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Editorial theme | Latest advances in microbiome interventions

Oct 28, 2020

The intestinal microbiome is a large and diverse population of microorganisms which mostly lives in symbiosis with the host. During disease states the microbiome may be disrupted resulting in an exacerbation of the condition. The link between graft-versus-host disease (GvHD) and intestinal dysbiosis, also known as microbial imbalance, has been a topic of great interest in recent years and the impact of hematopoietic stem cell transplantation (HSCT) on the intestinal microbiome has been extensively investigated. New treatment methods that influence and support the integrity of microbiome are being developed as its importance has been recognized.

Over the next months, the GvHD Hub will be focusing on a new editorial theme: ‘Latest advances in microbiome interventions’, summarizing talks and posters presented at the virtual 46th Annual Meeting of the European Society for Blood and Marrow Transplantation (EBMT); the GvHD Hub is excited to explore this topic in more detail.

Supporting the microbiome

Microbial metabolites

Daniela Weber discussed the impact of microbial metabolites in her talk.1 Out of the plethora of metabolites produced by microorganisms within the gut, several have been identified as being beneficial to support the integrity of intestinal epithelial cells. For example, short chain fatty acids (SCFAs) increase interleukin (IL)-18 signaling, which aids cellular repair and integrity. Further information regarding the impact of SCFAs can be found in an article previously published by the GvHD Hub here.

The secretion of IL-17A by T helper and endothelial cells promotes integrity of the gut barrier and is strongly stimulated by riboflavin metabolites from lactic acid bacteria. Indoles and their derivatives originate from the microbial metabolism of tryptophan and can activate interferon signaling which protects the intestinal mucosal barrier and lessens the effects of GvHD.

Butyrate, in particular, was noted to play a valuable role in protecting the gut by acting as a histone deacetylase inhibitor, thereby reducing apoptosis of epithelial cells. The protective effect of SCFA is mediated by G protein-coupled receptor (GPR)43. In murine models, local administration of butyrate, or butyrate-producing Clostridiales, improved the junctional integrity of epithelial cells and reduced the severity of gastrointestinal (GI) GvHD. GPR43 expression was found upregulated in patients with non-lethal GI GvHD. In addition, butyrate producing bacteria are suppressed during GvHD, and following HSCT.

Preventive and therapeutic interventions in the microbiota

Florent Malard gave a presentation2 on the methods available to support the microbiome including:

  • Prebiotics
    • Non-digestible carbohydrates
    • Diet that selectively avoids or includes specific food

One example is resistant potato starch, a form of nondigestible carbohydrate that can be metabolized by gut fauna to produce butyrate. It has been shown to be well tolerated in a small study, but whether this will have a clinical impact is yet to be determined.

  • Postbiotics
    • SCFA (e.g., butyrate)
    • Indole derivates
    • Avoidance of foods that negatively impact the mucus barrier


  • Probiotics
    • Fecal microbiota transplant (FMT)
    • Engineered microbes
    • Rationally selected strains

FMT has been extensively investigated and can be used following allogeneic-HSCT, autologous-FMT to increase microbial diversity and return the microbiome more rapidly to normal levels. FMT can also be used for the eradication of multidrug resistant bacteria in patients with hematological malignancies. This therapy shows promise for the treatment of steroid resistant acute GI GvHD, and a number of small studies have reported positive initial data. Larger clinical trials are also in progress internationally to test FMT for the treatment and prevention of acute GvHD (aGvHD).

Microbiota biotherapeutics

Florent Malard also presented a poster on the successful and safe treatment of intestinal GvHD with pooled-donor full ecosystem microbiota biotherapeutics.3 During this trial, 11 patients with steroid-dependent or steroid-refractory intestinal GvHD, following allo-HSCT, were treated with a next-generation FMT product called MaaT013. This is a standardized solution of pooled-donor microbiota. At 28 days posttransplant:

  • 46% of patients showed a complete response
  • 18% had a very good partial response
  • 18% exhibited a partial response

In terms of adverse events, one patient experienced a potentially transplant-related episode of sepsis but fully recovered following treatment with antibiotics. A total of three cases of bacteremia occurred, which were also treatable by antibiotics. There was one case of septic arthritis but following sequencing, it was determined that the strain causing this infection was present in the patient prior to transplantation.

