Antibiotics have been one of the most valuable modern medicines since their discovery by Alexander Flemming in the early 20th Century. But, their many benefits have come with a price. Over prescribing has led to increased bacterial resistance and many antibiotics are becoming ineffective. This is because antibiotics are indiscriminate killing machines and will destroy the both the bad and the good. Increasingly we are learning the “good” microbiome is very important to our health.


Most doctors are now more judicious prescribing antibiotics and the wider population is more informed about their risks and side effects. However, there are times when the best option for your health and recovery is to take them.


Why you should care about your microbiome


Healthy gut flora is important for nutrient supply, production of vitamins and protecting the body from pathogens. An imbalance in your gut microbes is implicated in obesity 1. One of the reasons agriculture uses antibiotics is to help animals gain weight quickly. There is also research supporting their role in mental health through the production of neurotransmitters 2. As you can see our good bugs are working pretty hard for us!


Some research has suggested it can take between 4-12 months to restore our intestinal flora depending on the type of antibiotic and the duration of the prescription 3.


Is there anything you can do to ensure you get optimal results from your antibiotic? How can you help to restore your good microbiome?


While taking antibiotics


B Vitamins

Many of the B vitamins require bacteria in to make or activate them.

B vitamins are involved a multitude of processes in our bodies but two of the most relevant here are energy production and immunity. Two important things if you’ve been unwell. Take a good quality B Complex supplement to ensure you don’t miss out! The only caution here is they may be contraindicated if you are taking an antibiotic from the tetracycline family so check with your doctor.


Vitamin C and D

As immune supporting nutrients both vitamin C and D have been shown to enhance the effectiveness of antibiotics and reduce recovery time 4.


Saccharomyces boulardii

As noted earlier antibiotics kill off the good with the bad and this often results in an overgrowth of the less desirable strains such as Staphylococcus spp. and Escherichia coli and Clostridium difficile. These are often the culprits in antibiotic associated diarrhoea. Saccharomyces boulardii (SB) is a probiotic yeast resistant to antibiotics. This means you can take it at the same time as antibiotics. SB inhibits the growth of pathogenic strains and also improves the ability of your intestinal cells to fight the infection 5. Various studies have shown considerable benefit for SB in reducing antibiotic associated diarrhoea6.


After your course of antibiotics


Now we know how important the microbiome is to our health we need to restore it. This involves 2 key things: probiotics and prebiotics


Probiotics to seed

Probiotics help seed the digestive system with beneficial bacteria. There is some debate amongst health practitioners about whether to take probiotic concurrently with antibiotics or not. I prefer to use SB with the antibiotic and prescribe a course of probiotics afterwards. This is because most prescriptions for antibiotics are twice a day and it’s difficult to place the probiotic far enough away from them to ensure the bacteria aren’t destroyed.

When evaluating a probiotic to take post antibiotic look for one containing multiple strains (5 or more is ideal) and a CFU (colony forming unit) count of at least 10 billion.


Consuming fermented foods such as natural yoghurt, kefir, kombucha, sauerkraut, kimchi, miso, tempeh will also support the return of a healthy microbiome.


Prebiotics to feed

Prebiotics are a type of non-digestible fibre, which ferment in the small intestine. Prebiotics are important for post antibiotic recovery and beyond. While probiotics seed the good bacteria prebiotics feed the healthy microbes so you don’t need to keep taking probiotics 7. Dietary fibres classified as having high prebiotic effects includes inulin, fructo-oligosaccharides and galacto-oligosaccharides. The good news is these are really available in foods8. Make prebiotic foods a regular part of your diet to maintain healthy bacteria. If you find it difficult to get enough of these foods in your diet there are also supplements available.

Vegetables Jerusalem artichoke, chicory, garlic, onion, leek, shallots, spring onion, asparagus, beetroot, fennel bulb, snow peas, savoy cabbage
Legumes Chickpeas, lentils, red kidney beans
Fruit Custard apples, nectarines, white peaches, tamarillo, watermelon, grapefruit, pomegranate, dried fruit (dates and figs)
Grains Barley, cous cous, wheat bran, oats
Nuts & Seeds Cashews, pistachio nuts


Other nutrients to support this phase


You can also continue with your B, C & D vitamins.


How long for?


I recommend your antibiotic recovery plan should run for about 4-6 weeks after you complete your course of antibiotics. This will give you a chance to get your good gut bugs back into balance.


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  1. Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016;8(1):39. doi:10.1186/s13073-016-0294-z.
  2. De Palma G, Collins SM, Bercik P. The microbiota-gut-brain axis in functional gastrointestinal disorders. Gut Microbes. 2014;5(3):419-429. doi:10.4161/gmic.29417.
  3. Zaura E, Brandt BW, Joost M, et al. Same Exposure but Two Radically Different Responses to Antibiotics : Resilience of the Salivary Microbiome versus Long-Term Microbial. Am Soc Microbiol. 2015;6(6):1-11. doi:10.1128/mBio.01693-15.Editor.
  4. Zojaji H, Talaie R, Mirsattari D, et al. The efficacy of Helicobacter pylori eradication regimen with and without vitamin C supplementation. Dig Liver Dis. 2009;41(9):644-647. doi:10.1016/j.dld.2008.09.008.
  5. Htwe K, Khin SY, Tin M, Vandenplas Y. Effect of Saccharomyces boulardii in the treatment of acute watery diarrhea in Myanmar children: A randomized controlled study. Am J Trop Med Hyg. 2008;78(2):214-216.
  6. Szajewska H, Mrukowicz J. Meta-analysis: Non-pathogenic yeast Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Aliment Pharmacol Ther. 2005;22(5):365-372. doi:10.1111/j.1365-2036.2005.02624.x.
  7. Vyas U, Ranganathan N. Probiotics, prebiotics, and synbiotics: gut and beyond. Gastroenterol Res Pract. 2012;2012(872716):1-17. doi:10.1155/2012/872716.
  8. Kolida S, Tuohy K, Gibson GR. Prebiotic effects of inulin and oligofructose. Br J Nutr. 2002;87(S2):S193-S197. doi:10.1079/BJNBJN/2002537.


Need help with your gut health?

Norelle Hentschel is an experienced Naturopath with a clinic in Stones Corner, Brisbane who enjoys supporting her clients to reach their health goals.


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