Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after Fecal Microbiota Transplant in Inflammatory Bowel Disease

Abstract

Background: Fecal Microbiota Transplant (FMT) has proven effective in treating recurrent Clostridioides difficile infection (rCDI) and has shown some success in treating inflammatory bowel diseases (IBD). There is emerging evidence that host engraftment of donor taxa is a tenet of successful FMT. However, there is little known regarding predictors of engraftment. We undertook a double-blind, randomized, placebo-controlled pilot study to characterize the response to FMT in children and young adults with mild to moderate active Crohn's disease (CD) and ulcerative colitis (UC).

Results: Subjects with CD or UC were randomized to receive antibiotics and weekly FMT or placebo in addition to baseline medications. The treatment arm received seven days of antibiotics followed by FMT enema and then capsules weekly for seven weeks. We enrolled four subjects with CD and 11 with UC, ages 14-29 years. Due to weekly stool sampling, we were able to create a time series of alpha diversity, beta diversity and engraftment as they related to clinical response. Subjects exhibited a wide range of microbial diversity and donor engraftment as FMT progressed. Specifically, engraftment ranged from 26% to 90% at week 2 and 3% to 92% at two months. Consistent with the current literature, increases over time of both alpha diversity (p< 0.05) and donor engraftment (p< 0.05) correlated with improved clinical response. Additionally, our weekly time series enabled an investigation into the clinical and microbial correlates of engraftment at various time points. We discovered that the post-antibiotic but pre-FMT time point, often overlooked in FMT trials, was rich in microbial correlates of eventual engraftment. Greater residual alpha diversity after antibiotic treatment was positively correlated with engraftment and subsequent clinical response. Interestingly, a transient rise in the relative abundance of Lactobacillus was also positively correlated with engraftment, a finding that we recapitulated with our analysis of another FMT trial with publicly available weekly sequencing data.

Conclusions: We found that higher residual alpha diversity and Lactobacillus blooms after antibiotic treatment correlated with improved engraftment and clinical response to FMT. Future studies should closely examine the host microbial communities pre-FMT and the impact of antibiotic preconditioning on engraftment and response.

Keywords: Crohn’s disease; fecal microbiota transplant; inflammatory bowel disease; microbial therapeutics; microbiome; ulcerative colitis.

Figure 1.

A. Consort Diagram. B. Clinical symptom scores (PUCAI for UC and PCDAI for CD) for individual participants (top) and for responders vs non-responders (bottom).

Figure 2.

A. Stool alpha diversity (Shannon index) time series for all patients, clinical non-responders (blue) vs. clinical responders (red) and for individual patients, each in a unique shade of gray (inset). B. Correlation between clinical symptom score (PUCAI for Ulcerative Colitis, PCDAI for Crohn Disease) and alpha diversity (Shannon index) for clinical responders (top) and non-responders (bottom). C. Correlation between PUCAI and alpha diversity at the post FMT timepoint (left, red, large panel). Smaller panels: top panels show correlation between PUCAI and alpha diversity at the pre- and post-antibiotic timepoints, bottom panels show correlation between the late post-FMT PUCAI and earlier (pre- and post-antibiotic) alpha diversity metrics.

Figure 3.

A. Percent Donor Engraftment, as estimated by SourceTracker, in responders vs. non-responders as well as for each individual patient, each in a unique shade of gray (inset) B. Beta diversity plots (Bray-Curtis) for three example responders. C. Beta diversity plots for three example non-responders. D. Correlation between alpha diversity (Shannon Index) and engraftment at the pre-antibiotic (Left) and post-antibiotic (Right) timepoints. E. Beta-diversity plots comparing eventual high engrafters (blue) and low engrafters (red) at the pre-antibiotic (Left) and post-antibiotic (Right) timepoint.

Figure 4.

A. Important features (on the genus level) from a random forest classifier using the post-antibiotic microbiome to classify high vs. low engrafters (AUC = 1.00). All taxa are genera, lowest identified taxonomic level is labeled. *Asterisks denote members of the Family Lactobacilliaceae. B. Boxplot of relative abundance (proportion of total reads) of species in the Family Lactobacillaceae that were detected in at least 3 individuals. ***, FDR p-value < 0.001; **, FDR p-value < 0.01; *, FDR p-value < 0.05. C. Time series of relative abundance of genus Lactobacillus (top left) and 3 species within genus Lactobacillus, comparing high (each participant represented in a unique shade of blue) vs. low (each participant represented in a unique shade of orange) engrafters in this study. D. Time series of relative abundance of genus Lactobacillus (top) and 2 species within genus Lactobacillus, comparing responders (each participant represented in a unique shade of blue) vs non-responders (each participant represented in a unique shade of orange) in an independent (n = 6) FMT study in IBD (Chu et al.).