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Understanding the Gut Bugs Trial: Case Study

The case study below explores the aims, research approaches and preliminary findings of the Gut Bugs pilot trial. It explains the complex, collaborative work that was undertaken by a large team of researchers who contributed to the project in different ways by drawing on different skills and expertise.

Research Questions

Researchers in the Gut Bugs trial wanted to examine the effectiveness of lean donor gut microbiome transfer (GMT) using encapsulated faecal material for the treatment of obesity in adolescents.


Teenagers who were living with obesity were chosen as the test population for the trial because, according to Professor Cutfield, “If we can reverse [obesity] in teens, they are less likely to have complications”. For example, a morbidly obese adult, who has been affected by obesity for decades, is more likely to have health problems such as heart disease that ar very difficult to reverse. They can lose weight, but this won’t reverse the damage done from heart disease. However, if you can support young people to achieve and maintain a healthy weight, any long-term health effects related to conditions of overweight or obesity are also more likely to be reversed.


Read about some of the Gut Bugs scientists:

Photo of Wayne Cutfield.
Photo of Thilini N. Jayasinghe.
Photo of Justin O'Sullivan and Thilini N. Jayasinghe in the lab.
Photo of Karen Leong.

The Research Team

Complex clinical projects such as the Gut Bugs trial often involve a wide range of expertise across many different disciplines. The research team consisted of about 12-14 people who worked together and consulted with each other. The clinical team liaised with participants and carried out the medical testing and diagnostics. The laboratory team processed the stool (poo) samples to separate out the bacteria and did the genotyping of the bacteria. Nutritionists advised the research team and participants. A group of specialised statisticians (called Bioinformaticians) used computer software for statistical analysis of the biological material.

Research Ethics

All research proposals and clinical trials need to go through a process of ethical review and approval before the research can begin. The ethics process is like a pre-flight check to ensure that risks of harm have been eliminated or minimised. Ethics requires that potential participants are informed about any risks and that they knowingly consent to taking part in the trial.



What did the researchers think or hope would happen? The overall hypothesis was that gut microbiome transfer (GMT) from healthy and lean donors would lead to weight reduction and improvement in metabolism in adolescents affected by obesity. Some possible outcomes of the Gut Bugs trial were:

  • The microbiome of adolescents impacted by obesity will change to be like that of the healthy, lean donor
  • There will be no change in the recipient’s gut microbiota 
  • The recipients could lose weight and keep it off for a long time
  • The recipients may lose weight, but this weight loss may last for a short time
  • There is no weight loss effect


There are many other factors to consider. For example, if the treatment does initially work, will the recipients need to adopt a healthy diet in order to maintain the health benefits?


If GMT could be proven to be a safe, effective technique, it could be further developed into a large scale treatment for one of our biggest health crises. Benefits of GMT as a treatment for obesity include:

  • Low cost
  • Relatively simple treatment
  • Relatively non-invasive

Research Methods

The trial was designed in two phases. First, a pilot study with a smaller number of participants was conducted. The research could only progress to the main trial involving 90-100 participants once the pilot was completed. The pilot was an important ‘proof of concept’ phase, and the research team were extremely meticulous in their study design.


Problem Solving

In the beginning there were many unknowns: 

  • Who is the ideal donor? Is the treatment more effective if the donor is related to the recipient?
  • How often should recipients be given the treatment?
  • Is there a risk of introducing or transferring diseases from donor to recipient? Donors needed to be screened for a wide range of conditions such as irritable bowel syndrome, chronic fatigue syndrome, diarrhoea, Giardia, HIV, Hepatitis, drug use, recent travel to high risk areas, recent tattoos or body piercings. 
  • Will there be other adverse side-effects?
  • Will we get enough volunteers to participate?
  • What if no one is willing to try the treatment? The ‘yuck factor’ was one of the reasons that the treatment was named GMT (gut microbiome transfer) rather than FMT (faecal microbiome transplant).
  • How best to recruit participants - both donors and recipients?
Image of a question mark.

More unknowns were associated with collection and preparation of the donor faeces. Practical and safety issues to consider and overcome included:

  • Fresh or frozen faeces?
  • How can the live donor microbes be packaged? (e.g. in suspension/emulsion, in a capsule).
  • How to get the material into capsules?
  • How long will the bacteria live for and under what conditions should they be stored?
  • How will participants receive the donor microbes? Will they swallow capsules or liquid? Would a nasojejunal tube be an effective method of delivery? (A nasojejunal tube is put in through the nose and down through the stomach to the small intestine). Rectal administration via enema was another option that was considered.

