Josh Michener

Josh Michener

Staff Scientist


Dr. Josh Michener is a microbiologist and metabolic engineer in the Biosciences Division at ORNL. He received his PhD in Bioengineering at Caltech in 2012, where he worked with Christina Smolke and Frances Arnold to use engineering and evolution to optimize heterologous enzyme activities. He was also a Nordic Research Fellow with Jens Nielsen, where he studied the stresses that heterologous metabolic pathways place on their host. He then moved to Harvard Organismic and Evolutionary Biology, where he worked with Chris Marx and Eric Alm to study microbial evolution after horizontal gene transfer, as an analogy to the processes that occur after the deliberate transfers of genetic material in synthetic biology. In 2015 he moved to ORNL, where he has been applying rational and evolutionary approaches to discover and optimize metabolic pathways for the conversion of lignocellulosic biomass into fuels and chemicals.


Wigner Fellowship (2015-2018)
NIH NRSA Postdoctoral Fellowship (2013-2015)
Nordic Research Fellowship (2011)
NSF Graduate Fellowship (2008-2011)
Roger de Friez Hunneman Prize (2006)
Phi Beta Kappa (2006)


Close D, Cooper SJ, Wang X, Giannone RJ, Engle NL, Tschaplinski TJ, Hedstrom L, Parks JM, and Michener JK*, Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis.

Cecil JH, Garcia DC, Giannone RJ, and Michener JK*, Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds in Novosphingobium aromaticivorans.

Standaert RF, Giannone RJ, and Michener JK*. Identification of parallel and divergent optimization solutions for homologous metabolic enzymes. Metab Eng Comm 2018. 6:56-62

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 Aug 31;83(18).

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. Frontiers in Microbiology 2016.

Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, et al. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. PLoS Comput Biol 2015; 11(8): e1004400.

Michener JK, Camargo Neves AAC, Vuilleumier S, Bringel F, and Marx CJ. Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife. 2014;10.7554/eLife.04279

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

Michener JK and Smolke CD. Synthetic RNA switches for yeast metabolic engineering. Methods in Molecular Biology, Yeast Metabolic Engineering. 1152:125-36

Michener JK, Nielsen J, and Smolke CD. Identification and treatment of heme depletion due to over-expression of a lineage of evolved P450 monooxygenases. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19504-9.

Michener JK and Smolke CD. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metabolic Engineering. 2012 Jul; 14(4):306-16.

Michener JK, Thodey K, Liang JC, and Smolke CD. (2011) Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metabolic Engineering. 2012 May; 14(3):212-22.