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Can the Microbiome Be Used as Medicine?
What if we could use our knowledge of the microbiome to treat or even prevent disease? This is exactly what microbiome-based therapeutics are aiming to do. This blog post will define and explore seven different types of microbiome-mediated interventions: dietary interventions, prebiotics, probiotics, synbiotics, faecal microbiota transplant, live biotherapeutics, and microbiome mimetics.
1. Dietary Interventions: Shaping the Microbiome Through Food
Dietary interventions — changing the food that we consume — is probably one of the most obvious and accessible ways to shape the microbiome. Fermented foods have been consumed for thousands of years by humans, long before we understood what the microbiome even was. While dietary change is not a ‘therapeutic’ in the traditional sense, it is sometimes recommended for patients with IBS (Irritable Bowel Syndrome) and has been researched in the context of other diseases.
2. Prebiotics: Feeding Beneficial Bacteria
Prebiotics are specific components of food — usually indigestible dietary fibres — that are used by key bacteria in the gut. Unlike probiotics, prebiotics do not introduce new microorganisms; instead, they are intended to directly promote the growth of specific ‘beneficial’ bacteria already present.
Some examples include fructooligosaccharides and galactooligosaccharides, which can be found in infant formula routinely given to newborns. Although a wealth of prebiotic products are available, there is currently no formal recommendation for using prebiotics to treat any specific disease. That said, one study showed that the prebiotic PHGG (partially hydrolysed guar gum) was able to alleviate bloating symptoms in patients with irritable bowel syndrome.
3. Probiotics: Live Microorganisms for Gut Health
Probiotics — defined by the World Health Organisation as ‘live microorganisms that confer a health benefit on the host’ — are one of the most well-known microbiome-based interventions. Common bacteria found in probiotic products include Bifidobacteria spp. and Lactobacilli spp.
Despite the abundance of products available, there are currently no formal recommendations for using probiotics as a sole treatment for any specific disease. However, there is evidence that probiotics taken after completing a course of antibiotics can help restore a diverse microbial community.
4. Synbiotics: Combining Prebiotics and Probiotics
Synbiotics are a synergistic combination of prebiotics and probiotics. Think of it as giving specific ‘beneficial’ bacteria their favourite food to take with them on their journey through your gut. The idea of synergy means that the two components together offer a greater benefit than either would alone. Synbiotics have been explored in some studies, but a lot more research is needed before firm conclusions can be drawn.
An important note: prebiotics, probiotics, and synbiotics are all currently regulated as food products, not therapeutics. There are no formal clinical recommendations for using these products to treat specific diseases — so always be cautious when you see bold claims about what a particular product can or cannot do.
5. Faecal Microbiota Transplant (FMT): Replacing a Disrupted Microbiome
One of the most well-known microbiome-based interventions is faecal microbiota transplant, or FMT. This is specifically used to treat people with recurrent infections caused by the bacterium Clostridioides difficile, which can cause abdominal pain, nausea, and diarrhoea — and in some patients, recurs even after antibiotic treatment.
FMT is essentially what it sounds like: taking a stool sample from a healthy, screened donor and transplanting it into a patient, with the goal of replacing a disrupted microbial community with a healthy one. While the concept might seem far-fetched, the results from early clinical trials were so effective that researchers had to stop the trial — it would have been unethical for the patients not receiving FMT to continue suffering without access to it.
6. Live Biotherapeutics: A More Targeted Approach Than FMT
The remarkable success of FMT led researchers to ask: do we really need to transplant entire faecal samples, or could a more targeted approach work just as well? This is where live biotherapeutics come in. Similar to probiotics in that they contain living microbes, live biotherapeutics are distinguished by a key requirement — they must demonstrate an established clinical benefit in the treatment of a specific disease. This makes them a far more regulated and clinically rigorous category than standard probiotic products.
7. Microbiome Mimetics: Replicating Microbiome Function Without Live Bacteria
Microbiome mimetics are products designed to mimic the interactions between the microbiome and the host — replicating the activity or function of the microbiota for therapeutic benefit, without introducing actual live bacteria. This includes bioactive substances such as microbial proteins or peptides, and metabolites such as short-chain fatty acids (SCFAs). This approach could allow for highly specific and targeted therapeutic applications.
The Future of Microbiome-Based Therapeutics
It is clear that there are many different ways to work with the microbiome, and the potential to develop new therapeutic approaches is enormous. What is particularly promising is that, as research expands, future treatments will hopefully become far more targeted than the general “good bacteria” approach you typically hear about. The microbiome field is moving fast — and we are only at the beginning.
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