Nutrition and the microbiome

The importance of diet and its impact on the microbiome were investigated in a poster presented by Skaarud et al.4 It is unknown whether diet can alter the diversity of GI microorganisms and affect the clinical outcome following allo-HSCT. This two-armed randomized controlled trial included 47 patients. About half had their energy and protein intake optimized and the other half were controls. Sequencing of 16S ribosomal RNA was used to assess the results. In the intervention group, 26% patients died during a 1-year follow-up, while 25% died in the control group. In the control group, 75% of patients had grade 0−1 aGvHD compared with 78% in the treatment group, while five in the intervention group and six in the control group developed grade 2−4 GvHD.

The microbiota profiles of both groups were similar at the start and at 3 weeks post allo-HSCT. As it has been reported previously, a loss of microbial diversity was seen posttransplant, and this was more severe in a patient who died within the first year compared with patients who did survive the first year. In addition, loss of the genus Blautia was shown to be associated with reduced survival at 1 year. However, dietary modulation did not appear to affect intestinal microbial diversity in this study.

The impact of a choline-rich diet on GvHD development has been analyzed by Kunpeng Wu and colleagues, which has been covered previously by the GvHD Hub and can be found here.

Impact of antibiotics on microbiome integrity

Maria Gavriilaki and colleagues presented a poster on a meta-analysis investigating the impact of antibiotics on the outcome following allo-HSCT.5 A total of 15 studies were included in the analysis which found a significant decrease in the incidence of grade II−IV aGvHD in patients who did not receive antibiotics (p = 0.0006). An association was noted between patients who received antibiotics as prophylaxis or treatment for neutropenic fever and a 10% reduction in overall survival (OS), although this was not statistically significant (p = 0.23). Transplant-related mortality increased by 75% in patients treated with antibiotics (p = 0.07). Higher microbial diversity was associated with an 86% increase in OS compared with patients with lower diversity (p = 0.07). However, it must be noted that there was no consensus on how to measure diversity across the different studies which resulted in a high degree of heterogeneity.  

In her talk, Daniela Weber highlighted the fact that antibiotic use is often necessary for the treatment of neutropenic infections in patients following HSCT. However, the use of antibiotics is a major risk factor for intestinal dysbiosis and may be linked to a poor outcome following HSCT due to the loss of the protective effects of commensal bacteria. The time of initiation of antibiotic treatment impacted the mortality rate in patients receiving allo-HSCT in a retrospective analysis of 621 patients. Patients who received no antibiotics had a transplant-related mortality rate of only 7%, whereas those receiving antibiotics after HSCT had a mortality rate of 21%. Mortality was even higher in patients who were treated with antibiotics before transplant (34%).1

Razan Mohty and colleagues presented a poster discussing the relationship between antibiotics exposure and risk of severe aGvHD in patients undergoing allo-HSCT.6 In this study, 318 patients who had received allo-HSCT were included.

Antibiotic exposure was split into three groups:

  1. No antibiotics
  2. Early exposure (from start of conditioning to Day 1 of engraftment)
  3. Late exposure (treated from Day 0 to neutrophil engraftment)

In this retrospective study, a 2-year OS of 74.3% was recorded for the early exposure group compared with 79.5% in the late exposure group (p = 0.11). Progression-free survival at 2-years was 63.6% in the early group compared with 70.8% in the late exposure group. Multivariate analysis was also performed, and early antibiotic use was identified as the only factor associated with a significantly increased risk of Grade 3−4 aGvHD (p = 0.02).

A study by Sung-Eun Lee and colleagues also demonstrated an association between the use of broad-spectrum antibiotics and an increased risk of GI aGvHD, which was reported earlier by the GvHD Hub and can be found here.

A shift away from clostridial to enterococcal flora within the gut has been identified with the use of broad-spectrum antibiotics; therefore, choosing antibiotics that protect these key butyrate-producing Clostridiales, remains a goal for treatment. Florent Malard discussed a study by Yusuke Shono et al. in which it was found that patients treated with aztreonam or cefepime showed a reduced GvHD-related mortality compared with patients receiving imipenem or piperacillin-tazobactam. Even more surprising was the finding that patients receiving 4th generation antibiotics showed improved survival compared with those who received no antibiotic treatment. Antibiotics with anaerobic coverage seem to be associated with a poorer outcome following HSCT.1

However, Daniela Weber’s group did not achieve the same results with 4th generation antibiotics and found that only rifaximin monotherapy was able to protect intestinal diversity during HSCT in a study from 2019.1 In addition to the effect on microbial diversity, the impact of antibiotics on GPR expression and butyrate producing bacteria was explored. Broad-spectrum antibiotics caused a complete suppression of GPR expression and reduction in the levels of butyrate-producing bacteria in patients with acute GI GvHD.

