Do's and Dont's of Probiotic Use

Do you take a daily probiotic? Or you have been told that you should for good general health? While I often prescribe probiotics to may patients, it is important to know that not everyone needs a probiotic and that there are different types of probiotic strains that do different jobs in the body, so you should always know where your probiotic is from and what job you want it to do. To help, this is my little guide to the do's and dont's of probiotic use. 


  • Don't believe that when you take a probiotic that strain colonises your gut. When you take a probiotic, the bacteria in there don't hang around for any longer than a week. They simply live in your colon for a little while (which can be great when treating infection or other conditions, more below), but then we poop those strains out.  For the long term, the best way to influence an increase in your good gut flora is eating prebiotic foods. Prebiotic foods and nutritional supplements feed your own gut bacteria and also increase diversity,  to help make your own to improve your gut and overall health. My favourite prebiotic foods are onions, garlic, brown rice, chickpeas, asparagus, dark cocoa and pumpkin seeds. When people have had long-term digestive issues, antibiotic or other medication use I will also prescribe prebiotic supplements to aid in building microbiota. 
  • Don't feel the need to take a probiotic daily for general health. As I spoke about above eating prebiotic foods is the key to getting and keeping a healthy diverse gut microbiota. Therefore if you are in good health (and even if not so!), include prebiotic and polyphenol-rich food in your diet for maintaining good gut bacteria. This is generally a diet that is high in plant-based foods such as vegetables, fruit, whole grains, legumes, nuts, seeds, with essential fats from fish, olive oil, avocado and small amounts of animal protein. Minimal to no refined sugar and trans fats (ie processed foods) should be consumed. 
  • Don't give probiotics to breastfed babies unless directed by your naturopath or nutritionist. Human breast milk has an amazing way of determining a baby's needs with immune cell complex travelling through the mother's body, picking up bacteria from her intestines and then transferring these to the breast milk. Breast milk also has the ability to feed and seed a baby's gut, so it is not only providing bacteria but also feeding the bacteria at the same time. When a probiotic is given to a baby it is potentially disrupting the gut microbiome by introducing unknown species. Probiotics can be great for helping with conditions such as thrush and colic in the baby, but they should always be given to the baby through the mother. Therefore the mother takes the probiotic and the bacteria will be transferred through the milk. This only occurs with certain strains, and why it is so important to speak to your naturopath first before treatment to get the best possible outcome. 
  • Don't just take any probiotic if you would like to use them for treatment, be aware probiotic strains all have different roles.  If you have allergies, parasite infections, IBS and IBD, autoimmune disease, low immunity, chronic fatigue syndrome,  depression, anxiety, chronic UTIs, trouble with weight loss or blood sugar issues and more, probiotics can all be useful in treatment. BUT, there is not one probiotic that treats all of these conditions, so it is important to know what strain you need. For example, Lactobacillus rhamnosus GG is great for helping with eczema, but may not be as useful as the strain Lactobaccillus rhamnosus GR-1 or Lactobacillus reuteri RC-14 for bacterial vaginosis. Confused yet? Yep well it's no surprise, a lot of healthcare professionals can't get their head around this! Different strains for different conditions! Just the same way that we have the species 'dogs', but then we have different types that have different qualities. We wouldn't ask a chihuahua to pull a sled we would get the husky to do that, just the same way that different probiotic strains have different conditions to treat. 

So now we have covered some of the do not's for probiotics use, let's have a look at some of the great things they can do!


  • Do use to treat conditions such as IBD, weight loss, depression, anxiety, autoimmune disease, chronic fatigue syndrome, allergies, skin conditions. Because probiotics have achieves amazing results in helping treat these conditions. But always make sure to use the right strain for your condition (see above). 
  • Do test, don't guess: if you have a long history of taking medications such as anti-inflammatory medications or antibiotics, have a suspected parasite or candida infection, or you have long-term chronic health issues, it is best to test your stool (poo) first before treatment, so you can be sure you are building up the correct bacteria through prebiotics and probiotic support. I think the Ubiome Gut Explorer is the best microbiome test we have currently available to use in Australia. I have moved away from culture-based tests, as believe they are inaccurate. 
  • DO use during antibiotic use. Many people think that they can't take probiotics while they are on an antibiotic. Taking probiotics while on antibiotics can prevent antibiotic-associated diarrhoea and thrush infections that often occur- just be sure to see a healthcare professional so you are using the right strains! It is best to take your probiotic away from your antibiotic by at least 4 hours, however, so the antibiotic does not kill the probiotic strains. 
  • Do be cautious if you Small intestinal bacterial overgrowth (SIBO)- SIBO is when there is an accumulation of gut bacteria in the small intestine that should generally only have a small number of bacteria. This can cause symptoms such as bloating, pain, excess gas, constipation diarrhoea, along with exacerbating symptoms of endometriosis, allergies, and pain conditions. The majority of  IBS patients, actually have SIBO. If you take a probiotic when you have SIBO, this could potentially make the condition and your symptoms worse. So it is important to seek the advice of someone that has knowledge in treating SIBO first. 

I hope the above has been a helpful little guide. If you have any questions, please write them in the comments below. 

If you are suffering from long-term digestive issues or another condition such as an autoimmune disease, endometriosis, depression or anxiety and you would love to learn how probiotics and other natural therapies can help, please send me an email at I would love to help you achieve great health and wellness. 

Yours in wellness,