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Supporting a balanced gut microbiome (& what to do when taking antibiotics)


PART 1: The Gut Microbiome


After having to take a recent course of antibiotics for a tooth infection which resulted in a few side effects (skin issues etc. I was caught off guard and wasn't super prepared), I wanted to share a little about the gut microbiome and ways in which we can support our gut both during and following antibiotics. I'll be covering a little about the gut microbiome first, so if you're just here for the tips, skip to part 2!

An abundance of research has been emerging over the past decade or so, demonstrating the importance of the gut microbiome for the health of the digestive system, but also way beyond the gut. The gut microbiome plays a major role in everything from immunity to skin health to hormonal balance and behaviour, but what is the gut microbiome?

The gut microbiome is made up of trillions of microorganisms, which live within the digestive system, the majority within the large intestine. This microbiome is made up of bacteria, but also archaea (similar to bacteria but not), viruses and eukaryotic organisms such as fungi. In a healthy gut, all of these different microbes live in harmony, keeping each other in balance.

We know from the research that a healthy microbiome can look different from one person to the next. However, we also know that diversity, meaning a diverse range of bacteria found within the gut, is a strong sign of a healthy gut microbiome. On the other hand, we know that dysbiosis or disruption to the delicate balance of the microbiome can cause a whole host of issues. When levels of good bugs are depleted, this allows more harmful bugs to overgrow and cause issues, both within the gut and beyond.

So what influences the microbiome? The microbiome begins to develop early in life, with genetics, parental health, delivery (vaginal or caesarean) and feeding (breastmilk or bottle fed) all influencing microbiome development. Beyond this, the food you consume, stress levels, exercise and medication to name a few, greatly impact the health of the microbiome.

Most notably, we know that antibiotic use can have a negative impact on the gut microbiome by reducing the healthy diversity we discussed earlier, as well as causing antibiotic-associated diarrhoea. Antibiotics revolutionised the way infections are treated, but despite this, we know that there're concerns about overprescribing and misuse of antibiotics which have contributed to antibiotic resistance, meaning some bacteria can become resistant and no longer respond to antibiotics.

Whilst antibiotics have both short-term and long-term consequences, there are times when antibiotics are 100% necessary and in some cases life-saving. So the question is, when necessary, how can we can support the health of our gut, both during and following antibiotic use?




PART 2: Tips & Tricks

Fermented foods:

The fermentation process of typical foods like vegetables and milk allows for bacteria to convert carbohydrates (sugars) into lactic acid and allows for the growth of beneficial bacteria including lactobacillus species, all whilst reducing pathogenic bacteria.

The process of fermenting foods can provide various benefits including enhancing nutrient content, improving nutrient absorption, reducing pathogens found in food and providing a rich source of probiotics to support a healthy, diverse and balanced gut microbiome.

Some of my favourite fermented foods include:

  • Sauerkraut

  • Kimchi

  • Pickles

  • Yoghurt

  • Kefir

  • Miso

  • Kombucha

Typically we want to look for fermented foods which contain active cultures and have undergone minimal processing, as processing can reduce the amount of probiotics in the final product. You'll typically find these products in the fridge section of your grocery store. In addition, different products contain different strains of beneficial bacteria, so consuming a wide range of fermented foods can help to support microbial diversity and a more balanced gut.

When introducing fermented foods, it's always wise to include them slowly. It's important to note that fermented foods are typically high in histamine, so if you have symptoms of a histamine intolerance or irritable bowel syndrome, just be mindful to introduce fermented foods in small quantities and introduce slowly, building up as tolerated.

Prebiotic foods:

You can think of prebiotics as the fuel your good bugs need to thrive. Simply put, prebiotics are typically non-digestible carbohydrates that pass through the digestive system and are fermented by bacteria, allowing them to grow and produce byproducts which are beneficial for health. Some non-carbohydrate sources can also have prebiotic actions, such as the polyphenols we can find in foods like berries and green tea. The best way to get in enough prebiotics is to include plenty of diversity of plant-based foods in your diet, not just sticking to the same three vegetables for dinner each week. Experiment by including different coloured vegetables, fruits and herbs in your meals.


