Stephen R Lindemann

Stephen R Lindemann Profile Picture

Assistant Professor of Food Science and Nutrition Science
Ph.D., Microbiology, University of Iowa, 2010
B.S., Microbiology, Molecular Biology, Biochemistry, and Genetics, Purdue University, 2004

Contact Info:

Training Group(s):
Microbiology, Immunology and Infectious Diseases
Computational and Systems Biology

Active Mentor - currently hosting PULSe students for laboratory rotations and recruiting PULSe students into the laboratory; serves on preliminary exam committees

Current Research Interests:

Broadly, Prof. Lindemann’s interests lie in identifying the principles that govern structure-function relationships in microbial communities and how host-microbe and microbe-microbe interactions govern their dynamics and emergent properties. Specifically, he is focused on using molecular microbial ecology techniques to understand: how diet influences the composition and stability of the gut microbiome; how gut microbiome metabolism of dietary components influences production and absorption of bioactive microbial metabolites; how metabolic interactions between microbes alter polysaccharide fermentation and nitrogen metabolism; and how interactions between beneficial microbes exclude pathogenic organisms and modulate inflammation in the colon. Our research employs genome-enabled systems biology (“-omics”) approaches coupled with genetic techniques, computational biology, and modeling. We envision a world in which dietary solutions can be reliably employed to improve nutrition and reduce acute and chronic gut illness.

Selected Publications:

Renslow, R. S., S. R. Lindemann, and H.-S. Song. “A generalized spatial measure for resilience of microbial systems.” Front. Microbiol. 7:443.

Lindemann, S. R.  H. C. Bernstein, H.-S. Song, M. Fields, W. Shou, D. R. Johnson, J. K. Fredrickson, and A. S. Beliaev (2016). “Engineering microbial consortia for controllable outputs.” ISME J 10:2077-2084.

Nelson, W. C., Y. Maezato, Y-W. Wu, M. F. Romine, and S. R. Lindemann (2016). “Metagenomic sequencing of parallel consortia enables genome reconstruction of rare and closely-related organisms.” AEM 82(1):255-267.

Song, H.-S., R. S. Renslow, J. K. Fredrickson, and S. R. Lindemann (2015). “Integrating ecological and engineering concepts of resilience in microbial communities.” Front. Microbiol. 6:1298.

Konopka, A. E., S. R. Lindemann, J. K. Fredrickson (2014). “Dynamics in microbial communities: unraveling mechanisms to identify principles.” ISME J. 9: 1488-1495.

Cole, J. K., J. R. Hutchison, R. S. Renslow, Y.-M. Kim, W. B. Chrisler, H. E. Engelmann, A. C. Dohnalkova, D. Hu, T. O. Metz, J. K. Fredrickson, and S. R. Lindemann (2014). “Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.” Front. Microbiol. 5:109.

Babauta, J. T., E. Acti, P. T. Ha, S. R. Lindemann, T. Ewing, D. R. Call, J. K. Fredrickson, and H. Beyenal (2014). “Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.” Front. Microbiol. 5:11.

Lindemann, S. R., J. J. Moran, J. C. Stegen, R. S. Renslow, J. R. Hutchison, J. K. Cole, A. C. Dohnalkova, J. Tremblay, K. Singh, S. A. Malfatti, F. Chen, S. G. Tringe, H. Beyenal, and J. K. Fredrickson (2013). “The epsomitic, phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.” Front. Microbiol. 4:323.

Lindemann, S. R., K. Peng, M. E. Long, J. R. Hunt, M. A. Apicella, D. M. Monack, L.A.H. Allen, and B.D. Jones (2011). “F. tularensis mutants in O-antigen and capsule biosynthesis induce early cell death in human macrophages.” Infect. Immun. 79(2): 581-94.

Lindemann, S. R., M. K. McLendon, M. A. Apicella, and B. D. Jones (2007). “An in vitro model system used to study adherence and invasion of Francisella tularensis live vaccine strain in nonphagocytic cells.” Infect. Immun. 75(6): 3178-3182.

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