The Crucial Elements of Safety and Efficacy in Fecal Microbiota Transplantation: A Comprehensive Analysis of Donor Screening, Universal Stool Banks, and Manufacturing Standards

Fecal microbiota transplantation (FMT), a procedure that involves transferring a donor’s healthy gut microbiome from their stool into the recipient's gut, with the aim of restoring a healthy gut microbial community 1–4, has emerged as a groundbreaking treatment. Currently, FMT is an approved and very effective treatment for patients with recurrent Clostridium difficile infections (rCDI) who are non-responsive to antibiotic therapy, with success rates of up to 90% 5–14

Over the past decade, the scientific and medical communities have witnessed a growing interest in understanding how FMT can modulate the gut microbiome to address various gastrointestinal (GI) and non-GI disorders beyond rCDI 1,4,5,15,16.  As the efficacy of FMT becomes evident in treating a range of conditions, the spotlight on safety intensifies. Two pivotal components for ensuring the safety of FMT are donor screening and high-quality manufacturing standards. This article delves into these critical aspects, emphasizing their role in guaranteeing the safety and efficacy of FMT and the need to focus on universal stool banks.

Why Donor Screening is critical.

Donor screening serves as the initial line of defence against potential risks associated with FMT. The primary objective is to exclude donors carrying known pathogens, minimizing the risk of transmitting infectious diseases and other undesirable traits 17–20. To determine a donor's health and eligibility, comprehensive screening must be implemented, including health and wellness questionnaires and blood and stool testing 17,18,21–27.

The significance of a donor's medical background cannot be overstated. This information is pivotal in determining a donor's suitability and identifying potential issues not detectable through routine blood and stool screening 21–23.  This initial screening examines the risk of infectious diseases, the history of disorders potentially associated with dysfunction of the gut microbiota and the use of treatments and/or medications that can affect the gut microbiota 22,23,25 which excludes a substantial percentage of potential donors, between 50% and 90% 14,28–30.  

Those who pass the initial health and wellness screening undergo extensive laboratory analysis of blood and stool samples 22,23. Comprehensive laboratory analysis is paramount to the safety of FMT and helps to identify potential pathogens possibly transmissible during FMT to reduce risks to patients 21–23. The regular repetition of these tests further underscores the commitment to ongoing safety evaluation.

At Novel Biome, a leading player in FMT product manufacturing, the donor screening process is notably stringent, with initial donor screening exceeding industry standards 17,18,21–27 and over 120 testing parameters to evaluate blood and stool. Donors meet specific criteria, including being vaginally born, breastfed, antibiotic-free throughout their lives, adhering to a diverse omnivorous diet, and undergo rigorous regular evaluation to ensure only the highest quality donor pool.

High-Quality Product Manufacturing: Expensive but Necessary

The safety of FMT is equally contingent on the quality of manufacturing processes. Incorporating pharmaceutical-grade laboratory spaces, equipment, and production standards is imperative but often expensive 17,22,24,25. The challenges include finding suitable laboratory spaces, securing high-quality personnel, and establishing stringent and consistent manufacturing processes 17,22,24,25.

In FMT manufacturing, upholding the highest standards of Good Laboratory Practices (GLP) and Good Manufacturing Practices (GMP) is non-negotiable. This commitment extends across various facets, including personnel quality, facility and laboratory equipment, test systems, processes optimization, manufacturing processes, quality assurance, standard operating procedures, and stringent donor screening protocols, ensuring all products are processed and meet the same standards as other pharmaceuticals. While these are high barriers to overcome, expertise in FMT manufacturing techniques and the use of proper equipment are critical 17,22,24,25.

At Novel Biome, the commitment to quality is evident through adherence to Good Laboratory Practices (GLP) and ongoing efforts to obtain Health Canada DEL and Good Manufacturing Practices (GMP) certifications.

The Importance of Safety in FMT: Where Universal Stool Banks Come In.

As FMT gains greater acceptance and interest, there is a growing need for high-quality FMT products to support hospitals, clinics, physicians and research organizations providing treatment and conducting research to prove FMT’s value in new indications.  While regulations around FMT are still developing around the world, there is a consensus around the need for stringent donor screening and that there is a need for universal donor banks to help scale access to this vital treatment 17,21–25,30–35. Universal stool banks can allow for donor screening and FMT product manufacturing to be centralized and standardized, allowing expanded access to quality FMT products and improving the safety, quality and reduced costs 21,31,36,37.  Stool banks address many logistical limitations, helping to minimize the delay in treating patients by providing physicians with access to well-screening, quality FMT products when needed 31,36,37.

While there is still a need for refinement of universal stool banking guidelines and best practices, such as the creation of best practice protocols and harmonized guidelines for screening and manufacturing, the implementation of universal stool banks following stringent and standardized guidelines will allow better donor screening, increased accessibility and reduced costs 17,21–25,30–35.


In the evolving landscape of FMT, where its applications extend beyond rCDI, safety, standardization, and efficacy are paramount. Donor screening protocols, universal stool banks, and adherence to manufacturing standards are integral to ensuring FMT therapies' success. As scientific knowledge and regulations progress, ongoing evaluation and adaptation of safety measures will be crucial in maintaining the integrity of FMT therapies and unlocking their potential to address unmet medical needs. To best support the growth of FMT and ensure the best quality products are utilized, Novel Biome is committed to exceeding industry standards in donor screening and manufacturing by focusing solely on manufacturing high-quality FMT products from our well-screened donor network, allowing for support of a broad range of treatments and research and increase access to help more people.

At Novel Biome, we're passionate about the importance of the gut microbiome and the transformative potential of Fecal Microbiota Transplantation (FMT) treatment to restore health. As an FMT contract manufacturer, we leverage our years of experience in FMT to manufacture high-quality FMT products utilizing our highly-screened donors and stringent manufacturing standards. If you are interested in learning more about our FMT products and manufacturing capabilities, please contact us HERE or to register as a clinical partner to order FMT products, click HERE.

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