Survey Reveals Varying Physician Opinions on Gut Microbiota Modulation for IBD

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Although respondents agreed on the relevance of the gut microbiota in IBD, attitudes toward the clinical application of microbiome-based therapies varied.

Responses to a cross-sectional survey are providing an overview of physicians’ beliefs, attitudes, and experiences regarding gut microbiota modulation through probiotics, antibiotics, and fecal microbial transplant (FMT) for various intestinal conditions.

Although participants primarily agreed on the relevance of the gut microbiota in inflammatory bowel diseases (IBD), survey responses highlighted challenges and knowledge gaps in the clinical application of microbiome-based therapies, including the limited use of microbial composition analysis in daily practice, infrequent use of probiotics for IBD, conflicting views on the benefits and risks of antibiotics for IBD, and varying opinions regarding the perceived safety and efficacy of FMT.1

“Given the prominent role of the gut microbiota in the pathogenesis of IBD and other gastrointestinal disorders, attempts to modulate it have been proposed. These include the use of probiotics, prebiotics, synbiotics, antibiotics, dietary interventions, fecal microbiota transplantation (FMT), and bacteriophage therapies,” wrote investigators.1 “However, drawing general conclusions on the efficacy and safety of these approaches is often difficult due to the variability in the interventions, doses, timing of administration, and the inevitable heterogeneity of host microbiome profiles and intestinal conditions.”

Although its exact etiology is unknown, genetic risk, environmental factors, and gut microbiota are thought to act together to influence IBD, with emerging evidence supporting a bidirectional relationship between disease progression and changes in microbiota. Microbiome-based IBD therapies are in development but still lag behind pharmacological treatments for inhibiting inflammation. Thus, little is known about their use in clinical practice and physicians’ attitudes regarding these treatment options.2

Tommaso Lorenzo Parigi, MD, of San Raffaele Hospital in Italy, and a team of investigators sought to examine the current practices, preferences, challenges, and expectations of physicians in assessing gut microbiome composition and to identify factors influencing decision-making processes in clinical practice. To do so, they administered a cross-sectional survey to gastroenterologists and other specialists involved in the management of gastrointestinal disorders. Survey questions addressed issues pertaining to microbiota modulation in gastrointestinal disorders with a particular focus on IBD.1

The survey invitation was circulated through email using the mailing list of IBDscope, a webinar platform targeting physicians with an interest in IBD. The survey was open from May 17, 2023, to July 30, 2023, and was completed by 142 healthcare professionals from 60 countries. The average age of respondents was 54 (Standard deviation, 13.6) years, 61% were male, and 86% were adult gastroenterology specialists. More than half of participants practiced in academic centers (53%) and 70% worked in the field of IBD for more than 10 years.1

In total, 41% of respondents reported feeling averagely knowledgeable about microbiota while 18% and 29% reported somewhat below- and above-average competence, respectively. Despite differences in expertise, there was broad agreement regarding the gut microbiota’s relevance to IBD pathogenesis. However, only 3% of respondents reported using microbiota composition analysis regularly and 63% said they never use it, citing a lack of reference values, variability, lack of reimbursement, lack of application to clinical practice, and difficulty in interpreting the results.1

Survey questions about probiotic use revealed physicians prescribed them most frequently for pouchitis (54%) and never or very rarely prescribed them for Crohn disease (30% and 31%, respectively) and ulcerative colitis (19% and 26%, respectively). For FMT, participants indicated the greatest perceived efficacy was for pouchitis, UC, and IBS-D, while IBS-C and CD were thought to benefit the least from this treatment. Still, 61% of respondents said they believed FMT was less effective than approved advanced medications for IBD.1

Investigators pointed out differing opinions on the position of FMT in the therapeutic algorithm for IBD, with 37% of respondents answering they did not know, followed by one-third placing FMT as the last medical option before surgery, 22% after the first medical failure, and 8% proposing it as a first-line treatment. FMT was not considered an option for IBD by 29% of participants and 12% said they were unsure if they would prescribe it. FMT was considered safe by two-thirds of participants, with main concerns including safety issues and a lack of evidence or guidance for its use.1

Among all participants, 26% performed, prescribed, or administered FMT at least once - 67% used it for UC, 42% for CDI, 28% for IBS, 11% for CD, and 8% for other indications. Respondents with FMT experience viewed its efficacy positively, with 47% saying it was very effective and 50% finding it somewhat effective. Of note, no respondent reported a negative impact of FMT on the disease. In cases of FMT for IBD, FMT was frequently combined with ongoing IBD medication. It was found most efficacious in the induction of remission by 42% of respondents and 53% said it worked well for both induction and maintenance.1

“While there is consensus on the relevance of the gut microbiota in IBD, the survey highlights several challenges and knowledge gaps in the clinical application of microbiome-based therapies. These findings underscore the need for further research, standardization of techniques, and evidence-based guidelines to optimize the use of probiotics, antibiotics, and FMT in clinical practice. As our understanding of the gut microbiome continues to evolve, these insights will contribute to more informed and personalized approaches to managing gastrointestinal conditions,” concluded investigators.1


  1. Parigi TL, Vieujean S, Paridaens K, et al. Efficacy, Safety, and Concerns on Microbiota Modulation, Antibiotics, Probiotics, and Fecal Microbial Transplant for Inflammatory Bowel Disease and Other Gastrointestinal Conditions: Results from an International Survey. Microorganisms. 2023; 11(11):2806.
  2. Shan Y, Lee M, Chang EB. The Gut Microbiome and Inflammatory Bowel Diseases. Annu Rev Med. 2022;73:455-468. doi:10.1146/annurev-med-042320-021020