Argonne National Laboratory

Theodore Flynn

Theodore M. Flynn

Assistant Staff Scientist

Dr. Flynn is a microbial ecologist working in the Biosciences Division who specializes in understanding the links between microorganisms and biogeochemical cycles. His academic training was a combination geochemical modeling and hydrogeology with molecular microbial ecology, metagenomics, and microbial physiology. His research focuses on the biogeochemical cycling of elements, particularly Fe, S and C, and the ecological mechanisms that control the structure and function of microbial communities in such diverse environments as aquifers, wetlands, and the mammalian gut. 

Dr. Flynn came to Argonne in 2011 as a Director's Postdoctoral Fellow in the Molecular Environmental Science group working with Dr. Ken Kemner and Dr. Ed O'Loughlin. Following his postdoctoral fellowship, he joined the Computation Institute at The University of Chicago as a researcher while continuing his work at Argonne with both the MES group as well as Dionysios Antonopoulos’ Microbial Systems group. As an Argonne staff scientist, he collaborates with these and other members of the Argonne Biosciences Division such as Jack Gilbert

Dr. Flynn is an expert in molcular microbial ecology and has extensive experience in both laboratory work (extraction of DNA from diverse environmental matrices, PCR, and high-throughput DNA sequencing) as well as computation (phylogenomic analysis of amplicon and whole-genome shotgun sequence data, metagenomics, genome assembly, and multivariate statistical analysis of large microbial community datasets). He also has expertise in geochemical modeling, cultivation of aerobic and anaerobic bacteria, and analytical geochemistry (ion and gas chromatography). 

Dr. Flynn is currently an editor for the journal mSystems, published by the American Society for Microbiology. He was the co-organizer of the 2014 Midwest Geobiology Symposium and is a member of the International Society for Microbial Ecology, the American Society for Microbiology, the American Geophysical Union, and the Geochemical Society. 


Ph.D., Department of Geology, University of Illinois at Urbana-Champaign, 2011

B.Sc., Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 2004

Select Publications

Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O’Loughlin EJ, Cann IKO, Mackie RM, Locke RA, Weber JR, Egan SM, Fouke BW (2016) “Isolation and characterization of Orenia metallireducens sp. nov., a novel metal-reducing Firmicute from the deep subsurface,” Applied and Environmental Microbiology. doi: 10.1128/aem.02382-16.

Dong Y, Sanford RA, Boyanov MI, Kemner KM, Flynn TM, O’Loughlin EJ, Locke RA, Weber JR, Egan SM, Fouke BW (2016) “Tepidibacillus decaturensis sp. nov.: an anaerobic, moderately thermophilic iron-reducing bacterium isolated from a depth of 1.7 km in the Illinois Basin, USA,” International Journal of Systematic and Evolutionary Microbiology. doi: 10.1099/ijsem.0.001295.

Leavitt WD, Flynn TM, Suess MK, Bradley AS (2016) “Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios in Desulfovibrio alaskensis G20,” Frontiers in Microbiology, Vol. 7(918), p. 1–14.

Houghton JL, Foustoukos D, Flynn TM, Vetriani C, Bradley AS, Fike DA (2016) "Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry," Environmental Microbiology. doi: 10.1111/1462-2920.13232.

Kirk MF, Wilson BH, Marquart KA, Zeglin LH, Vinson DS, Flynn TM (2015) “Solute concentrations influence microbial methanogenesis in coal-bearing strata of the Cherokee basin, USA,” Frontiers in Microbiology, Vol. 6(1287), p. 1–14.

Bunker JJ, Flynn TM, Koval JC, Shaw DG, Meisel M, McDonald BD, Ishizuka IE, Dent AL, Wilson PC, Jabri B, Antonopoulos DA, Bendelac A (2015) "Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A," Immunity, Vol. 43(3), p. 541–553.

Flynn TM, O’Loughlin EJ, Mishra B, DiChristina TJ, Kemner KM (2014) “Sulfur-mediated electron shuttling during bacterial iron reduction,” Science, Vol. 344(6187), p. 1039–1042. 

Dong Y, Kumar CG, Chia N, Kim P-J, Miller PA, Price ND, Cann IKO, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong P-Y, Tamaki H, Liu W-T, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Mackie RI, Fouke BW (2014) “Halomonas sulfidaeris-dominated microbial communities inhabits a 1.8 km-deep subsurface Cambrian sandstone reservoir,” Environmental Microbiology, Vol. 16(6), p. 1695–1708. 

Flynn TM, Sanford RA, Ryu H, Bethke CM, Levine AD, Ashbolt NJ, Santo Domingo JW (2013) “Functional microbial diversity and substrate utilization explain groundwater chemistry in a pristine aquifer,” BMC Microbiology, Vol. 13(1), p. 146(1–15). 

O’Loughlin EJ, Boyanov MI, Flynn TM, Gorski CA, Hofmann SM, McCormick ML, Scherer MM, Kemner KM (2013) “Effects of bound phosphate on the bioreduction of lepidocrocite (γ-FeOOH) and maghemite (γ-Fe2O3) and the formation of secondary minerals,” Environmental Science & Technology, Vol. 47(16), p. 9157–9166. 

Flynn TM, Sanford RA, Bethke CM, Iker B, Levine AD, Ashbolt NJ, Santo Domingo JW (2012) “The active bacterial community in a pristine, confined aquifer,” Water Resources Research, Vol. 48, p. W09510. 

Bethke CM, Sanford RA, Kirk MF, Jin Q, Flynn TM (2011) “The thermodynamic ladder in geomicrobiology,” American Journal of Science, Vol. 311(3), p. 183–210. 

Flynn TM, Sanford RA, Bethke CM (2008) “Attached and suspended microbial communities in a pristine confined aquifer,” Water Resources Research, Vol. 44, p. W07425.