Scott Hamilton-Brehm | Microbiology | SIU

Southern Illinois University



College of Science

Scott Hamilton-Brehm

Assistant Professor

Scott Hamilton-Brehm


Life Science III 1009
Phone: 618-453-3818
Fax: 618-453-8036

Research Specialities: Anaerobic and aerobic cultivation of microorganisms, environmental sampling. 


PhD, 2008, University of Georgia, Athens, GA

Courses Taught:

MICR 201: Elementary Microbiology
MICR 423: Geomicrobiology

Research Interests:

My lab focuses on microbial diversity in oligotrophic, geothermal, and ‘ancient’ environments. Microbes from these environments have deep implications that could greatly influence applied research through the enhancement of fundamental knowledgebase in extant/extinct microbial biomes, characterizing pathways for alternative biofuels, and piecing together the mechanisms of the origins of life.

While my research interests cover many areas of microbial biochemistry, the two research themes that my lab is currently pursuing are 1) Characterizing deep subsurface microbes and 2) Screening oral microbiota and sequencing mitochondrial genomes of ancient peoples of Southwestern North America.

Subsurface Microbes. There is a vast reservoir of prokaryotic microbes that very likely amount to more biomass than all the life on the surface of the Earth. Subsurface microbial metabolisms typically mean subsisting on a carbon and energy source not driven by the sun. We know very little about the vast subsurface microbial ecosystem. I have isolated a bacterium, strain name DRI-14, that belongs to the class Clostridia from a water sample taken from over 900 meters underground in the Nevada desert. By 16S rRNA gene sequence this microorganism appears to be a novel family or order that is found around the subsurface world (Japan, S. Africa, Denmark, and North America). While DRI-14 appears to be a significant subsurface environmental bacterium by Illumina sequencing, the method by which this microorganism derives energy and carbon is poorly understood. By characterizing DRI-14’s metabolism, we can determine the role DRI-14 plays in subsurface carbon cycling. I am looking for a determined graduate student who is persistent to pursue cultivation of fastidious bacteria, mapping metabolic pathways, and who enjoys discovering answers.

Ancient DNA. Cold and desert environments can preserve biological samples for thousands of years (half-life of ~3,000 years for 100 bp DNA in bone) by slowing the decomposition processes. Coprolites (desiccated feces) and quids (chewed plant material) offer a window through time to view the microbiota and mitochondrial DNA of ancient humans and animals. In a preliminary study, an undergraduate and I have been analyzing a subset of 21 quids from a rock shelter located in the Spring Mountains of Nevada. The plant materials of the quids were radiocarbon dated to ~300 to 1000 years before present. Total DNA was extracted from the chewed plant material and human mitochondrial DNA (hu-mtDNA) was amplified using specific primers by PCR. Through sequencing small sections of the hu-mtDNA we were able to analyze the maternal-inherited single nucleotide polymorphisms (SNPs) found in specific haplogroups known to be found in populations of Native American people. The next step will be to completely sequence the hu-mtDNA using next generation sequencing (NGS) to map the range of haplogroups present in the quid collection. Furthermore it may be possible to determine the human oral microbiota of these ancient people who chewed the quids using NGS. This research will provide a genetic pattern of occupancy over time and a comparison of ancient microbial oral biomes to the present.  I am looking for an inquisitive and dynamic graduate student with experience in microbiology, molecular biology, and interest in archaeology and anthropology.

Undergraduates who want to learn laboratory research techniques and are interested in contributing to ongoing projects are encourage discuss ideas/opportunities with me.


