Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant

Abstract

Antibiotic treatment can deplete the commensal bacteria of a patient's gut microbiota and, paradoxically, increase their risk of subsequent infections. In allogeneic hematopoietic stem cell transplantation (allo-HSCT), antibiotic administration is essential for optimal clinical outcomes but significantly disrupts intestinal microbiota diversity, leading to loss of many beneficial microbes. Although gut microbiota diversity loss during allo-HSCT is associated with increased mortality, approaches to reestablish depleted commensal bacteria have yet to be developed. We have initiated a randomized, controlled clinical trial of autologous fecal microbiota transplantation (auto-FMT) versus no intervention and have analyzed the intestinal microbiota profiles of 25 allo-HSCT patients (14 who received auto-FMT treatment and 11 control patients who did not). Changes in gut microbiota diversity and composition revealed that the auto-FMT intervention boosted microbial diversity and reestablished the intestinal microbiota composition that the patient had before antibiotic treatment and allo-HSCT. These results demonstrate the potential for fecal sample banking and posttreatment remediation of a patient's gut microbiota after microbiota-depleting antibiotic treatment during allo-HSCT.

Fig. 1.. The gut microbiota is disrupted during allo-HSCT.

A total of 3237 fecal samples from 753 patients who underwent allo-HSCT were obtained, and the microbiota composition was analyzed using high-throughput 16S rRNA amplicon sequencing. (A) Antibiotics with a varying spectrum of activity were given over the course of allo-HSCT, either as prophylaxis or for treatment of infections. Antibiotics with anti-anaerobic activity included β-lactams, carbapenems, metronidazole, clindamycin, and vancomycin (oral only); these antibiotics were defined as microbiota perturbing in the study protocol (see the Supplementary Materials). (B) The α-diversity of each microbiota sample was measured using the IS index. Intestinal microbiota diversity dropped sharply as patients progressed through allo-HSCT treatment, reaching very low levels (IS < 4 or lower). (C) The average diversity trend showed that the drop in average microbiota diversity began several days before hematopoietic stem cell infusion, during the conditioning regimen and antibiotic prophylaxis treatment.

Fig. 2.. Timeline for a study patient undergoing allo-HSCT and randomized to receive auto-FMT.

(A) Allo-HSCT for study patient T5 was initiated with pretransplant conditioning [chemotherapy and total body irradiation (TBI)], followed by allogeneic hematopoietic stem cell infusion (day 0). Various antibiotics were given throughout this period for prophylactic and treatment purposes. (B) Neutrophil count reached a nadir but later recovered after hematopoietic stem cell engraftment. (C) The subject’s intestinal microbiota composition was altered as shown by sequencing of longitudinally collected fecal samples obtained before allo-HSCT and up to day 91 after transplant. After stem cell engraftment, randomization assigned patient T5 to the treatment arm and the patient received an auto-FMT on day 49 using the patient’s initial pretreatment feces, which had been collected and stored before allo-HSCT (initial feces collected at day −21). The intestinal microbiota was restored to that before transplant in terms of (D) its diversity (α-diversity quantified by the IS index) and (E) its percent similarity to the initial fecal microbiota.

Fig. 3.. Auto-FMT improves gut microbiota diversity and composition in allo-HSCT patients.

(A) t-SNE plot provides visualization of gut microbiota composition during allo-HSCT. t-SNE plots were constructed from 3237 fecal samples collected from allo-HSCT patients since 2010; the patients were randomized in the auto-FMT trial. The plot shows a large region of high diversity (IS > 4) and clusters of low diversity corresponding to domination by specific bacterial species, for example, Enterococcus and Klebsiella. (B) Each patient followed a unique trajectory in the t-SNE space. The control patients (C) and those receiving auto-FMT treatment (T) were ranked by post-randomization gut microbiota recovery. The patient’s number and the percentage similarity of the gut microbiota to the initial fecal sample are shown. Patients started with a diverse gut microbiota composition, but then many progressed to domination states with loss of diversity due to the impact of antibiotic and chemotherapy administration. The microbiota composition in patients after auto-FMT (patients T1 to T14) moved closer to the initial composition than it did for control patients (patients C1 to C11). (C) Effect sizes of clinical parameters quantified by a mixed-effects model (along with a 95% CI) show that auto-FMT for allo-HSCT patients improved gut microbiota diversity (left-hand plot; P = 5 × 10⁻⁶) and recovery of the original gut microbiota composition (right-hand plot; P = 5 × 10⁻⁶).

Fig. 4.. Auto-FMT restores commensal members of the gut microbiota in allo-HSCT patients.

(A) Commensal species (ranked by their abundance) in the initial fecal sample from allo-HSCT patients disappeared after allo-HSCT before randomization to the auto-FMT or control arm (Pre-Rand); they reappeared after auto-FMT (Post-Rand) compared to the control group, who did not receive auto-FMT. Sixty percent of the patients enrolled in this trial (15 of 25) had a gut microbial diversity of IS < 4 before randomization; after randomization, 3 of 11 (27%) control patients but only 1 of 14 (7%) patients receiving auto-FMT retained this depleted diversity. The percent recovery also showed that auto-FMT helped to reconstitute the original gut microbial composition. Only 3 of 11 (27%) of the control patients had a composition 75% or more similar to their initial fecal sample, whereas 11 of 14 (79%) of the auto-FMT–treated patients showed 75% or more recovery. The bacteria in the left-hand grayscale heat map represent the top 50 bacterial strains present in the patient’s initial fecal sample; the right-hand grayscale heat map highlights seven bacterial species that increased after allo-HSCT (colors underlying the heat maps are defined in the key in Fig. 2). (B) Bacterial taxa from the patient’s initial fecal sample were classified on the basis of their presence in pre- and post-randomization fecal samples from the same patient. This is shown for all taxonomic groups (bottom panel) and for three important taxonomic groups (top three panels). A taxon was considered lost (red) if it was not detected in both pre- and post-randomization samples, restored (blue) if it was lost in the pre-randomization sample but was present in the post-randomization sample, and never lost (gray) if it remained detectable throughout the study (note that the initial sample of patient T4 did not have detectable Bacteroidetes).