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Shall i take probiotics after antibiotic treatment?

Updated: Nov 16, 2022



Probiotics are often presented in media headlines in two completely polarised ways. Either it’s a panacea for every existing disease or it’s a totally useless waste-of-money health pursuit.


Recently I had to undergo unexpectedily heavy antibiotic treatment that left behind an overly sensitive, disturbed and painful gut with a significant dysbiosis. Antibiotics for guts is like a nuclear bomb, it wipes out everything - good and bad bacteria. They completely disbalance this fragile and complex homeostatic relationship between billions of bacteria, fungi and viruses we are hosting in our intestines. So I was weighing pros and cons for specific interventions that would potentially help my damaged guts to accelerate the recovery.


One of them was probiotics. But I decided against this option, and let me explain why.


While the logic behind probiotics benefits might seem sound, it is clear that we have a long way before understanding the complexity of the microbiota and the effects that probiotics might have - good or bad. Each of us has a very unique gut microbiome, and the effects of different bacteria on individual levels are very likely to be variable.



Personally, I consider gut microbiome as complex as genetics, and I'm very sceptical about dropping a mix of just a few bacteria into this ocean of complexity, hoping to restore the integrity of inflamed guts. It’s like throwing a couple of bricks to a giant ruined building after the huge earthquake, naively believing it’s sufficient.


Our baseline knowledge on gut bacteria and their interactions is unfortunately very limited, and the commercial use of probiotics is massively outpacing the science. Having said that, I don't mean probiotics are useless and for some specific diseases, such as gastroenteritis for example, they have a potential benefit. My point is that in the case of post-antibiotic recovery I haven't seen any strong data supporting the use of any single specific strain of bacteria or a mix of them in large scale human trials.

In the best case scenario, it might have a harmless placebo effect, but in the worst case, it might actually disturb a natural recovery process.


In fact, I've actually seen an interesting 2018 study published in the prestigious journal Cell showing that probiotics induced a delayed and persistently incomplete stool/mucosal microbiome reconstitution. Researchers investigated the recovery of the gut microbiota after antibiotic treatment in humans and found that probiotics might perturb rather than aid this process. The probiotics rapidly colonised the gut but prevented the normal microbiota from repopulating for up to 5 months.


Other researchers also argue that colonisation happens in highly individualised patterns, with some people's gastrointestinal tracts rejecting probiotics and others allowing colonisation by the probiotic strain, meaning that many individuals taking probiotic supplements are simply wasting their money.


In the defence of probiotics, i believe that in the future it can be a game-changer but on a very personalised approach. That would include an assessment of individual microbiome and a targeted selection of specific genera/species/strain.

However, commercially available products might not contain the correct strains or quantities of bacteria to provide benefits, and most probiotic supplements contain only single strains, vastly oversimplifying the complexity of the microbiota.


Let me grab your attention for 2 more minutes and explain the basic classification of bacteria.


Do you know that when we refer to bacteria such as Lactobacillus or Bifidobacterium, we are just simply referring to the genera.



But, when you read Lactobacillus reuteri DSM 17938, for example, on a probiotic product label, it includes the genus (Lactobacillus), species (reuteri) and strain (DSM 17938).


Referring just to Lactobacillus is like referring to the general population, without specific ethnicity or individual differences.


Probiotics aren’t created equal. Different probiotics may have the same genus, but differences in the strain and species will have a different impact on your digestive health.


Think of probiotics like a family! So you and your siblings have the same family tree (the genus) and share the same name (the species) but you are very unique and different from your sister or brother (the strain).


So commercially available probiotics have different compositions and very different quantities of bacteria, but how to know which one is the best for you individually?



Remember, your microbiome is very different from anyone else. Moreover, there is no guarantee you will respond to the treatment in a similar way as others.


Now let’s get back to my antibiotic case.


After a reflection, I decided that the best approach would be to focus on my diet. It’s safe and proved to be effective! Diet and the environment have the most important long term impact on your gut microbiome than anything else.


Here are just a few important steps to implement in the unfortunate case of antibiotic treatment.



  • Removing or limiting any kind of gut-irritating food products from the diet for a month (or longer, depending on individual gut sensitivity). It includes alcohol, caffeine, spicy foods, citrus fruits, fried foods, too much fiber, beans and processed foods.


  • Drastically limiting sugary foods, at least for 8 few weeks after antibiotics. The simple reason behind - bad bacteria will thrive on excess of dietary sugar and fructose. Just after the antibiotic treatment, gut bacteria will immediately start repopulating the place but at very different speeds. It's a highly competitive environment! So you really want to optimise the process and prioritise good bacteria, rather than pathogenic proliferation. Diet high in sugar will most likely benefit the bad bacteria overgrowth, shifting the balance toward the negative health outcome.


  • Getting as much diversified diet as possible. It’s important that your gut has a high variety of different bacteria and fungi. Think of it as a garden, the more diverse and resilient the environment of the soil - the better quality produce grown on such rich soil.


  • Slowly introducing natural fermented foods, such as sauerkraut, kefir, miso, etc. These foods are rich in probiotics. By the way, do you know that naturally fermented kefir has multiple amounts of bacteria compared to commercially available probiotics. But it has to be a careful approach because it might simply be too harsh on a hypersensitive gut.


  • Trying not to overload the digestive system. Remember, post-antibiotic gut milieu is very compromised and fragile, so the last thing you want to do is to overload your system with heavy meals.


  • Exposing yourself to nature. Once we are immersed in the great outdoors, we’re literally bombarded by environmental microbiota—a thimble-full of soil containing billions of microbes, far more than there are humans on our planet. This abundance of environmental microbiota means our gut microbiome has countless choices when it comes to selecting which microbes to propagate. Fresh country air offers a microbial diversity that avoids the accumulation of harmful microbes.


By doing these simple gestures, I'm convinced you will achieve much more than just taking a pill.


We shouldn't underestimate the importance of gut health. We know now that by way of the gut microbiota, our digestive health influences not only the immune system, but also the development of chronic disease, and even mental and emotional health. In my case, it was a primary cause of my allergy and eczema for more than 10 years.


My approach to whether suggesting a specific probiotic to a client is the following:


I look at the whole picture including symptoms, health history, diet, and I also like to take into account individual gut microbiome picture thanks to various available functional lab tests. But before recommending any specific probiotics, I try to understand if there is any research evidence about specific strains, and whether it might have a desired impact on the health and wellbeing of myself and my clients. And it really has to be done jointly with other dietary and lifestyle interventions.


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1 Comment


George Graham
George Graham
May 08, 2021

Great post- I’ve often wondered about this. Not sure about probiotics in general- the effect they have in ’pushing’ out the bad stuff can be uncomfortable - happy to stick with the dietary approach! Hope you are feeling better!

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