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:
NLSN 3215

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 microbes compete for - and cooperate in - degradation of complex substrates and how this division of metabolic labor influences gut microbiome fermentation of dietary fiber polysaccharides. We are interested in how differences in physical and chemical structures influence gut microbiome structure and function, and how structural differences influence health outcomes. Finally, we are interested in 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:

Tuncil, Y. E. (P)*, R. D. Thakkar (G), S. Arioglu-Tuncil, B. R. Hamaker, and S. R. Lindemann*. “Subtle variations in dietary fiber fine structure differentially impact the composition and metabolic function of gut microbiota.” In press, mSphere. 

Thakkar, R. D. (G), Y. E. Tunçil (P), B. R. Hamaker, and S. R. Lindemann*. “Maize bran particle size governs the community composition and metabolic output of human gut microbiota.” In press, Frontiers in Systems Microbiology.

Lawson, C. E., W. R. Harcombe, R. Hatzenpichler, S. R. Lindemann, F. E. Löffler, M. A. O’Malley, H. García-Martin, B. F. Pfleger, L. Raskin, O. S. Venturelli, D. G. Weissbrodt, D. R. Noguera, and K. D. McMahon* (2019). “Common principles and best practices for engineering microbiomes.” Nature Microbiology 17:725-741. 

Song, H.-S.*, J.-Y. Lee, S. Haruta, W. Nelson, D.-Y. Lee, S. Lindemann, J. Fredrickson, and H. Bernstein (2019). “Minimal Interspecies Interaction Adjustment (MIIA): inference of member-dependent interactions in microbiomes.” Frontiers in Systems Microbiology 10:1264.

S. R. Lindemann* (2019). “Microbial Ecology: Functional “Modules” Drive Assembly of Polysaccharide-Degrading Marine Microbial Communities.” Current Biology, 29(9): R330-R332.

Zengler, K., K. Hofmockel, N. S. Baliga, S. W. Behie, H. C. Bernstein, J. B. Brown, J. R. Dinney, S. A. Floge, S. P. Forry, M. Hess, S. A. Jackson, C. Jansson, S. R. Lindemann, J. Pett-Ridge, C. Marans, E. A. Shank, O. S. Venturelli, M. D. Wallenstein, and T. Northen* (2019). “EcoFAB: Advancing microbiome science through standardized fabricated ecosystems.” Nature Methods 16: 567-571.

Tuncil, Y. E.* (P), R. D. Thakkar (G), S. Arioglu-Tuncil, B. R. Hamaker, and S. R. Lindemann*. “Fecal microbiota responses to bran particles are specific to cereal type and in vitro digestion methods that mimic upper gastrointestinal tract passage.” (2018) Journal of Agricultural and Food Chemistry 66(47):12580-12593.

Tuncil, Y. E. (P), R. D. Thakkar (G), A. D. Romero Marcia (V), B. R. Hamaker, and S. R. Lindemann*. “Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions.” (2018) Scientific Reports 8(1):16655.

Lindemann S. R.*, J. M. Mobberley, J.K. Cole (I), L. M. Markillie, R. C. Taylor, E. Huang, H. S. Wiley, M. S. Lipton, W. C. Nelson, J. K. Fredrickson, and M. F. Romine (2017). “Predicting species-resolved macronutrient acquisition during succession in a model phototrophic biofilm using an integrated’omics approach.” Front. Microbiol. 8:1020.

Ha, P. T., S. R. Lindemann, L. Shi, A. C. Dohnalkova, J. K. Fredrickson, and H. Beyenal* (2017). “Syntrophic anaerobic photosynthesis via direct interspecies electron transfer.” Nat. Comm. 8:13924.

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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