon is known for its warm and sweet flavour, but it has a lot more to offer than its culinary applications. Cinnamon has been valued for centuries for its medicinal properties, and research shows it can be effective in reducing high blood pressure, regulating glucose levels, reducing inflammation, and improving cognition.

Cinnamon is rich in polyphenols, which are plant compounds known for their antioxidant properties. These polyphenols, including procyanidins and cinnamaldehyde, exhibit strong antioxidant activity, protecting cells from oxidative stress and damage caused by free radicals. Cinnamaldehyde has been shown to inhibit the release of pro-inflammatory cytokines in the gut, thus aiding in the reduction of gut inflammation and promoting gut health.

Cinnamon also exhibits prebiotic-like activity, supporting the growth of beneficial gut bacteria and suppressing the growth of pathogenic bacteria, positively impacting the balance of the gut microbiome. Several studies in healthy adults have demonstrated that cinnamon extract significantly increased the abundance of Bifidobacteria, Akkermansia and Lactobacillus, all known for their beneficial effects on gut health.

Studies have also shown that cinnamon oil can improve the oral microbiome by exhibiting a broad range of antimicrobial activity against the microbes causing dental caries. This is significant as dental caries is a risk factor for heart disease and Metabolic Syndrome.

Cinnamon also has many nutritional benefits. Adding one teaspoon (2-4 grams) of cinnamon powder a day provides calcium, potassium, vitamin A as well as small quantities of fibre and trace amounts of many other vitamins and nutrients.

So be bold and start adding cinnamon to your food and reap the benefits of its exotic taste whilst also supporting your gut microbiome and promoting optimal health.

REFERENCES

Jeong. et al. (2021). Antibacterial and antibiofilm activities of cinnamon essential oil nanoemulsion against multi-species oral biofilms. Sci Rep 11, 5911. DOI: 10.1038/s41598-021-85375-3

Kim et al. (2019). “Severity of dental caries and risk of coronary heart disease in middle-aged men and women: a population-based cohort study of Korean adults, 2002–2013.” Scientific Reports 9:10491 DOI: 10.1038/s41598-019-47029-3

Lu et al. (2019). “Mixed Spices at Culinary Doses Have Prebiotic Effects in Healthy Adults: A Pilot Study” Nutrients 11, no. 6: 1425. DOI: 10.3390/nu11061425

Lu et al. (2017). “Prebiotic Potential and Chemical Composition of Seven Culinary Spice Extract” Journal of Food Science Aug; 82(8): 1807–1813 DOI: 10.1111/1750-3841.13792

Mollazadeh et al. (2016). “Cinnamon effects on metabolic syndrome: a review based on its mechanisms.” Iran J Basic Med Sci. Dec; 19(12):1258-1270. DOI: 10.22038/ijbms.2016.7906.

Rao PV, Gan SH. (2014). “Cinnamon: a multifaceted medicinal plant.” Evid Based Complement Alternat Med. 642942. DOI: 10.1155/2014/642942

Vicky Ellenport BHSc NUT is a registered Nutritionist and Microbiome Analyst who uses a food first approach in her treatment protocols.

Research shows that the digestive condition known as leaky gut (or intestinal permeability), is a common factor in the biological mechanism that leads to the onset of autoimmune disease.

While it is easy to make the connection between the gut and digestive conditions such as food allergies, Celiac disease, Crohn’s Disease, and Ulcerative Colitis, the link to autoimmune disorders such as Type 1 Diabetes, Multiple Sclerosis or Rheumatoid Arthritis etc can be a little harder to grasp.

So, let’s break it down….

Firstly what exactly is the Gut?

The word gut is another way of referring to your gastrointestinal tract (GIT) or digestive system. Put simply, the gut is the passage through which food enters your body through your mouth, is digested (or broken down) in your stomach, beneficial nutrients are absorbed in your intestines (the small and large bowel) and then toxins and wastes are expelled via the rectum.

The innermost surface of the gut is known as the intestinal barrier.

This barrier is semipermeable as it allows certain substances to pass through it but not others.  It is the role of this barrier to protect the body by only allowing nutrients, water and electrolytes to cross into the blood stream while preventing undesirable substances from entering the body by retaining them in the gut to be excreted as waste.

How does the gut become leaky?

