Stephen Lindemann

Educational Background

  • B.S., Microbiology, Molecular Biology, Biochemistry, and Genetics, Purdue University, 2004
  • Ph.D., Microbiology, University of Iowa, 2010
  • Post-Doc, Microbial Ecology, Pacific Northwest National Laboratory, 2013

Dissertation Title

Exploring the genetic basis of intracellular pathogenesis in Francisella tularensis


  • Whistler Center for Carbohydrate Research
  • PULSe: Microbiology, Inflammation and Infectious Diseases, and Computational and Systems Biology Training Groups
  • Editor, mSystems
  • Associate Editor, Frontiers in Systems Microbiology
  • International Society for Microbial Ecology
  • American Society for Microbiology


Dr. Lindemann’s research targets the ways that dietary influences shape the gut microbiome and the effects of those shifts on health (such as inflammation and gut colonization by pathogens) with the goal of identifying dietary solutions to health problems. 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 in the colon; and how these interactions between beneficial microbes exclude pathogenic organisms and modulate inflammation in the colon.

Discovery Publications

  1. Bernstein, H.C., Brislawn, C., Renslow, R.S., Dana, K., Morton, B., Lindemann, S.R., Song, H.-S., Atci, E., Beyenal, H., Fredrickson, J.K., Jansson, J.K., Moran, J.J. “Trade-offs between microbiome diversity and productivity in a stratified microbial mat.” ISME J, in press.
  2. Renslow, R.S., Lindemann, S.R., Song, H.-S. “A generalized spatial measure for resilience of microbial systems.” Front. Microbiol. 7:443.
  3. Lindemann, S.R., Bernstein, H.C., Song, H.-S., Fields, M., Shou, W., Johnson, D.R., Fredrickson, J.K., Beliaev, A.S. (2016) “Engineering microbial consortia for controllable outputs.” ISME J 10:2077-2084.
  4. Zachara, J.M., Moran, J.J., Resch, C.T., Lindemann, S.R., Felmy, A.R., Bowden, M.E., Cory, A.B., Fredrickson, J.K. (2016) “Geo- and biogeochemical processes in a heliothermal hypersaline lake.” Geochim. Cosmochim. Ac., 181:144-163.
  5. Renslow, R.S., Lindemann, S.R., Cole, J.K., Zhu, Z., Anderton, C.R. (2016) “Quantifying element incorporation in multispecies biofilms using NanoSIMS image analysis.” Biointerphases 11:02A322.
  6. Nelson, W.C., Maezato, Y., Wu, Y.-W., Romine, M.F., Lindemann, S.R. (2016) “Metagenomic sequencing of parallel consortia enables genome reconstruction of rare and closely-related organisms.” AEM 82(1):255-267.
  7. Song, H.-S., Renslow, R.S., Fredrickson, J.K., Lindemann, S.R. (2015) “Integrating ecological and engineering concepts of resilience in microbial communities.” Front. Microbiol. 6:1298.
  8. Ha, P.T., Renslow, R.S., Atci, E., Reardon, P.N., Lindemann, S.R., Fredrickson, J.K., Call, D.R., Beyenal, H. (2015) “Regulation of electron transfer processes affects phototrophic mat structure and activity.” Front. Microbiol. 6:909.
  9. McDermott, J.E., Bruillard, P.J., Overall, C.C., Gosink, L.J., Lindemann, S.R. (2015) “Prediction of multi-drug resistance transporters using a novel sequence analysis method.” F1000Research 4:60.
  10. Konopka, A.E., Lindemann, S.R., Fredrickson, J.K. (2014) “Dynamics in microbial communities: unraveling mechanisms to identify principles.” ISME J. 9:1488-1495.
  11. Moran, J.J., Doll, C.G., Bernstein, H.C., Renslow, R.S., Cory, A.B., Hutchison, J.R., Lindemann, S.R., Fredrickson, J.K. (2014) “Spatially tracking (13)C-labeled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry.” Environ. Microbiol. Rep. 6(6).
