My research, and that of the unculturable group in the Antimicrobial Discovery Center at Northeastern University, is focused on growing previously unculturable bacteria, and identifying the molecular mechanisms responsible for uncultivability. It is estimated that 99% or more of all bacteria in the environment do not grow under standard laboratory conditions, drastically limiting the diversity of microorganisms that are available for research. It is likely that within this ‘missing’ diversity, there are novel classes of antibiotics and other biologically active compounds that will remain hidden, unless it becomes possible to culture the organisms that manufacture them. We use a combination of growth in the natural environment and co-culture with neighboring bacteria to identify factors inducing growth, and increase the diversity we are able to cultivate in the lab.

The projects and techniques we use are described in the Unculturables Group section.

Previously, at the Faculty of Medicine, Paris Descartes University, INSERM U571, I worked as an EMBO and FRM Post Doctoral Fellow and INSERM Young Investigator on aging and phenotypic variability in bacteria, particularly those which reproduce by apparently symmetric division. During this work, we discovered that, contrary to theories of aging, these organisms display the phenotypes of aging, suggesting that perfect repair is either prohibitively costly, or impossible for the cell. We also determined that the presence of damaged proteins (in the form of inclusion bodies) correlated with almost half of the aging phenotype, suggesting that the accumulation of damage components is responsible for some cellular aging.

As a graduate student, I worked in the lab of Jon Beckwith at Harvard Medical School, where I studied the role of two thio-disulfide redox pathways in the model bacterium, Escherichia coli. I identified a previously cryptic gene encoding a new thioredoxin-like protein, and demonstrated the role of both thioredoxins in the cytoplasm in oxidizing proteins under specific conditions, a reversal of their normal role in cysteine reduction. In addition, I characterized DsbD, a key protein responsible for transducing reducing potential from the cytoplasm to the periplasm.
During the course of obtaining a B.S. in Microbiology at Penn State University, I carried out research in the lab of Dr. Robert Bernlohr on the role of EF-Tu in starvation sensing in E. coli.

Publications:

D'Onofrio A.*, Crawford J.M.*, Stewart E.J., Witt K., Gavrish E., Epstein S., Clardy J., Lewis K. (2010) Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria. Chemistry & Biology 17(3):256-264.
*Both first authors contributed equally [PDF]

Babic A., Lindner A.B., Vulic M., Stewart E.J.., Radman M. (2008) Direct Visualization of Horizontal Gene Transfer. Science 319: 1533-1536 [PDF]

Veening J.W.*, Stewart E.J.*, Berngruber T.W., Taddei F, Kuipers O.P. and Hamoen L.W. (2008) Bet-hedging and epigenetic inheritance in bacterial cell development. PNAS 105(11): 4393–4398
*Both first authors contributed equally [Link]

Lindner A.B., Madden R. Demarez A., Stewart E.J., Taddei F. (2008) Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. PNAS 105(8): 3076–3081 [Link]

Fontaine F., Stewart E.J., Lindner A.B., Taddei F. (2008) Mutations in two global regulators lower individual mortality in Escherichia coli. Molecular Microbiology 67(1): 2–14 [Link]

Stewart E.J., Madden R., Paul G., Taddei F. (2005) Aging and Death in an Organism that Reproduces by Morphologically Symmetric Division. PloS Biology, 3(2): e45. [Link]

Guyon J., Bize A., Paul G., Stewart E.J., Delmas J-F., Taddei F. (2005) Statistical Study of Cellular Aging. ESAIM Proc., 14: 100-114. Proceedings of CEMRACS 2004: Mathematics and Applications in Biology and Medicine. [PDF]

Stewart E.J., Katzen F., Beckwith J., (1999) Six conserved cysteines of the membrane protein DsbD are required for the transfer of electrons from the cytoplasm to the periplasm of Escherichia coli. EMBO J. 18(21): 5963-5971 [Link]

Stewart E.J., Åslund F., Beckwith J., (1998) Disulfide bond formation in the Escherichia coli cytoplasm: an in vivo role reversal for the thioredoxins. EMBO J. 17(19): 5543-5550 [Link]

Murphy C.K., Stewart E.J., Beckwith J., (1995) A double counter-selection system for the study of null alleles of essential genes in Escherichia coli. Gene 155(1): 1-7 [Link]