Faecal microbiota transplants have the potential to offer health benefits and are already used to treat C. difficile infections, but what can poo do for you and why should you look after your gut flora?
What is a faecal microbiota transplant?
The humble faecal microbiota transplant (FMT) has a long history, first being described 1700 years ago by a Chinese philosopher named Ge Hong, under the moniker of ‘yellow soup.’
The concoction – dried or fermented stool – was administered orally as a treatment for diarrhoea. With respect, an effective if not entirely palatable fix.
Similar uses have been documented in the veterinary world, as well as during times of war as an effective treatment on the front line, such as to treat bacterial dysentery in WWII.
Nowadays, we have other methods of administering the yellow soup. Techniques can involve freeze-dried capsules or colonoscopy. Perhaps not ideal, but certainly an improvement over Ge Hong’s technique.
What is your gut microbiota?
So, what is in your guts and how can a dose of poop make things better for you?
Your gut doesn’t just contain this morning’s breakfast, rather it hosts trillions of bacteria – up to 2kg of them! These bacteria (and some viruses and yeasts) are your gut microbiota. In recent years we have discovered links between your gut microbiota and your physical and mental health. Previous estimates thought that the bacterial cells in your gut outnumbered your own intestinal cells by ten to one, though more recent estimates have lowered this to just over 50% of your cell count.
You wouldn’t go amiss treating your microbiota as an organ, such is its impact on our health and wellbeing. Another way to look at it is that our genome isn’t just our human genome, but also our microbiota’s genome. As Professor Sarkis Mazmanian, a microbiologist from Caltech, put it, “What makes us human is, in my opinion, the combination of our own DNA, plus the DNA of our gut microbes”.
What do we gain from this relationship with our gut microbiota? Our microbiota help digest food into available nutrients for us to absorb; it helps form and matures our intestinal immune system. Additionally, the microbiota blocks colonisation of our guts by harmful bacteria in a process known as colonisation resistance, which can be summed up simply as our bacteria forming a barrier against colonisation by alien species of bacteria. Our guts are valuable real estate, so keeping a happy, beneficial compliment can keep the riff-raff from moving in. In turn, our microbiota is provided with a lovely, warm home and regularly fed.
We get our first colonisation of bacteria as we are being born, with lasting consequences. Bacteria from a mother’s gut and vaginal canal colonise newborn babies. In fact, for vaginally-born babies, arguably this is your first faecal transplant. Caesarean babies first meet the skins’ microbiota and have demonstrated a higher incidence of developing allergies than vaginally-born babies. Don’t worry caesarean babies (of which I am one), we can influence and cultivate a ‘good’ gut microbiome.
What constitutes a ‘good’ gut microbiome?
Like all things, a one-size-fits-all approach doesn’t work; just as everyone is unique, so is their microbiome. That notwithstanding, the main factor that constitutes a ‘good’ microbiome is simple: diversity. Much like the saying, don’t put all your eggs in one basket, having a diverse microbiome is beneficial. In fact, type microbiota diversity into Google Scholar and just read the titles of the top results. The general trend is that low diversity = an unwell host.
Most healthy adults share many of the same bacterial species in their microbiota. For example, Firmicutes and Bacteroidetes and to a lesser extent, the Actinobacteria and Proteobacteria. Our gut is also a host to yeasts and viruses. Whilst we loosely share many of the same bacteria, the proportions vary dramatically between individuals. Interestingly, what varies less – in healthy adults – is the functional gene profile of our guts. Whilst there may be quite a varied bacterial presence, the actual functions of the genes are similar and fulfil similar roles – such as amino acid metabolism.
Factors such as age, genetics, environment and diet can help shape our microbiota. Additionally, our use of antibiotics can have a drastic effect on our microbiota.
If we wanted to shape our microbiome, we can adopt a few strategies. Ultimately the most ‘natural’ medicine we can take is just a change of diet. A change of diet for ten days can affect our microbiota. A healthy, diverse bacterial population ultimately wants a diverse diet. This would contain fresh vegetables, fruit, fibre and interestingly, fermented foods such as kimchi.
Our doctors prescribe us a balanced diet, but this applies just as well for our gut. Imagine you recreated Supersize Me (don’t) and ate a Big Mac meal every day. The bacteria that crave fatty, sugary food will be ecstatic and will do well in the process. They may outcompete other bacteria and lead to a less diverse microbiome. There are also studies suggesting that your microbiome can influence what you want to eat. This could lead to a negative self-perpetuating cycle.
How do probiotics fit in?
The other routes you can follow are the probiotics and prebiotics. Prebiotics are the food for your bacteria, whereas probiotics are a delivery of bacteria to your guts. A good analogy is that prebiotics are the fertiliser for your garden, whilst probiotics are the seeds. Much like your actual garden, you wouldn’t deliver seeds without fertiliser to help them grow.
Prebiotics are essentially non-digestible fibre from food. They pass through our stomachs and serve as food for the ‘desirable’ bacteria. Foods such as onions and garlic can supply your prebiotic needs.
