Human disease-related pathways increasing with opportunistic pathogens bloom in intestinal microbiome after vancomycin exposure and restoration with fecal transplantation by simulator of the human intestinal microbial ecosystem (SHIME)

Abstract

Background: Antibiotics are growing reported to cause human intestinal microbial disorders with increasing abundances of opportunistic pathogens, and fecal microbiota transplantation (FMT) has been confirmed to restore the dysbiosis of gut flora in many kinds of intestinal disease. However, to date, few studies have focused on the bloomed opportunistic pathogens associated human disease-related pathways as well as antibiotic resistance genes (ARGs) after vancomycin exposure, and there is limited information on using FMT for restoration of intestinal microbiome affected by antibiotics. Methods: This study investigated effects of vancomycin on the opportunistic pathogens, human disease-related pathways as well as ARGs in human gut, and the restoration of intestinal microbiome by FMT. Using the simulator of the human intestinal microbial ecosystem (SHIME), two reactors (representing the ascending and descending colon, respectively) were inoculated with human intestinal microbiota from a healthy adult volunteer who did not suffer from gastrointestinal diseases or take any antibiotic in the previous six months. Samples were collected from the reactors at six-time points (before treatment, after seven days of individual 10 mg/L, 100 mg/L, 1000 mg/L vancomycin treatment, 14 days following the termination of vancomycin and 14 days following FMT). The intestinal microbiome composition and function were analyzed using 16S rRNA gene sequencing and High-throughput Quantitative PCR (HT-qPCR).Results: Vancomycin treatment substantially increased human disease-related pathways and decreased abundances of ARGs. Besides, the bloomed opportunistic pathogens including Achromobacter, Klebsiella, and Pseudomonas, caused by vancomycin exposure, were positively correlated with human disease-related pathways. The microbiota abundance and genes of human disease-related pathways and antibiotic resistance showed a remarkable return towards baseline after FMT, but not for natural recovery. Conclusions: These findings suggest that impacts of vancomycin on human gut are profound and FMT will be a promising strategy in clinical application that can restore the dysbiosis of gut microbiota, which may be valuable for directing future work.