Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro

Abstract

Fecal microbiota transplantation (FMT) is a proposedly useful strategy for the treatment of gastrointestinal (GI) disorders through remediation of the patient gut microbiota. However, its therapeutic success has been variable, necessitating research to uncover mechanisms that improve patient response. Antibiotic pretreatment has been proposed as one method to enhance the success rate by increasing niche availability for introduced species. Several limitations hinder exploring this hypothesis in clinical studies, such as deleterious side effects and the development of antimicrobial resistance in patients. Thus, the purpose of this study was to evaluate the use of an in vitro, bioreactor-based, colonic ecosystem model as a form of preclinical testing by determining how pretreatment with the antibiotic rifaximin influenced engraftment of bacterial strains sourced from a healthy donor into an ulcerative colitis-derived defined microbial community. Distinct species integrated under the pretreated and untreated conditions, with the relative rifaximin resistance of the microbial strains being an important influencer. However, both conditions resulted in the integration of taxa from Clostridium clusters IV and XIVa, a concomitant reduction of Proteobacteria, and similar decreases in metabolites associated with poor health status. Our results agree with the findings of similar research in the clinic by others, which observed no difference in primary patient outcomes whether or not patients were given rifaximin prior to FMT. We therefore conclude that our model is useful for screening for antibiotics that could improve efficacy of FMT when used as a pretreatment.IMPORTANCE Patients with gastrointestinal disorders often exhibit derangements in their gut microbiota, which can exacerbate their symptoms. Replenishing these ecosystems with beneficial bacteria through fecal microbiota transplantation is thus a proposedly useful therapeutic; however, clinical success has varied, necessitating research into strategies to improve outcomes. Antibiotic pretreatment has been suggested as one such approach, but concerns over harmful side effects have hindered testing this hypothesis clinically. Here, we evaluate the use of bioreactors supporting defined microbial communities derived from human fecal samples as models of the colonic microbiota in determining the effectiveness of antibiotic pretreatment. We found that relative antimicrobial resistance was a key determinant of successful microbial engraftment with rifaximin (broad-spectrum antibiotic) pretreatment, despite careful timing of the application of the therapeutic agents, resulting in distinct species profiles from those of the control but with similar overall outcomes. Our model had results comparable to the clinical findings and thus can be used to screen for useful antibiotics.

Keywords: antibiotic pretreatment; bioreactor; fecal microbiota transplantation; human gut microbiome; in vitro model; microbial ecosystem therapeutics; rifaximin.

FIG 1

Partial least squares discriminant analysis of compositional and metabonomic data. Microbial community compositional data were generated from gDNA-extracted bioreactor samples that were 16S rRNA profiled by Illumina sequencing, with subsequent processing and center log-ratio transformation, and from ¹H NMR metabolite data from filtered (0.2-μm pore size) bioreactor samples. The bioreactors were seeded with a defined microbial community representing a fecal sample from an ulcerative colitis patient. Data points are labeled by the following sample characteristics: (i) day of the bioreactor run (D), (ii) replicate number (R), and (iii) the assignment to rifaximin treatment (C for control and T for treatment). Coloring is used to distinguish the experimental groups, as indicated. Before, samples collected prior to rifaximin treatment or application of MET; Abx, rifaximin pretreatment.

FIG 2

Differential abundance changes in the ulcerative colitis-associated microbial community after microbial replenishment by rifaximin pretreatment. Pairwise effect sizes of processed and center log-ratio-transformed Illumina 16S rRNA profiling data were generated from gDNA-extracted bioreactor samples seeded with a defined microbial community representing a fecal sample from an ulcerative colitis patient. Shown are the species with absolute effect sizes greater than 1, when abundances before treatment (Before) and after microbial ecosystem therapeutic replenishment conditions, both untreated (MET) and pretreated with rifaximin (Abx-MET), were compared. Dotted lines are at the −1 and 1 effect sizes for reference.