Application & Fecal Microbiota Transplantation (FMT)

Fecal Microbiota Transplantation (FMT) = introduction of gut bacteria from a healthy donor into a patient, through transfer of an infusion of a fecal sample via nasogastric tube, Nasoduodenal tube, rectal enema or the biopsy channel of a colonoscope
NICE (National Institute for Health and Care Excellence) 2014 NICE Interventional Procedure Guidance 2014: 485

The clinical findings are influenced by the methodology rather than the concept of fecal microbiota transplantation.
Cui et al. 2016 Gastroenterology 150(1): 285-6

How to handle the FMT suspension

There is no unified standard or recognized procedure for preparing fecal suspensions in laboratories
Gong et al. 2025 Front Microbiol 16: 1637673

The processing of fecal matter for transplant is not standardized and requires experimental validation to ensure optimal efficacy. Despite this, the general principle remains largely universal. The donated stool is initially mixed with a saline solution to create a homogenized liquid sample. This mixture is then filtered to remove any solid feces that could interfere with the transplant process.
Marotz & Zarrinpar 2016 Yale J Biol Med. 89: 383–388

Mixing feces with saline and filtering out large particles has little effort to purify or enrich microbial fractions. Thus, FMT's benefits might partly come from the abiotic part (soluble components)
Hanssen et al. 2021 Cell Metab 33(6):1098-1110

To standardize fecal matter processing, studies have compared the efficacy of frozen versus fresh stool samples before processing and transplantation. These studies have not shown any significant difference in primary outcomes
Hamilton et al. 2012 Am J Gastroenterol 107(5): 761-7
Lee et al. 2016 JAMA 315(2): 142-9

Many institutions use a polyethylene glycol colon preparation. This is done before FMT. It helps the transplanted microbiome colonize the gut. This applies whether FMT is introduced in the upper GI tract or via colonoscopy. However, no evidence shows this preparation improves FMT outcomes
Zarrinpar & Loomba 2012 Aliment Pharmacol Ther 36(10): 909-21

How the FMT suspension is applied

Fecal microbial transplantation can be delivered to the lower gastrointestinal tract via colonoscopy or enema or the upper gastrointestinal tract via Nasoduodenal tube or capsules
Hvas et al. 2019 Gastroenterology 156: 1324–32
Chande et al. 2020 Inflamm Bowel Dis 26: 843-851

The delivery method will differ based on clinical context. Each method has advantages and disadvantages that should be considered on a case by case basis. The delivery methods include upper endoscopy, nasoenteric tubes, or capsules for upper gastrointestinal tract transplant delivery, and colonoscopy, flexible sigmoidoscopy, or enema for lower gastrointestinal tract transplant delivery
Allegretti et al. 2019 Lancet 394: 420-31

The route of administration often varies from study to study; for the treatment of CDI, no statistically significant difference in outcome is reported between the methods of administration. It is unclear whether this also applies to the treatment of other diseases such as IBD or obesity. Validation is to be sought.
Kassam et al. 2013 The American journal of Gastroenterology 108(4): 500-8
Youngster et al. 2014 Clin Infect Dis 58(11): 1515-22

Impact of FMT on Gut Microbiota

What gets transferred is diverse and strongly influences the outcome of both scientific studies and clinical practice: Microbiota and soluble components obtained from the dry mass of the feces. Regarding the microbiota, the focus is mainly on transferring bacteria, but other FMT components often get overlooked. These are:

• Bacteria


• Funghi


• Archaea


• Virusses (95% Bacteriophages)

Hanssen et al. 2021 Cell Metab 33(6):1098-1110

The abiotic part (soluble components) that is examined in only a few studies means:

• Mucus


• Proteins


• Fat


• Small molecues (bile acids, metabolites)


• Short-chain fatty acids (SCFAs)

Such therapies can also perturb the microbiota quite broadly (Smith et al. 2014 Nature 506: 290-291), as the FDA has also warned (United States Food and Drug Administration 2019).
Inda et al. 2019

How the composition of the graft is determined

While some studies have utilized 16S rRNA sequencing before and after processing to assess sample loss, it is important to note that fecal matter contains 99% anaerobic species, which may not survive vigorous aerobic blending. Additionally, 16S rRNA sequencing does not differentiate between viable and dead cells.
van der Waaij et al. 1994 Cytometry 16(3): 270-9
Cui et al. 2016 Gastroenterology 150(1): 285-6

What determines the effectiveness of FMT

Despite these challenges, the numerous positive results from fecal microbiota transplantation (FMT) in treating Clostridioides difficile infection (CDI) patients suggest that either the viability of the cells is relatively unimportant, or that a small proportion of surviving cells is sufficient to induce a change in the recipient’s microbiome and achieve a therapeutic effect.
Marotz & Zarrinpar 2016 Yale J Biol Med. 89: 383–388

FMT is easy to perform. But methods vary widely between institutions. Some give patients multiple doses of doxycycline or vancomycin. This aims to reduce the native, dysbiotic population
Grehan et al. 2010 J Clin Gastroenterol 44(8): 551-61

Metagenomics (Scholz et al. 2016 Nat Methods 13: 435-438; Truong et al. 2017 Genome Res 27: 626–638) often struggles with the complexity of clinical samples, particularly in detecting low-frequency organisms or distinguishing closely related strains (Ye et al. 2019 Cell 178: 779-794; Sczyrba et al. 2017 Nat. Methods 14: 1063-1071). Current FMT donor guidelines focus on microbial diversity and exclude pathogens. However, they often overlook engraftment potential that is crucial for FMT success. It relies on strain-level compatibility between donor and recipient (Zmora et al. 2018 Cell 174: 1388–1405; Xiao et al. 2020a Nat Commun 11: 3329; Chen-Liaw et al. 2025 Nature 637: 422-429).

see also:
Adverse Events / Safety & Fecal Microbiota Transplantation (FMT)
Analytic Microbiome / Methodology
Fecal Microbiota Transplantation (FMT)
Fecal Microbiota Transplantation (FMT) & Adiposity / Obesity
Fecal Microbiota Transplantation (FMT) & Clostridioides difficile infection (CDI) (recurrent)
Fecal Microbiota Transplantation (FMT) & Inflammatory Bowel Disease (IBD)
Approvals / Regulatory affairs & Fecal Microbiota Transplantation (FMT)
Manipulation / Modulation of Gut microbiota
Shotgun metagenomics