Gut microbiome: do poo transplants or probiotics really help?

Written by: Dr Aathavan Loganayagam
Published: | Updated: 12/04/2023
Edited by: Laura Burgess

Scientists are searching what’s now turning out to be the most important organ in the body – the gut microbiome, which is a complex ecosystem of bacteria and home to the immune system. The microbiome plays a critical role in the digestion and absorption of nutrients, hormone balance, cognitive function, skin appearance and heart health.

But when the gut microbiota goes awry (which is known as dysbiosis) we may turn to treatments such as probiotics and faecal (poo) transplants for restoration. Here, expert gastroenterologist Dr Aathavan Loganayagam explains whether these options can re-engineer our gut bacteria and what the future of probiotics looks like.

What are the treatment options for infections in the gut?

The treatment options for infection in the gut include:

Poo transplants

Faecal transplants are the transfer of a faecal sample from a healthy donor to a recipient. This can be done via nasogastric tubes (inserted into the nostril, down the throat and into the stomach) or inserted directly into the colon.

Faecal transplants have had spectacular success with treating Clostridium difficile infections. This bacterium causes severe diarrhoea and inflammation. Recurrent infections are extraordinarily debilitating and life-threatening. Trials of faecal transplants typically show a 90 per cent success rate in treating this condition.

But C. difficile disease is a special case. The disease has one main cause and a consequence of the infection is a greatly reduced microbiota. In the “empty” gut environment of such patients, it’s easy to introduce new organisms. The removal of one problem organism is an easy target.

Most conditions involving gut health – such as obesity, inflammatory bowel disease, and irritable bowel syndrome – have more complex causes and the gut retains a high-density complex combination of bacteria.

For complex gut health issues, the effectiveness of faecal transplants is either much lower, or not proven. Of two published studies of faecal transplants for inflammatory bowel disease, for instance, one found a low effect and one no effect.

Although clinical trials of faecal transplants have reported few problems, we should be alert to the risk. There have been reports of patients showing unexpected weight gain after treatment, for instance. This may be attributable to the engineered microbiota, or may simply reflect that they are no longer seriously ill.

For issues of long-term safety and effectiveness, there are still far more questions on faecal transplants than there are answers. 


Modern lifestyle changes in diet and hygiene have dramatically changed what microbes we are exposed to and how successful they are in colonising us. Our microbiome has changed and we seem to have lost some benefits.

Probiotics aim to restore these. Probiotic can be a confusing term since its use in marketing creates the perception that any product for human consumption that contains specific live bacteria is a probiotic. This contrasts with the definition used by health regulators around the world: probiotics are live bacteria that, when taken in sufficient amounts, confer a health benefit.

The issue revolves around whether the specific bacteria being ingested are what is actually delivering a particular health benefit. There is a lot of marketing hype around products containing good bacteria that “may improve” wellbeing or immune function.

Products that contain live bacteria, such as yoghurt, fermented milk drinks, or pills, contain bacteria that are considered beneficial and are generally recognised as safe. But this is not to say that consuming the product will deliver a known health benefit (the probiotic definition).

There are many examples where probiotics have been shown to be useful in controlled clinical trials. One example is the use of probiotics in preterm births. Premature babies are at high risk of developing a serious illness because they lack beneficial microbes. Probiotic treatments have consistently been found to lower the risk.

Probiotics work most effectively when directly addressing the cause of a disease. For more complex issues or general health improvement, the story with probiotics is less clear cut. Most probiotic bacterial strains do not actually permanently colonise your gut. So to get any benefit for chronic conditions, you need to continually take them.

The next generation of probiotics is starting to address these issues. 

What does the future of probiotics look like?

There is great optimism when it comes to what the next generation of microbiome-based therapies will offer. You don’t restore a complex ecosystem by throwing in one species and expecting it to survive, let alone fix everything. New approaches to probiotics aim to change the ecology of the gut.

Recent studies, using cocktails of probiotic species, have had encouraging results in experimental studies of mice with inflammatory bowel conditions. The goal is to inoculate with networks of bacteria rather than a single strain. Such networks are more able to deliver complex functions or to displace problem bacteria.

A new generation of biotech companies is developing microbiome-based probiotic pills (capsules) as alternatives to faecal transplants for treating C. difficile. Although early studies were very promising and hailed as a breakthrough therapy, a recent phase two trial was less successful. It’s clear there is potential here, but further work is needed.

Although we are in the early stages of the microbiome-engineering era, the future is bright.



Make an appointment with Dr Loganayagam now if you're worried about your gut health. 

By Dr Aathavan Loganayagam

Dr Aathavan Loganayagam trained in medicine at Guy’s, King's and St. Thomas’ medical schools. He then underwent rigorous structured specialty training in gastroenterology and general internal medicine in the well respected South London training programme.

He then spent two years during postgraduate training as a research and endoscopy fellow at Guy’s and St Thomas’ Hospitals, London. His research was in the fields of pharmacogenetics, inflammatory bowel disease and gastrointestinal malignancy. He has received awards and grants for outstanding research work, including the prestigious NHS Innovation London Award.

Dr Loganayagam has numerous publications in peer reviewed journals on all aspects of gastroenterology. He is actively involved in clinical research. He has particular local expertise in the practice of personalised medicine and the utilisation of novel therapeutic agents in the treatment of complex inflammatory bowel disease. He is currently the lead clinician for endoscopy at Queen Elizabeth Hospital, Woolwich.

Diagnostic and advanced therapeutic endoscopy remains a major part of his clinical expertise, including assessment and treatment of inflammatory bowel disease, strictures, polyps and cancers.

Dr Loganayagam is an approachable doctor who takes pride in his communication skills with patients. He is keen to ensure that patients are fully informed and involved in all aspects of their care.

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