Periodontitis is an inflammatory disease of the oral cavity induced by anaerobic bacteria, that remains to be the primary cause of tooth loss in adults worldwide. Finding an anti-microbial therapeutic to selectively target periodontal pathogens has proven to be difficult, and current treatment modalities only provide a transient benefit. Amixicile is a non-toxic, readily bioavailable novel antimicrobial that targets strict anaerobes through inhibition of the activity of Pyruvate Ferredoxin Oxidoreductase (PFOR), a major enzyme mediating oxidative decarboxylation of pyruvate, a critical step in metabolism. Our study aimed to evaluate the efficacy of amixicile in inhibiting the growth of bacteria harvested from the complex sub-gingival biofilm of patients with chronic periodontitis. We hypothesize that amixicile will selectively inhibit pathogenic anaerobic bacteria collected from patients, with the same efficacy as metronidazole, the current accepted treatment modality. Plaque samples were harvested from patients with severe chronic periodontitis and cultured under anaerobic conditions. The microbiomes were grown in the presence of amixicile and metronidazole and the growth was compared to that of bacteria grown in the absence of the antimicrobials. Following 24 hour incubation, bacterial DNA was isolated and bacterial quantity was evaluated by quantitative PCR (qPCR) using primers specific for 12 bacterial species: P. gingivalis (Pg), P. intermedia (Pi), F.nucleatum (Fn), S.gordonii (Sg), S. anginosus (Sa), V. atypical (Va), L. acidophilus (La), A.actinomycetemcomitans (Aa), T.denticola (Td), S.mutans (Sm), S.sanguis (Ss), and 16s. Individual qPCR runs were combined to represent an overall average of CT value differences. Amixicile treatment groups exhibited statistical significant reductions (PP. intermedia, F. nucleatum and Veillonella atypical. When comparing amixicile to metronidazole, amixicile performed with similar efficacy with the largest effect seen for PFOR bacteria. Our conclusion supports amixicile as a potent inhibitor of anaerobic bacteria, and could be a potential new therapeutic antimicrobial in the treatment of periodontal disease