Two recent studies have recently been published that cast doubt on taking probiotics to help recover from a course of antibiotics. Crazy right? Ask anyone and they would tell you the opposite (as I would have). However sometimes research comes out that contradicts what we would previously have thought, and we have to be open to the idea that what we believed was in fact incorrect. The saturated-fat-heart-disease hypothesis is a clear example of dietary dogma that has been turned on its head* (and the difficulty that people have getting their heads around).
Gut health 101: The gastrointestinal (GI) tract is like a hollow tube, and the cells of the GI tract are covered by a thick protective gel, and that is the mucus layer (the inside cells of the gut are called the lumen). Each of these areas have a distinct microbial community, however these are rarely studied as they are difficult to get to (unless you have an invasive colonoscopy). The stool microbiome is also part of this gut picture and is the most often studied proxy marker as the gut microbiome and these are often used interchangeably (i.e. the bacteria you see in the stool is what we would expect to find in the gut). Interestingly, one study found that the stool microbiome is not representative of the gut mucosal or lumen microbiome, which really presents a challenge to any practitioner or patient who wants a better understanding of their gut health. It also doesn’t tell us about the gut endothelial microbiome which may be the closest to explaining our gut health as it is the closest bacteria to the gut tissue. They found that there was only a 20% correlation between the stool and the gut microbiome. While stool testing can be helpful for identifying pathogens or parasites, it’s not so useful for us to understanding the presence of ‘good’ or ‘bad’ bacteria. Stool testing is one piece of the puzzle, but it’s better alongside other tests (such as a SIBO test).
When you take probiotics, the presence of these in your gut is transient, and this is something that people are unaware of. Hundreds of trials have showed the safety and efficacy of probiotics in benefiting people, but it’s not typically through the colonisation of our gut. Like many things, we are different in the level of colonisation that occurs when bacteria is introduced into the gut – some people are more permissive than others, and some are really resistant to it. The researchers were not able to determine exactly what makes someone a ‘permissive’ coloniser and a ‘resistant’ coloniser, however suggested that the presence of certain bacteria in the gut may play a role in this. However, they are still beneficial despite this – with significant changes in the gene expression of people who took the probiotics (19 downregulated and 198 upregulated genes), confirming the idea that probiotics work at a cellular level and can enhance the activity of genes in the gut, aid in digestion, stimulate the immune system etc.
A surprising finding from a second study was that probiotics slowed the recovery of the gut microbiome after a round of fairly potent antibiotics. In fact, this is what I (and other practitioners) always recommend their clients do. Flooding the system with good bacteria has been thought to prevent the adverse effects of the antibiotics. The study wanted to see how the probiotics affect the long-term gut ecosystem after a single dose of the broad-spectrum antibiotic ciprofloxacin and metronidazole (to ensure all gut microbiome was wiped out). This particular study (conducted in both mice and humans) split the participants into three groups: one took no probiotic and were left to spontaneously recover; one group took an 11 strain bacteria probiotic for four weeks immediately upon finishing the antibiotics and the final group actually had what is called an autolagus fecal microbiome transplant (aFMT) – this is when a person takes capsules of their own fecal matter that had previously been collected when their gut is in a good space. Remember, the gut doesn’t like change, so what better than to replace the bacteria with some of your own? The results found that treating the gut with a course of probiotics delayed the return of the normal gut microbiota by as long as five months after stopping the probiotic treatment, and microbiota diversity stayed low too – well lower than the group who took nothing. In fact, the researchers found the group left to their own spontaneous recovery had no major differences in their stool microbiota within 21 days post-antibiotics. This is so different to what we understood about the ability of the gut to recover post-antibiotics. Again, there will be differences in what practitioners recommend, but to the best of our knowledge we thought that it took a good 18-24 months for the gut to fully recover from a round of potent antibiotics. This is actually incorrect too: previous research (when you delve further) shows that this may be the case for one or two strains of bacteria, but the majority actually recover fairly quickly and the composition of the gut microbiota resembles pre-treatment composition.
The gut microbiome is resilient, perhaps more so than what I (and others) had believed. This is only good news!
The researchers found the lactobacillus in the probiotic was what prevented the colonisation of the native bacteria in those that took the probiotic. This is the most commonly used bacteria in most probiotic strains. Again, this doesn’t mean that probiotics are NOT helpful in general (from the immune regulating benefits and what I’ve mentioned above) and we also don’t know how other probiotics which don’t contain the lactobacillus bacteria affect the gut (such as the yeast saccharomyces boulardis). There are so many different combinations of antibiotics and probiotics out there – and this is specific to this particular strain of probiotics and the type of antibiotic used. So it’s by no means the nail in the coffin for probiotics post-antibiotics, however it does call into question the broad recommendation and is something worth talking to your health practitioner about.