Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity

Abstract

Background: Fecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients' phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients' phageome composition.

Results: Donor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients' phageome toward the donors' composition and increased phageome alpha diversity and variability over time.

Conclusions: FMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient's microbiome.

Trial registration: The Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174 . Video Abstract.

Keywords: Donor microbiome diversity; Fecal microbiota transplantation (FMT); Microbial engraftment; Microbial population dynamics; Phageome composition.

Fig. 1

Schematic representation of the Gut Bugs Trial. Whole stools were collected from 8 healthy lean donors (4 females and 4 males). Following the first donation, a single male donor (DM05) was replaced by another (DM12). Donor stool and saline solution were administered in a double-blind manner to FMT (n = 42) and placebo (n = 45) recipients, respectively. Recipient stool samples were collected at baseline and at 6, 12, and 26 weeks post-intervention to investigate the effects of FMT on recipient microbial populations

Fig. 2

Donor phage engraftment was associated with phageome alpha diversity. a Donors differed in the number of engrafted vOTUs donated and in engraftment efficacy. b Donors differed in phageome alpha diversity (Shannon diversity). Each dot represents a different donation. c Positive correlation between the donor’s phageome alpha diversity and phage engraftment efficacy (assessed by Pearson correlation)

Fig. 3

FMT recipients’ phageome composition shifted towards donor profiles. Bray–Curtis dissimilarities between donor and recipient vOTU profiles, stratified by sex-matched donors and time point. Significant shifts towards individual donor profiles were assessed using linear mixed-effects models (LMM) including a treatment by time point interaction (fixed effect) and subject ID (random effect). The p values were collectively adjusted using the FDR correction, and only statistically significant differences (i.e., q ≤ 0.05) were reported

Fig. 4

FMT and placebo recipients had distinct phageome compositions. The phageome compositions of a FMT and b placebo recipients were categorized according to the origin of the vOTUs: (1) vOTUs shared with the donors (i.e., shared with donors); (2) vOTUs that were initially identified at baseline within the FMT or placebo recipients (i.e., conserved from baseline), (3) vOTUs that were identified at time points subsequent to the transplantation in FMT or placebo recipients (i.e., novel)

Fig. 5

Increase in phageome variability and alpha diversity in FMT recipients post-transplantation. a Bray–Curtis dissimilarities between participants’ week 6 phageome and phageomes from subsequent follow-up time points. Comparisons between treatment groups were performed using Wilcoxon rank sum tests with FDR correction. b vOTUs identified in FMT recipients were less stable than the vOTUs identified in placebo individuals. Inter-group differences were assessed using Pearson’s chi-squared tests. To determine which variables contributed to the overall inter-group differences, a post hoc analysis was performed, and the p values were adjusted using the FDR correction. c Female FMT recipients exhibited an increase in phageome alpha diversity at 6 weeks following the transplantation. The differences in variation in alpha diversity post-FMT between FMT and placebo recipients were assessed using linear mixed-effects models. The p values were collectively adjusted using the FDR correction, and only statistically significant differences (i.e., q ≤ 0.05) were reported

Fig. 6

The total abundance of temperate phages increased post-FMT. Total abundance of temperate and virulent phages in a FMT and b placebo recipient microbiomes. Treatment differences in variation in the total abundance of the temperate and virulent phages post-FMT between FMT and placebo recipients were assessed using linear mixed-effects models. The p values were collectively adjusted using the FDR correction within sexes. Only statistically significant differences (*q < 0.05, ***q < 0.001) were reported