The Gut Bugs trial looked at many factors: weight loss, fat in body tissue, diabetes risk, heart disease risk, blood pressure, mood, bowel function. While the primary hoped-for outcome was weight loss, the benefits of GMT could be wider. For this reason, the team decided to assess a wide range of clinical factors.


Image of a group of people icons.

Recruiting Participants

If you can’t get participants recruited for a trial or if they drop out, then that is the end of the study. Recruiting participants for the trial was a mammoth task and initially the researchers were unsure about how best to do this. They considered visiting schools and talking to students, but eventually it was decided to recruit via Facebook. There was a huge amount of interest and a large number of people (600) responded. Of these, over 300 people were spoken to for further testing.


Potential participants and their caregivers were given an information sheet which told them what would happen in the trial and what they would be required to do if they agreed to take part. Eight young people were wanted for the pilot trial - four men and four women. However, eight young women were chosen, as only women responded.


The Donors

Faecal matter was taken from lean, physically active donors. One donor stool (faeces) would produce enough material for two same-sex recipients. Potential donors were screened to make sure they were free of infectious and chronic diseases and drug use (including nicotine and alcohol). These procedures were similar to those used for blood donation in New Zealand. Donors were interviewed to make sure they had not been exposed to other risk factors such as recent travel to high-risk countries. They were tested for leanness (low BMI) and for high levels of physical fitness and activity. 


Of the 21 donors that volunteered for the pilot trial, only four passed the screening stage. 


To collect the faeces, donors would come in to the Liggins Institute on a regular basis, about once a month. They would have something to eat, maybe drink a coffee, and then hopefully, they would be able to produce a stool sample. This sample was processed into capsules immediately. The donors’ stool samples were checked at 6, 12 and 26 weeks to ensure their gut microbiomes remained stable. 

Who Donated the Faeces?

Criteria for Gut Bugs Donors

Age 18-28 years
BMI Between 18.5 and 30.0 kg/m²
Body fat Under 29% (females) and under 19% (males)
Bowel habits Healthy, regular (at least once a day)
Food intake Well-balanced diet
High levels of fruits and vegetables
Medications No regular oral medications
No antibiotics within previous 6 months
Pregnancy Not eligible if pregnant
Physical activity Moderate-vigorous physical activity at least 3.5 hours per week
Overseas travel No overseas travel in previous 3 months
Drugs and alcohol No smoking or drugs
Less than 7 standard drinks per week
Disease Free of Hep A,B,C, HIV, syphilis, C. difficile, as well as other bacterial and viral pathogens, cancer, diabetes, irritable bowel syndrome or coeliac, multidrug-resistant organisms, intestinal parasites 
Table 1: Criteria for Gut Bugs Donors (Jayasinghe, 2019, p. 99; Leong et al., 2018, Table 1).

Gut Bugs Trial Design

Diagram of the Gut Bugs trial study design.
Figure 1. Study design of the Gut Bug Trial - pilot project. Adapted with permission from Jayasinghe, 2019, p. 99, Figure 4-1.
An inforgraphic detailing the 'Gold Standard' of clinical trials. Clinical trials that follow the 'Gold Standard' are double-blind, meaning neither the participants nor the researchers know who is getting the treatment. They are also placebo-controlled meaning that a control group of participants receive 'dummy' or placebo pills. They are also randomised meaning that a computer programme is used to assign participants into the treatment or control group.

The research team designed the trial to what is known as the ‘gold standard’ of clinical trial designs: double-blind, placebo-controlled and randomised. This is the most reliable method for testing new treatments and drugs.

The placebo effect is a form of patient bias. This is when the treatment leads to improvement or reported improvement through patients believing that the treatment works, yet they have only been given the dummy or placebo.

It is possible that health changes noticed in the trial might be caused by other factors. Researchers wanted to be able to identify that the GMT was working, and tried hard to reduce this risk. If participants suddenly started changing or reducing their food intake, or exercising more, they might lose weight, but this weight loss could not be attributed to the treatment. Participants were asked to eat healthy food but to continue as much as possible with their normal lifestyle. Changes were also tracked by recording a wide range of information about the recipients, such as height, weight, questionnaires about diet, physical activity and mental health, and a DEXA scan to measure any changes in the amounts of lean muscle and fat in their bodies.


Image of a speech bubble with the quote, "The capsules are just like hand-made chocolates."

