The Good, The Bad and The Microbiome

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I am absolutely delighted to bring you guys an article today in honour of World Microbiome Day (June 27th!), written by Irish registered dietitian Sarah Killeen, who is currently immersed in gut health research. Here is a little foreword from Sarah and about her research before you read into the article.

From Sarah: I am a Registered Dietitian and I am currently doing my PhD on probiotics with the UCD Perinatal Research Centre in Dublin. My team, which is led by Prof. Fionnuala McAuliffe are running an exciting new study called the GetGutsy study. We are testing a new probiotic which may have health benefits for some women. We need volunteers to take part and help us with this research.  To find out more, you can email or visit our website at: For more on probiotics and the microbiome, our colleagues in Cork have lots of useful resources: and


The Good, The Bad and The Microbiome

Bacteria and other “bugs” are everywhere! They live on and inside our bodies, in our environment and are essential to life as we know it. No matter how well we wash, we are covered in microbes. In fact, we carry more cells from microbes than our own (that’s 100 trillion microbes)! This large family of microbes is called the human microbiota and is unique to every person. The microbiome is the name for the genetic information (genes) of our microbiota.

Today (June 27th) is World Microbiome Day! On this day we recognise the important role microbes play in our health The gastrointestinal (GI) tract is the home of about 95% of all of our microbes. The most welcoming part of the GI tract for microbes to live is the large intestine and this is where the majority of our gut microbiota is found. We can become aware of our gut microbiota in everyday life when we get a “gut instinct” or “gut feeling” however they are constantly working inside us and can affect many parts of the body, from the brain to our immune system. They can break down food which we would otherwise be unable to consume and this helps us get more energy from the food we eat. They can also make vitamins in the gut which we can absorb.


Our microbiota is not fixed and can change in response to lots of things such as what we eat and how much we move. Unfortunately, not all of our little microbes are “good” and some can cause us harm. When the amount and types of microbes in the gut change, this can be helpful or unhelpful depending on whether we have gotten more “good” or “bad” microbes. Antibiotics for example, are medications which we need to fight certain infections. They kill the “bad” bacteria that are causing us to be sick but in the process, can also kill “good” bacteria. This creates space for either “good” or “bad” bacteria to fill. What we eat can help encourage “good” bacteria to grow and help us maintain the overall health of our gut microbiota.

Prebiotiotics are parts of foods which “good” bacteria like to use for energy and to grow. Eating prebiotics supports the growth of “good bacteria” in the gut. Most prebiotics in foods are types of fibre, however, some types of fibre are not prebiotics because they are not broken down by bacteria. These types help us in different ways by adding “bulk” to our diet and encourage a healthy gut transit. Foods which contain prebiotics include onions, garlic, bananas, and some wholegrains. Another option to encourage shifting the balance in your gut to “good” bacteria is to eat foods which contain “good” microbes. This includes foods such as yogurts or fermented milk drinks which contain live “good” bacteria.


Fermented foods are foods which use microbes to make them (e.g. to achieve a certain taste or texture). Examples include yogurt, kefir and sauerkraut. Not all fermented foods contain live microbes in the final product however, as they may be killed during a later step in the manufacturing process or during storage. Take for example sourdough bread which is baked – this kills the bacteria used earlier in production. Cheese is another example which may or may not contain live bacteria. Certain cheeses are heated to a level which kills the bacteria (e.g. cottage cheese) and others are aged for so long that the levels of live bacteria become very low as the bacteria die over time. Finally food additives which are intended to prolong shelf life may reduce the levels of live bacteria in the product e.g. picked dill pickles.

Probiotics are live bacteria which have been shown to have a health benefit to the consumer when a specific amount of them are taken.  Therefore, all probiotics are live bacteria, however, not all live bacteria are probiotics. To be officially recognised as a probiotic, microbes must have a proven health benefit. They also must contain enough of the helpful microbes in the product to produce the health benefit. Probiotics can be taken in lots of different ways, including as tablets, capsules, powders on their own or can be added to foods. They can also be given through special medical devices.


There are lots of probiotics out there and they each of work a little bit differently in the body. When you are choosing a probiotic, you must first think about why you are taking the probiotic and what it is you want to improve. There are certain probiotics which work well in situations such as after an antibiotic and others work better for diagnosed digestive issues (e.g. Irritable bowel syndrome or inflammatory bowel disease), reduced immunity or stress. For maximum benefit, it is important to look at which probiotics have been shown to support the benefit you want – it is not a one size fits all! It is also very important to give probiotics enough time to work (at least 4 weeks) and if they work, to keep taking them, usually every day. Certain probiotics may work better in some people compared to others so depending on your specific situation, it might take longer or a few different options to find the right probiotic for you. Probiotics must have a proven health benefit backed up by science.

I hope you guys enjoyed the article! Do let me know what you thought – you know where to find me, @theirishbalance on Instagram/Twitter/Facebook!

Ciara 🙂 x

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