Probiotics are foods that contain a healthy bacterial profile – the chief sources include yoghurts and fermented food such as sauerkraut. Often, these foods come sterilised in the supermarket. If you see sauerkraut in a jar, it likely doesn’t have any live bacteria left. It will taste nice though, so can still be enjoyed with a wurst of your choosing.
Whilst eating well and cultivating a diverse microbiota is good practice all year round, there are times when your microbiota will need a boost. Such a time is when you’ve taken a course of antibiotics.
Antibiotic effects on microbiota
The effect antibiotics have on your microbiota, to continue the lawn analogy, are effectively an indiscriminate weed killer. Sure, some unwanted bacteria may be killed, but so will your lovely green lawn. As mentioned before, having a diverse microbiota is a good thing. It is important to ensure that you are getting the right pre and probiotics after a course of antibiotics to boost your gut flora. A change in your microbial landscape can take months or even years to return to their original state. The expression of genes, the synthesis of proteins and general metabolic output of the microbiota can be affected on a long-term basis.
What also happens with antibiotic use is that ‘undesirable’ antibiotic-resistance bacteria remain. They no longer have to compete with the ‘good’ bacteria and therefore proliferate in your gut. This may lead to disease.
Antibiotic-associated diarrhoeas, caused by various bacteria, and most worryingly, by Clostridium difficile can cause long-term recurrent infections and even a form of colitis. C. difficile infections (CDIs) have been the subject of FMT trials already, but what exactly is C. difficile and how do we get infected?
C. Difficile infection
Clostridia are a family of bacteria that are ubiquitous in nature and prevalent in soil. They can be pathogenic and produce toxins which may produce inflammation in our guts. It is difficult to treat CDIs in a traditional manner with antibiotics as in many cases they are resistant to antibiotics. Antibiotic resistance is a major health concern worldwide and due its own article. Before I get around to writing one, have a Google for yourself.
It has been shown in mice that a post-antibiotic gut environment favours C. difficile germination and growth by reducing colonisation resistance and by increasing certain metabolites in the gut that can be exploited by C. difficile. Antibiotics are the traditional treatment for CDIs, so when put in the position where we have infections and proliferation of antibiotic-resistant bacteria we really are fighting a losing battle pursuing this course of treatment.
In the US, the antibiotics metronidazole and vancomycin are the first lines of defence, despite increasingly losing their efficacy. Their use keeps the gut in a weakened state by killing off the non-resistant bacteria that keep the gut running. This is a story repeating itself globally as we find many traditional antibiotics are impotent against bacterial infection.
Benefits of poo
What can we do to fight such a threat? The unorthodox-sounding FMT comes into play.
Antibiotic treatment for CDI is the norm, however, just cultivates an environment for remaining, and likely antibiotic-resistant, C. difficile to grow. Faecal transplants from a healthy donor reintroduce a bacterial profile to the gut.
This increases colonisation resistance, helping those suffering from CDI to recover on a long-term basis. The stool samples are prepped in a relatively simple fashion – collect a fresh sample, homogenise, dilute as necessary, strain and then administer orally or through colonoscopy.
In a previous trial, it was concluded that FMT resulted in better outcomes when compared with vancomycin therapy.
There may be benefits even if you don’t have a CDI. It doesn’t seem unreasonable to suggest that FMT would be beneficial after a course of antibiotics. It could serve as a ‘top up’ to your microbiota.
Surely there are downsides? It’s poo!
The problem with poo as a treatment is just that, it’s poo. We all have access to it. The only thing holding anyone back from administering their own FMT really is just willingness. It isn’t something I would advise. If your microbiota or gastrointestinal health is a concern, I would speak to a medical profession and evaluate your diet. Additionally, unlike most medicines, it is not a controlled substance, meaning there is no regulation over what you’re putting in.
FMT is still in its early stages, and many groups are looking to study it to isolate the beneficial complement of the faeces and prepare a more controlled and regulated treatment. You can screen healthy donors, but what they donate is ever changing and inconsistent.
Worth noting too is that we do not fully understand the mechanism by which it works. The theory is that it introduces a bacterial complement to the gut, but it is never that simple in biology.
Anecdotally, FMT has been shown to have side effects. Many clinics are registered to administer FMT in the US. One such case involved a 32-year-old woman receiving a faecal sample from her borderline obese daughter. A year later the naturally slim woman complained as she had undergone a weight gain, which she was unable to shift.
After reading this article you may be thinking, “Do I have a good microbiota? Do I need FMT? How do I find out?” I have seen adverts (more since I started writing this article – thanks cookies) popping up about microbiome test kits. Personally, I don’t think I would recommend this. Whilst I don’t doubt the efficacy of the tests – using 16S rRNA sequencing – it is the conclusions I’m concerned with. Your microbiota is ever-changing based on diet and medication. What the tests may well show you is whether you have an abnormal microbiota. The way I view it is if you are happy and otherwise healthy, you shouldn’t require these tests. Failing that, if you have concerns, go to a medical professional.
Eating well and exercising shouldn’t be a reaction to an illness, but rather treated as a medicine in itself.