The Recipients

Eleven recipients took part in the pilot trial. They were all young women who were living with obesity as no young men volunteered. The treatment and assessments were not always pleasant. All recipients took a laxative to clean their bowel the day before taking the capsules. The laxative caused diarrhoea-like watery bowel motions. This was to reduce the microbial population in the gut. The young women had to fast overnight before swallowing 16 capsules in the morning. They had to swallow 12 more capsules the next day.


The young women were followed for around six months. After initial testing (or baseline testing) was completed, recipients were tested again at 6, 12, and 26 weeks. Each time, the testing took 2-3 hours. The women needed to be very motivated to take part and to stay in the trial for the full six-month period, especially as they didn’t know if they had received the GMT or the placebo capsules.


Two types of data were collected - the gut microbiome and clinical (medical) diagnostics. 


The recipients provided stool samples so that the composition of their gut microbiome could be monitored. The microbial DNA and RNA were extracted and gene sequencing was used to analyse the type of microbes present in each sample. The researchers searched for ‘markers’, or short gene sequences that uniquely identify just one kind of microbe. A DEXA scan measured any changes in the amounts of lean muscle and fat in their bodies. Recipients had to do an oral glucose test (to test for diabetes or insulin resistance) which required them to drink a very sweet drink before having a blood test. They had to complete a three-day food diary and answer questions about their levels of physical activity. 

Who Got the Treatment?

Criteria for Gut Bugs Recipients

Age 14-18 years
BMI Above 30.0 kg/m2
Body fat Under 29% (females) and under 19% (males)
Bowel habits Healthy, regular

No antibiotics within previous 3 months

No regular medications that influenced weight or metabolism (e.g. oral contraceptives, antidepressants, glucose-lowering drugs, diet drugs, or inhaled, topical, oral steroids)


Free of gastrointestinal disease (including IBS, coeliac, and IBD), type 1 and 2 diabetes, chronic diseases (other than obesity-related conditions)

No known allergies to food

No allergies to the bowel preparation product (laxative)

No allergies to any over-the-counter medication

Table 2: Criteria for Gut Bugs Donors (Jayasinghe, 2019, p. 99; Leong et al., 2018, Table 2).


Capsule Preparation

Samples collected from donors needed to be processed and made into capsules immediately. The capsules were designed to remain intact as they pass through the oesophagus and stomach and small intestine before breaking up and delivering their contents to the large intestine.

Diagram detailing the capsule preparation steps.
Figure 2. Capsule preparation steps (Jayasinghe, 2019; Leong et al., 2018). Adapted with permission. Image of centrifuge adapted from
Diagram detailing gut microbiome transfer.


With such a small number of participants (11) in the pilot trial, findings were “50-50” in terms of a lot of aspects (e.g. it was difficult to ascertain significant weight loss). The most important result was that the participants’ gut microbiome shifted to resemble the donor’s microbiome and stayed that way for six months. No similar shift was observed in the control (placebo) group.  This means that there was engraftment and augmentation (increase in gut bacteria diversity), and showed that the gut microbiome transfer in adolescents affected by obesity was working. There was also evidence of changes in recipients’ bloodwork that were significant, even with such a small number. All of this evidence was enough to commence the main trial.


The main trial involving 80 participants started in July 2017, with the last participant finishing the six-month assessment period in March 2019. There are 51 females and 36 males in the main trial because again more females than males responded. The trial is ongoing. Researchers are still blinded while the results are analysed. This means that the final results are as yet unknown. There may have been changes noticed, but the researchers do not yet know the significance of these changes. The first results from the main trial are anticipated towards the end of 2019.


Next Steps

The pilot trial was the proof of concept. But in a way, the main trial is also proof of concept, just on a much larger scale. Professor Cutfield and Dr O’Sullivan point out that if the main trial is successful (i.e. shows that GMT supports teens who are living with obesity to lose weight and sustain that weight loss), then collecting donor stools will not be the way in which long-term and large scale treatment is undertaken. The process is too expensive, too labour-intensive and too reliant on humans. Also if successful, the demand for treatment would be so great that it would be difficult to get enough donors. Instead, researchers would identify which combinations of bacteria were most effective, and then try to culture (grow) them en masse in the laboratory. Another advantage of this method would be that the treatment could be guaranteed to be disease-free. 

However, Dr O’Sullivan explains that growing bacteria in the lab is not a simple process, and that this will require further investigation and problem-solving. It will not be possible to just take a sample of faeces and use them forever to grow bacteria in the laboratory. Organisms change as they are cultured in the lab - for example, the E. Coli grown in the lab are not the same as those bacteria in the gut.