Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel 13C-metabolite fingerprinting


  • Conflicts of interest: The authors declare that they have no conflict of interest.
  • Whitney D. Hollinshead and William R. Henson contributed equally to this work.


For rapid analysis of microbial metabolisms,13C-fingerprinting employs a set of tracers to generate unique labeling patterns in key amino acids that can highlight active pathways. In contrast to rigorous 13C-metabolic flux analysis (13C-MFA), this method aims to provide metabolic insights without expensive flux measurements. Using13C-fingerprinting, we investigated the metabolic pathways in Rhodococcus opacus PD630, a promising biocatalyst for the conversion of lignocellulosic feedstocks into value-added chemicals. Specifically, seven metabolic insights were gathered as follows: (1) glucose metabolism mainly via the Entner–Doudoroff (ED) pathway; (2) lack of glucose catabolite repression during phenol co-utilization; (3) simultaneous operation of gluconeogenesis and the ED pathway for the co-metabolism of glucose and phenol; (4) an active glyoxylate shunt in acetate-fed culture; (5) high flux through anaplerotic pathways (e.g., malic enzyme and phosphoenolpyruvate carboxylase); (6) presence of alternative glycine synthesis pathway via glycine dehydrogenase; and (7) utilization of preferred exogenous amino acids (e.g., phenylalanine). Additionally, a13C-fingerprinting kit was developed for studying the central metabolism of non-model microbial species. This low-cost kit can be used to characterize microbial metabolisms and facilitate the design-build-test-learn cycle during the development of microbial cell factories. Biotechnol. Bioeng. 2016;113: 91–100. © 2015 Wiley Periodicals, Inc.