Impact of Metronidazole Treatment and Dientamoeba Fragilis Colonization on gut Microbiota Diversity.

OBJECTIVES The intestinal parasite Dientamoeba fragilis (D. fragilis) is a common colonizer of children in Denmark. Metronidazole has been used to reduce gastrointestinal symptoms in children colonized with D. fragilis. We aimed to identify gut microbiota changes associated with i) D. fragilis carrier status and ii) metronidazole treatment of D. fragilis-positive children. METHODS The fecal microbiota of 275 fecal samples from children treated with metronidazole (n = 48) or placebo (n = 48) were characterized by ribosomal DNA sequencing. Samples collected before (T1), 2 weeks after (T2), and 8 weeks (T5) after treatment were included. Seventy fecal samples from 70 age-matched parasite-negative children served as controls. RESULTS The abundance of 24 bacterial genera differed significantly according to D. fragilis carrier status, with Flavonifractor being remarkably more abundant in children testing negative for D. fragilis. Eight bacterial genera changed significantly in abundance in children losing vs. keeping D. fragilis after metronidazole treatment. Of these, seven returned to pre-treatment (T1) levels at T5. Meanwhile, the abundance of Flavonifractor continued to differ at T5, whereas for Ruminococcus the abundance only remained high in children who were D. fragilis-negative at T2 and T5. Increases in Hungatella, Sutterella, and Streptococcus abundances observed at T2 were specific to metronidazole exposure and hence independent of D. fragilis colonization. CONCLUSIONS This study revealed that specific bacterial genera were associated with D. fragilis colonization. Metronidazole treatment had a short-term impact on the abundance of some bacterial genera, with most of these reverting to pre-treatment levels eight weeks after completed treatment.