  12. Cole, J.K., Hutchison, J.R., Renslow, R.S., Kim, Y.-M., Chrisler, W.B., Engelmann, H.E., Dohnalkova, A.C., Hu, D., Metz, T.O., Fredrickson, J.K., Lindemann, S.R. (2014) “Phototrophic biofilm assembliy in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.” Front. Microbiol. 5:109.
  13. Stolyar, S., Liu, Z., Thiel, V., Tomsho, L.P., Pinel, N., Nelson, W.C., Lindemann, S.R., Romine, M.F., Haruta, S., Schuster, S.C., Bryant, D.A., Fredrickson, J.K. (2014) “Genome sequence of the thermophilic cyanobacterium Thermosynechococcus sp. Strain NK55a.” Genome Announc. 2(1).
  14. Babauta, J.T., Acti, E., Ha, P.T., Lindemann, S.R., Ewing, T., Call, D.R., Fredrickson, J.K., Beyenal (2014). “Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.” Front. Microbiol. 5:11.
  15. Rasmussen, J.A., Post, D.M., Gibson, B.W., Lindemann, S.R., Apicella, M.A., Meyerholz, D.K., Jones, B.D. (2014) “Francisella tularensis Schu S4 lipopolysaccharide core sugar and O-antigen mutants are attenuated in a mouse model of tularemia.” Infect. Immun. 82(4):1523-39.
  16. Lindemann, S.R., Moran, J.J., Stegen, J.C., Renslow, R.S., Hutchison, J.R., Cole, J.K., Dohnalkova, A.C., Tremblay, J., Singh, K., Malfatti, S.A., Chen, F., Tringe, S.G., Beyenal, H., Fredrickson, J.K. (2013) “The epsomitic, phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling.” Front. Microbiol. 4:323.
  17. Long, M.E., Lindemann, S.R., Rasmussen, J.A., Jones, B.D., Allen, L.A. (2013) “Disruption of Francisella tularensis Schu S4 iglI, iglJ, and pdpC genes results in attenuation for growth in human macrophages and in vivo virulence in mice, and reveals a unique phenotype for pdpC.” Infect. Immun. 81(3):850-861.
  18. Lindemann, S.R., Peng, K., Long, M.E., Hunt, J.R., Apicella, M.A., Monack, D.M., Allen, L.A.H., Jones, B.D. (2011) “F. tularensis mutants in O-antigen and capsule biosynthesis induce early cell death in human macrophages.” Infect. Immun. 79(2):581-94.
  19. McCaffrey, R.L., Schwartz, J.T., Lindemann, S.R., Hollenback, C., Buchan, B.W., Jones, B.W., Allen, L.A. (2010) “Multiple mechanisms of NADPH oxidase inhibition by Francisella tularensis.” J. Leukoc Biol. 88(4):791-805.
  20. Buchan, B.W.,  McCaffrey, R.L., Lindemann, S.R., Allen, L.A., Jones, B.D. (2009) “Identification of migR, a regulatory element of the Francisella tularensis live vaccine strain iglABCD virulence operon required for normal replication and trafficking in macrophages.” Infect. Immun. 77(6):2517-2529.
  21. Schulert, G.S., McCaffrey, R.L., Buchan, B.W., Lindemann, S.R., Hollenback, C., Jones, B.D., Allen, L.A. (2009) “Francisella tularensis genes required for inhibition of the neutrophil respiratory burst and intramacrophage growth identified by random transposon mutagenesis of strain LVS.” Infect. Immun. 77(4):1324-1336.
  22. Lindemann, S.R., McLendon, M.K., Apicella, M.A., Jones, B.D. (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.


NUTR 59000 Techniques in Microbial Genomics and Metabolism.
Stephen Lindemann
Assistant Professor of Food and Nutrition Science

Office: NLSN 3215
Address: 745 Agriculture Mall Drive, West Lafayette, IN 47907
Phone: 765-494-9207

Department of Nutrition Science, 700 W. State Street, West Lafayette, IN 47907-2059(765) 494-8228, Fax: (765) 494-0674

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