Research into Alternatives to Fecal Microbiota Transplant

Fecal microbiota transplant (FMT) is an emerging technique showing high efficacy in the treatment of recurrent Clostridium difficile infection (RCDI) which is a disease of the gut caused by the overgrowth of this toxic microbe, and which makes up a fourth of antibiotic-associated diarrhea. The reason for the infection is the disruption of the normal gut microbiome by the administration of antibiotics. It is typically treated with prolonged courses of the antibiotics.

However, recurrences are common and may be discouraging and debilitating. RCDI is defined as the reappearance of the infection at any time following completion of antibiotic therapy. This recurrence is related to abnormal composition of the gut microbial community, or dysbiosis. Individuals who cannot, for whatever reason, restore the normal pattern of enteric bacterial colonization, are prone to RCDI. It is difficult to treat, and can lead to significant loss of quality of life and ill-health.

The place of FMT

In this situation, fecal microbiota transplant (or fecal bacteriotherapy) was hailed as a great breakthrough when it was found that introducing fecal microbes in the form of lightly processed stool samples from a carefully screened and healthy donor led to re-establishment of normal gut microflora and symptom relief, with the improvement being long-term.

FMT has also been suggested to be of benefit in many other conditions potentially arising out of dysbiosis. These include neuropsychiatric illnesses such as Parkinson’s disease, and metabolic conditions such as diabetes mellitus and obesity, beside allergies and gut disorders.

Drawbacks of FMT

However, some potential drawbacks include the possibility of transmissible donor infections, the unpleasant mental associations of fecal transfer, and thus lower than expected levels of patient acceptance. It is worth noting, however, that its acceptability is increasing, and over 500 cases of FMT have already been performed worldwide despite its very new status as a modern therapeutic intervention. Standardization of the manufacturing processes is also required to ensure efficacy and patient safety. Stool samples subjected to good manufacturing processes (GMP) regulation are also called full-spectrum microbiota (FSM) units.

Synthetic stool substitute

To achieve the benefits of FMT while avoiding its disagreeable and risky associations, and enable a standardized plan of therapy, researchers have come up with a synthetic stool substitute. This is based upon the premise that a mixture of pre-defined microbes isolated from donor stool can be effective in restoring the healthy gut microbiome. It is also termed microbiota ecosystem therapeutics (MET). This refers to a bacterial preparation derived by carefully combining strains of purified intestinal bacteria which were previously cultured.

In the pilot study, the synthetic stool substitute called REPOOPULATE was constituted from 33 strains obtained from a fecal sample of one healthy individual. The type of strain and the number of organisms per species in the final artificial stool formulation was determined based upon a profile of normal stool bacterial composition, and based upon antibiotic sensitivity studies. The selected isolates had to be relatively easy to grow, and had to be sensitive to a wide spectrum of antibiotics. The culturing process was carried out in a synthetic gut-like medium nicknamed the Robo-gut.

Once the fecal microbial mixture was ready, it was infused into the ascending and transverse colon in patients who had RCDI. The pre-treatment stool samples showed that the infused strains were rarely found in the patients’ intestines. The patients were advised to abstain from all probiotics but to have a fiber-rich diet.

Within three days, the patients reported that symptoms had resolved, and they continued to have normal bowel functioning even six months after treatment. The stool samples showed a change in microbial character. The infused strains now made up a fourth of the intestinal microflora in the patients, reflecting a durable change in the gut microbiome to include the cultured strains. The number of patients in this study was only two, as it was intended to provide a proof-of-concept by demonstrating clinical curability of RCDI using synthetic stool substitute as an alternative to FMT.

Another Danish study was earlier performed using 10 strains that were missing from the gut of patients with RCDI, and reported convincing success rates in clinical resolution of the condition.


The advantages of using such a formulation include:

  • Standardization of the bacterial composition of the infusate allows for control and duplication of the mixture for future use.
  • Such cultures can be kept stable for much longer without affecting the efficacy of treatment, as compared to fresh stool which is often recommended to be used within six hours of collection
  • It is possible to certify the absence of pathogenic agents in the infusate, and so prevent disease transmission via this procedure
  • Only antibiotic-sensitive organisms are used, which improves the safety of the procedure

Mechanism of MET

The pathogenesis of RCDI is considered to be the susceptibility of the intestine in affected individuals to overgrowth by pathogenic C. difficile, because it is unable to re-establish the normal microbiotic pattern. Following the infusion of synthetic stool substitute, the gut adopts the isolates as part of its microflora, without allowing them to wipe out its original bacterial population.

This increases the microbial diversity. A still more important factor, however, is the nature of the newly adopted organisms which are usually absent in the gut at first, but can colonize it in a stable manner. This contrasts with the temporary change in gut flora produced by the ingestion of probiotics. It is likely that the introduction of multiple organisms derived from a single community (the feces from one healthy donor) are inherently more able to produce stable colonies as a new community than randomly mixed isolates as in probiotics. It is noteworthy that one of the patients in this pilot study had to take multiple antibiotic courses for repeated cellulitic episodes, but the gut microbial composition remained stable in the new pattern.

Further research is needed to answer the questions of whether patients and donors should be matched for age, or for the gut microbiotic profile, and the effects of post-treatment antibiotic administration (for any cause) on the type of microbiome that is finally established. MET will also require an exacting set-up to ensure that all strains included in the reagent or infusate are able to grow in culture, which involves providing diverse conditions for growth.

The loss of just a few strains will make the mixture less complex and significantly less effective. Thus, manufacturing and regulatory conditions must meet the demand of these microbes in order to provide a healthy and resilient artificial ecosystem within the recipient gut.



Further Reading

Last Updated: Aug 23, 2018

Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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