Food-based sources of prebiotics include:

  • Onion

  • Garlic

  • Leek

  • Asparagus

  • Artichoke

  • Chicory root (you can typically find it in tea form)

  • Apples (specifically when cooked)

  • Berries

  • Green tea/matcha

  • Cacao

IBS & FODMAP intolerance:

Some individuals with IBS or symptoms of ongoing bloating, distension and gas may have an intolerance to something called FODMAPS, or fermentable oligosaccharides, disaccharides, monosaccharides and polyols.

FODMAPS are types of fermentable carbohydrates which are not fully digested. In some people, this fermentation can cause a lot of discomfort, bloating and pain. Although incredibly healthy, many prebiotic foods are also high in some FODMAPS. My recommendation is to start slow when increasing prebiotic foods, specifically those high in FODMAPS.

If digestive symptoms are causing you lots of concern, it could be worth looking at whether there is some sort of dysbiosis going on, such as a condition called SIBO (small intestinal bacterial overgrowth). Working with a naturopath to get the right testing and right treatment is my number one recommendation.


Supplements: Probiotics

Because we know antibiotics also delete beneficial bacteria, it's commonly thought that taking a probiotic during or following a course of antibiotics outweighs any negative effects of the antibiotic, make sense right? Unfortunately, it's not quite as simple as that.

The current understanding is that not all probiotic strains will directly colonise or replace the beneficial bacteria lost during antibiotic use, but they do still have a benefit. The studies we do have show that those who take probiotics have a greater ability to restore balance to the gut microbiome following antibiotics. Probiotics can also help to create an environment where harmful bacteria (pathogens) cannot overgrow.

This being said, it can take a while for the gut microbiome to restore to a healthy balance, especially following multiple rounds of antibiotics, so just keep in mind that probiotics do not cancel out the impact of antibiotics on the microbiome.

Based on my understanding of the research, I do think it's helpful to supplement with a probiotic both during and following antibiotic use, but it's always best to chat with your health practitioner before adding anything in. Just be careful to choose a product that’s high quality so it does its job and reaches the intestines where we want it to act. Best to chat with a practitioner about the best type for you!


Antibiotic-associated diarrhoea (AAD):

Diarrhoea is an absolutely dreaded side effect that occurs in anywhere from 5% to 39% of patients taking antibiotics. It occurs as a result of the depletion of beneficial bacteria we see as a consequence of antibiotic use. Probiotic use has been shown to be useful in reducing the risk of AAD. Two specific probiotic strains in particular have been shown to have the largest benefit, Lactobacillus rhamnosus GG and Saccharomyces boulardii.

To wrap it up:

  1. Focus on fermented foods daily, as tolerated. This could be as simple as having yoghurt for breakfast (greek, goats, coconut) and a small amount of fermented vegetables like sauerkraut on a sandwich or salad.

  2. Focus on prebiotic foods, again as tolerated. Try adding stewed apples to your breakfast and drinking green tea or matcha daily. Ensure plenty of diversity of plant foods in the diet by popping to your local greengrocer and picking a few fruits and veg that aren't on your usual rotation.

  3. Lastly, consider a good quality multi-strain probiotic to help reduce the negative side effects. Ideally take as soon as you start taking your antibiotic and continue for at least a few weeks after. Consider Lactobacillus rhamnosus GG and Saccharomyces boulardii if antibiotic-associated diarrhoea is a concern.



I hope that gives you a little insight and some easy steps to implement if you're wanting to support your gut the best you can. If you're experiencing chronic gut symptoms such as IBS, one on one consultations are available. If you're needing short-term support or recommendations for the best probiotic for you, feel free to book a quick 15 minute consult!!


Lauren xx




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