Amixicile targets anaerobic bacteria within the oral microbiome

Anaerobic bacteria are the major causative agents of periodontal disease. However, so far, targeted therapy aimed at reducing those pathogens has not been widely implemented. We have previously reported on a novel antimicrobial, amixicile, that targets anaerobic bacteria through inhibition of the function of the major anaerobic metabolic enzyme pyruvate ferredoxin oxidoreductase (PFOR), while not affecting aerotolerant organisms. It effectively inhibited the growth of oral anaerobes both in monocultures as well as in mixed in vitro mixed cultured however, amixicile's activity in in vivo-like conditions remained to be established.

Here, we expand our study using an ex vivo oral microbiome combined with metagenomic sequencing to determine the effect of amixicile treatment on the composition of the microbiome and compare it to that of metronidazole.

Our results show that in the complex microbiomes, anaerobic bacteria are selectively inhibited, while the growth of aerotolerant ones, such as Streptococcus, Klebsiella, Neisseria, and Rothia is unaffected. Veillonella was the most abundant anaerobic genus in our ex vivo microbiome, and we observed complete inhibition of its growth. In addition, growth of other anaerobes, Fusobacterium and Prevotella, was significantly inhibited. It is noteworthy that a change in abundance of bacteriophages, such as Siphoviridae and Myoviridae, associated with the oral microbiome was observed.

Collectively, our data expand on the so far reported inhibitory spectrum of amixicile and demonstrates that it inhibits anaerobic bacteria, including both clinical isolates and laboratory strains.