Screening donor samples for pathogen-free faecal microbiota transplants

July 26, 2023

Faecal microbiota transplantation (FMT) continues to earn itself a place in a gastroenterologist’s toolbox as a potential therapy for a range of conditions, including irritable bowel syndrome (IBS) and recurrent Clostridium difficile infection, with the latter approved by the National Institute for Health and Care Excellence (NICE) in 2022.1 However, suppliers of FMT donor stool material – such as independent manufacturer – face the challenge of standardising what is essentially an unusual medicine that by its very nature is highly variable. Patient safety, of course, takes precedence, which means performing rigorous donor screening and testing of stool samples to ensure that faecal products are free of serious pathogens. The global SARS-CoV-2 pandemic introduced a new virus to the mix, and quickly expanded its already comprehensive screening panel by adopting the GA-map® COVID-19 Fecal Test to guarantee the continued supply of high quality and safe products to medical professionals.

The lowdown on FMT and how it helps IBS patients

FMT is a clinical procedure that transplants beneficial gut microbiota – stool – from healthy donors to IBS patients via the gastrointestinal tract. It aims to alter the composition and activity of a patient’s microbiome, addressing any ‘dysbiosis’ – disturbance of the gut microbiome – and helping to alleviate IBS symptoms. However, there are still questions around the therapy, and the risk of adverse events from transmission of any infection has led manufacturers of FMT implants to recruit ‘super-donors’ to standardise the product and ensure positive outcomes for recipients. For, this begins with an intensive pre-screening clinical questionnaire to assess the donor’s medical history and lifestyle habits. The donor pool is whittled down on multiple criteria – including mode of delivery at birth, as well as past and present physical, mental and dental health – before the blood and stool testing schedules begin. These factors are investigated through a questionnaire that includes over 50 questions.

Regulation of FMT and careful screening protocols

Worldwide, there is no common classification for the practice of FMT, and there is no global consensus on specific guidelines for the manufacture of donor sample material. However, there are high expectations around safety – extrapolated from established guidelines for blood and organ transplantation – and that’s why manufacturers need carefully constructed screening procedures to provide high quality, pathogen-free stool samples.’s schedule tests for the presence of serious pathogens in blood and stool samples from potential donors. For example, blood samples are screened for major viruses including cytomegalovirus (CMV), Epstein-Barr virus (EBV) and all strains of hepatitis and human immunodeficiency virus (HIV). Additionally, if a stool sample contains pathogens such as Salmonella, Campylobacter or norovirus, the associated individual will be swiftly eliminated from the donor pool.

Keeping COVID-19 out of faecal samples

Despite this comprehensive panel of infective agents, safety concerns for FMT were raised again during the COVID-19 pandemic in 2020, when it was discovered that SARS-CoV-9 viral RNA could be detected in faeces.2 The FMT community became worried about the potential transmission of the virus from donor to recipient, and the FDA published a safety alert advising that donor specimens should be tested for the virus before transplantation.3,4 rapidly broadened its screening protocol to include the GA-map® COVID-19 Fecal test to detect any COVID-19 RNA traces in faecal samples, keeping its FMT sample bank free of serious pathogens and providing the highest protection for recipient patients. However, the rigorous preparation procedure doesn’t stop with testing – the specimens are then stored and quarantined for a minimum of 90 days before use – and retrospectively checks donor health status and microbiome stability before distributing samples to medical professionals for use in patients.

From current to future forms of FMT

Many of the potential risks of FMT are mitigated by this meticulous selection and screening process for prospective donors. While the future of FMT as a therapy for IBS might look much more complex – for example, involving donor microbiome characterisation – for now, a safe source of faeces as transplant material is the primary concern. Suppliers like are providing high quality and safe faecal products, screening donor blood and stool samples against a wide panel of serious pathogens, alongside exhaustive pre-screening interviews and post-donation sample handling quarantine procedures. Should another pathogen come on the scene, there is no doubt that the FMT community will rapidly adapt screening practices again, keeping faecal transplant material safe for all.


  1. Faecal microbiota transplant for recurrent Clostridioides difficile infection. NICE.
  2. Chen Y, Chen L, Deng Q, et al. The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients. J Med Virol. 2020;92(7):833-840. doi:10.1002/JMV.25825
  3. Ianiro G, Bibbò S, Porcari S, et al. Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: experience of a large-volume European FMT center. Gut Microbes. 2021;13(1). doi:10.1080/19490976.2021.1994834
  4. Safety Alert Regarding Use of Fecal Microbiota for Transplantation and Additional Safety Protections Pertaining to SARS-CoV-2 and COVID-19 | FDA. Accessed March 14, 2023.

About BIOHIT HealthCare

BIOHIT HealthCare is a Finnish biotech company, headquartered in Helsinki, that specialises in the development, manufacture and distribution of kits and assays for the screening, diagnosis and monitoring of digestive diseases. Its core disease focus areas include stomach health and dyspepsia, reflux and acid dysregulation, Inflammatory Bowel Disease (IBD), functional gastrointestinal disorders (FGID), Irritable bowel syndrome (IBS), and gut microbiota dysbiosis. Innovating for Health

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