Preparing the Gut with Antibiotics Enhances Gut Microbiota Reprogramming Efficiency by Promoting Xenomicrobiota Colonization

Abstract

Gut microbiota plays multiple important roles in intestinal and physiological homeostasis, and using fecal microbiota transplantation (FMT) to reprogram gut microbiota has demonstrated promise for redressing intestinal and physiological disorders. This study tested the alterations in reprogramming efficiency caused by different gut preparation procedures and explored the associated underlying mechanisms. We prepared the guts of mice for FMT by administering one of the three most-clinically used pretreatments [antibiotics, bowel cleansing (BC) solution, or no pretreatment], and we found that preparing the gut with antibiotics induced a more efficient modification of the gut bacterial community than was induced by either of the other two pretreatment types. The increased efficiency of antibiotic treatment appeared to occur via increasing the xenomicrobiota colonization. Further analysis demonstrated that antibiotic treatment of mice induced intestinal microbiota disruption, mostly by expelling antibiotic-sensitive bacteria, while the indigenous microbiota was maintained after treatment with a BC solution or in the absence of pretreatment. The amount of antibiotic-resistant bacteria increased shortly after antibiotics usage but subsequently decreased after FMT administration. Together, these results suggest that FMT relied on the available niches in the intestinal mucosa and that preparing the gut with antibiotics facilitated xenomicrobiota colonization in the intestinal mucosa, which thus enhanced the overall gut microbiota reprogramming efficiency.

Keywords: antibiotics; colonization efficiency; fecal microbiota transplantation; gut pretreatment; microbiota reprogramming.

FIGURE 1

Influence of pretreatment on FMT efficiency. (A,B) Principal coordinate analyses of mucosa microbiota plotted on the first two principal components in the jejunum (A) and colon (B). (C,D) Bray–Curtis dissimilarities using OTU taxa of the jejunum (C) and colon (D) mucosa bacterial communities after FMT compared with control mice. (E,F) Bray–Curtis dissimilarities of the mouse jejunum (E) and colon (F) mucosa bacterial communities after FMT compared with the donor bacterial community. (G,H) The altered taxa in abundance at the genus level in the jejunum (G) and colon (H). The significantly altered taxa compared with control mice are enclosed in boxes, and arrows indicate increased (↑) or decreased (↓) abundance. Only taxa with p < 0.05 are included. Data are presented as means ± SD. ^∗∗∗p < 0.001. For all figures: FMT, fecal microbiota transplant group; CON, control group; BC, bowel cleansing group; AT, antibiotics group.

FIGURE 2

Influence of antibiotic and bowel cleansing treatments on the intestinal mucosa bacterial community. (A–D) The mucosa bacterial community in the jejunum (A,B) and colon (C,D) were analyzed using OTU taxa; the principal coordinate analyses plotted on the first two principal components (A,C) and Bray–Curtis dissimilarities (B,D) are shown. (E,F) Alpha diversity of the mucosa bacterial community in the jejunum (E) and colon (F). (G,H) Taxonomic distribution of intestinal microbiota in the jejunum (G) and colon (H) mucus after AT or BC treatment. Taxa with a mean abundance of >10^-4 are shown. The internal tree presents the taxonomy at the phylum level: Bacteroidetes (red), Proteobacteria (blue), Firmicutes (green), and others (black). The four circular histograms indicate the taxa that are less abundant compared with control mice; from inside to outside, the first and third circular histogram present the taxa depleted by AT or BC treatment, respectively, and the second and fourth circular histogram denote the fold-change of taxa by AT or BC treatment, respectively. The taxa that are more or less abundant after treatment are highlighted in red and blue, respectively. The main bacterial taxa in the intestine are annotated in the outer circle. Data are presented as means ± SD. ^∗∗p < 0.01, ^∗∗∗p < 0.001.

FIGURE 3

Genus level dynamic changes in the mouse intestinal microbiota after antibiotic pretreatment and FMT. (A,B) Changed taxa in the jejunum (A) and colon (B) are indicated and clustered into three groups. Hierarchical clustering is based on the Euclidean distance. Taxonomic names of the taxa are listed, and names written in red belong to antibiotic-resistant bacteria according to the Antibiotic Resistance Genes Database (ARDB: http://ardb.cbcb.umd.edu/). Only taxa having a change with p < 0.05 are shown.

FIGURE 4

Diagram of the proposed mechanism for antibiotic pretreatment enhancement of FMT efficiency by promoting xenomicrobiota colonization in the intestinal mucosa. (A) Commensal bacteria resist xenomicrobiota colonization under normal conditions. (B) Antibiotic treatment induces commensal bacteria disruption, and these vacancies provide more available spaces for xenomicrobiota in the mucosa. (C) Xenomicrobiota colonization is promoted after antibiotic usage. Symbols in olive indicate commensal bacteria, and those in red indicate xenobacteria.