Disruption to the intestinal barrier in the large intestine causes damage to the tight bonds that hold the cells of the gastrointestinal lining together. When these bonds are broken, gaps form in the lining allowing contents of the gut to pass into the body via the bloodstream. This is known as increased intestinal permeability or leaky gut.

In leaky gut, pathogens, toxins, partially digested food and bacteria are able to leak through the gaps between the cells and enter the body. When these substances leak through the barrier, immune cells identify them as a potential threat and initiate an immune response in order to protect the body.

This immune response creates inflammation. In some cases, inflammation can become widespread throughout the body and contribute to many health issues, including autoimmune disease.

So, what causes disruption to the intestinal barrier?

1. Gluten. Zonulin is a protein secreted by the cells in the gut wall to stimulate the opening of gaps between cells in the intestinal barrier, to allow nutrients to pass through into the bloodstream. Gluten increases the production of Zonulin, resulting in numerous gaps in the intestinal barrier. It is believed that this mechanism is common to all autoimmune diseases and may be caused by proteins in all grains and pseudo-grains.
2. Dysbiosis. The gastrointestinal microbiome regulates the permeability of the intestinal barrier. An imbalance of good and bad bacteria living in the gut can lead to an overgrowth of pathogenic species. Pathogenic bacteria can cause inflammation in the gut lining causing damage to the intestinal barrier.
3. Sugar. Elevated blood glucose causes inflammation and alteration to intestinal cells that leads to intestinal barrier dysfunction.
4. Stress. Stress hormones can lead to inflammation which impacts the balance of gut bacteria by supporting the growth of pathogenic microbes that lead to dysbiosis and a leaky gut.
5. Alcohol. In addition to affecting the microbiome, alcohol has a direct effect on the intestinal barrier , causing cellular damage and increased permeability.

Finally, how does leaky gut lead to Autoimmune Disease?

For people with a predisposition to AID, the activation of the immune system, as a result of barrier disruptors entering the bloodstream, can lead to the production of autoantibodies – antibodies produced by the immune system that attack the body’s own tissue.

Autoantibodies are stimulated by the presence of inflammation when the body’s back-up system, which eliminates or regulates the cells that produce autoantibodies, fails and the immune system initiates an attack on the tissues.

Autoantibodies can attack local, gastrointestinal tissue leading to conditions such as Inflammatory Bowel Disease and Coeliac disease but they can also travel in the bloodstream and affect joints, organs and tissue anywhere in the body.

The good news is that leaky gut is reversible, and when your gut heals, it is possible to resolve Autoimmune Disease or achieve remission.

Using microbiome stool testing we can rebalance the bacteria in the gut. We can also use an elimination diet like AIP to reduce inflammation. By focusing on diet and lifestyle factors and microbiome modulation we can reverse leaky gut, regulate the immune system and resolve autoimmune symptoms.

Five Ways to Support Gut Healing:

1. Anti-inflammatory foods. Inflammation is one of the main drivers in AID and leaky gut. Including anti-inflammatory foods helps to heal the gut and manage AID symptoms. Anti-inflammatory foods include turmeric and Omega-3-rich oily fish (salmon, sardines, mackerel, anchovies, herring).
2. Probiotics. Eating fermented foods are an excellent way to increase beneficial bacteria in the gut to improve the microbiome balance. Non-dairy fermented foods include sauerkraut, kimchi, kombucha, coconut kefir and apple cider vinegar.
3. Prebiotics. Prebiotics are a type of dietary fibre that feed the good bacteria in your gut. Prebiotic foods include onion, garlic, leek, asparagus, artichoke and bananas. Using targeted supplements like PHGG or GOS can also be beneficial.
4. Glutamine. Glutamine is an amino acid which helps to tighten the gaps between the epithelial cells of the gut lining and improve barrier permeability. Glutamine is found in foods such as beetroot, cabbage, Brussel sprouts, grass-fed meat, seafood, bone broth, and grass-fed gelatin.
5. Reduce stress. Reducing stress is essential in order to reduce inflammation and to support gut healing and healthy immune function. Introducing techniques such as daily meditation, deep breathing or mindfulness practices helps to calm the nervous system, reduce stress and improve sleep.

To find out more about Leaky Gut or the Autoimmune Protocol and how it can work for you, book in for a Complimentary Discovery Session.