As a result of this work, Ernst Holler along with Daniela Weber and colleagues submitted a poster regarding changing practices for the use of antibiotics following allo-HSCT.7 A restrictive policy was introduced in their institution for the use of antibiotics in patients with fever and a high chance of cytokine release syndrome. The new policy ensured that the use of broad-spectrum antibiotics was postponed to the second episode of fever for at least 12 h. A total of 146 patients who had been treated with the previous permissive policy were compared with 131 patients treated with the new restrictive policy. The new policy resulted in a decrease in antibiotic use from 49.3% to 28.7% (p = 0.003), prior to the day of HSCT. Although there was a slight rise in the incidence of bacteremia in the restricted group compared with the permissive, 29.0% vs 18.5%, respectively, the policy change did not translate to an increase in severe neutropenic complications:

  • Neutropenic sepsis was 3.3% vs 10%, restrictive policy vs permissive, respectively
  • Treatment related mortality was 0.8% (restrictive) compared with 3.8% during the period of permissive antibiotic use.

The incidence of grade II−IV GI GvHD decreased from 14% (permissive) to 7% (restrictive; p = 0.07). Transplant related mortality showed a significant reduction from 17% to 9% permissive vs restrictive, respectively (p = 0.05). Multivariate analysis showed that the restricted antibiotic use remained significant even after inclusion of donor type, stage, and performance status (HR 0.39, 95% CI 0.18−0.84).


In summary, the link between loss of microbial diversity and increased risk of severe GI GvHD is becoming increasingly clear. The impact of the use of broad-spectrum antibiotics is also evident, but it remains to be seen if certain types of antibiotics such as 4th generation or narrower spectrum are more beneficial in terms of survival for patients treated with HSCT.

The microbiome is an incredibly diverse population of organisms and its relationship with the human host is complex, with more facets being revealed over time. The rise in different therapies focused on supporting the microbiome is very promising and there is a great deal of potential for the treatment of GI GvHD. However, many of these have only been tested in small studies so it remains to be seen how they will translate into use in the clinic.

The GvHD Hub aims to bring you the most up-to-date research on advances in microbiota interventions so stay tuned for more content coming soon!

  1. Weber D. Current understanding of the impact of microbiome on HSCT alloreactive phenomena and outcome. Presentation E2-1 (Session: Educational forum on microbiota and allogeneic HSCT). 46th Annual Meeting of the EBMT; August 29, 2020; Virtual.
  2. Malard F. Preventive and therapeutic interventions in the microbiota. Presentation E2-3 (Session: Educational forum on microbiota and allogeneic HSCT). 46th Annual Meeting of the EBMT; August 29, 2020; Virtual.
  3. Malard F, Legrand F, Cornillon J, et al. Successful and safe treatment of intestinal graft-versus-host disease (GvHD) with pooled-donor full ecosystem microbiota biotherapeutics. Poster #O073; 46th Annual Meeting of the EBMT; August 29–September 1, 2020; Virtual.
  4. Skaarud K, Hov JR, Hansen S, et al. Microbial diversity, survival, and acute GvHD in adult recipients of allo-HSCT after myeloablative conditioning: results of a nutritional intervention trial. Poster #B015; 46th Annual Meeting of the EBMT; August 29 –September 1, 2020; Virtual.
  5. Gavriilaki M, Sakellari I, Anagnostopoulos A, et al. The impact of antibiotic-mediated modification of the intestinal microbiome on outcomes of allogeneic hematopoietic cell transplantation: Systematic review and meta-analysis. Poster #A272; 46th Annual Meeting of the EBMT; August 29–September 1, 2020; Virtual.
  6. Mohty R, Duléry R, Battipaglia G, et al. Investigating antibiotic exposure and risk of severe acute graft versus host disease in patients undergoing allogeneic hematopoietic stem cell transplantation. Poster #A234; 46th Annual Meeting of the EBMT; August 29–September 1, 2020; Virtual.
  7. Holler E, Weber D, Hahn J, et al. Restrictive use of intravenous antibiotics in allogeneic SCT pts with fever due to cytokine release syndrome allows microbiota protection without increase of infections and TRM. Poster #A251; 46th Annual Meeting of the EBMT; August 29–September 1, 2020; Virtual.