Josh Michener

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Josh Michener


  • PhD, 2012, Bioengineering at Caltech
  • S.B. 2006, Chemical Engineering and Biology at MIT

Research Experience

  • Wigner Fellow, Biosciences Division, Oak Ridge National Lab
  • NRSA Postdoctoral Fellow in the Marx Lab, Harvard Organismic and Evolutionary Biology and Alm Lab, MIT Biological Engineering
  • Nordic Research Fellow in the Nielsen Lab, Chalmers Institute of Technology (Gothenburg, Sweden)
  • NSF Graduate Research Fellow in the Smolke Lab, Caltech/Stanford Bioengineering
  • UROP in the Endy Lab at MIT

Contact Info

Josh Michener
Biosciences Division
Oak Ridge National Laboratory
1 Bethel Valley Road
Oak Ridge, TN, 37830

Research Interests

No gene exists in isolation. To be useful, a gene must be functionally expressed and its host must be able to deal with any resulting stresses. Most genes have had sufficient time in their current host that the gene and host have co-evolved to minimize deleterious interactions. However, while this type of coexistence might be the rule, the exceptions can be both interesting and extremely consequential. When, for example, a microbe acquires new genetic material through horizontal gene transfer or synthetic biology, genes must function in an environment with which they did not co-evolve. Efficient use of a new ability will require careful integration into the existing metabolic and regulatory networks of the host. The interactions between gene and host, as well as their evolutionary outcomes, will determine whether a microbe can become pathogenic, remediate a polluted site, or produce a biofuel. Understanding these interactions and the strategies by which evolution optimizes them will allow us to better anticipate the emergence of new microbial phenotypes.



  • Cecil JH and Michener JK*. Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds. bioRxiv 2017. [1]

Research Articles

  • Clarkson SM, Giannone RJ, Kridelbaugh DM, Elkins JG, Guss AM*, and Michener JK*. Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables bioconversion of model aromatic compounds. Appl Env Microbiol. 2017; 83 (18), e01313-17 [2]
  • Michener JK*, Vuilleumier S, Bringel F, and Marx CJ. Transfer of a catabolic pathway for chloromethane in Methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. Front Microbiol 2016; 10.3389/fmicb.2016.01116 [3].
  • Michener JK, Carmargo-Neves AA, Vuilleumier S, Bringel F, and Marx CJ. Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement of the host. eLife 2014;10.7554/eLife.04279 [4].
  • Michener JK, Vuilleumier S, Bringel F, and Marx CJ. Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J Bacteriol. June 2014 196:2101-2107. [5]
  • Michener JK, Nielsen J, and Smolke CD. Identification and treatment of heme depletion due to over-expression of a lineage of evolved P450 monooxygenases. PNAS. 2012; 109(47):19504-9. [6]
  • Michener JK and Smolke CD. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng. 2012 Jul; 14(4):306-16. [7]

Methods and Reviews

  • Michener JK and Marx CJ. After horizontal gene transfers, metabolic pathways may need further optimization. Microbe, 2015 Feb. [8]
  • Michener JK and Smolke CD. Synthetic RNA switches for yeast metabolic engineering. 2014. Valeria Mapelli (ed.), Yeast Metabolic Engineering: Methods and Protocols, Methods in Molecular Biology, 1152:125-36. [9]
  • Michener JK, Thodey K, Liang JC, Smolke CD. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng. 2012 May; 14(3):212-22. [10]