Articles in Professional Journals

  • Sackett JD, Huerta DC, Kruger BR, Hamilton-Brehm SD, Moser DP. 2018. A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog. PLoS ONE 13(3): e0194404. Link
  • Hamilton-Brehm SD, Hristova LT, Edwards SR, Wedding JR, Snow M, Kruger BR, Moser DP. Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA. PloS one. 2018;13(3):e0194223. Link
  • Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG. A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E. Biotechnology for biofuels. 2014 Dec;7(1):165.
  • Vishnivetskaya TA, Hamilton-Brehm SD, Podar M, Mosher JJ, Palumbo AV, Phelps TJ, Keller M, Elkins JG. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park. Microbial ecology. 2015 Feb 1;69(2):333-45.
  • Wan, Q., Kovalevsky, A., Zhang, Q., Hamilton-Brehm, S., Upton, R., Weiss, K.L., Mustyakimov, M., Graham, D., Coates, L. and Langan, P. 2014. Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. Mar 1; 69(Pt 3):320-3.
  • Elkins, J.G., Hamilton-Brehm, S.D., Lucas S., Han J., Lapidus A., Cheng J.F., Goodwin L.A., Pitluck, S., Peters, L., Mikhailova, N., Davenport, K.W., Detter, J.C., Han, C.S., Tapia, R., Land, M.L., Hauser, L., Kyrpides, N.C., Ivanova, N.N., Pagani, I., Bruce, D., Woyke, T. and Cottingham, R.W. 2013. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T. Genome. Announc. Apr 11; 1(2).
  • Wan, Q., Zhang, Q., Hamilton-Brehm, S.D., Weiss, K., Mustyakimov, M., Coates, L., Langan, P., Graham, D.E., Kovalevsky, A. 2013. X-ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications for the Catalytic Mechanism of Retaining Glycoside Hydrolases. Acta. Crystallogr. D. Biol. Crystallogr. 2014 Jan; 70(Pt 1):11-23.
  • Wang, Z.W., Lee, S.H., Elkins, J.G., Li, Y., Hamilton-Brehm, S. and Morrell-Falvey, J.L. 2013. Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy. J. Environ. Sci. (China). 2013 May 1;25(5):849-56.
  • Hamilton-Brehm, S.D., Gibson, R.A., Green, S.J., Hopmans, E.C., Shields, J.P. and Elkins, J.G. 2013. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park. Extremophiles. Mar; 17(2):251-63. Link
  • Yee, K.L., Rodriguez, M. Jr, Tschaplinski, T.J., Engle, N.L., Martin, M.Z., Fu C., Wang, Z.Y., Hamilton-Brehm, S.D. and Mielenz J.R. 2012. Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach. Biotechnol. Biofuels. Nov 12; 5(1):81.
  • Blumer-Schuette, S.E., Giannone, R.J., Zurawski, J.V., Ozdemir, I., Ma, Q., Yin, Y., Xu, Y., Kataeva, I., Poole, F.L. 2nd, Adams, M.W., Hamilton-Brehm, S.D., Elkins, J. G., Larimer, F. W., Land, M.L., Hauser, L.J., Cottingham, R.W., Hettich, R.L. and Kelly R.M. 2012. Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J. Bacteriol. Aug; 194(15):4015-28. Link
  • Hamilton-Brehm, S.D., Vishnivetskaya, T.A., Allman, S.L., Mielenz, J.R. and Elkins J.G. 2012. Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass derived substrates. Methods. Mol. Biol. 908:153-68.
  • Elkins, J. G., Lochner, A., Hamilton-Brehm, S.D., Davenport, K.W., Podar, M., Brown, S.D., Land, M.L., Hauser, L.J., Klingeman, D.M., Raman, B., Goodwin, L.A., Tapia, R., Meincke, L.J., Detter, C.J., Bruce, D.C., Han, C.S., Palumbo, A.V., Cottingham, R.W., Keller, M. and Graham, D.E. 2010. Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47. J. Bacteriol. 192(22): 6099-100.
  • Wang, Z.W., Hamilton-Brehm S.D., Lochnerm A., Elkinsm J.G. and Morrell-Falvey, J.L. 2010. Hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis. Bioresour. Technol. 102(2011): 3155-3162. Link
  • Hamilton-Brehm, S.D., Mosher, J.J., Vishnivetskaya, T., Podar, M., Carroll, S., Allman, S., Phelps, T. J., Keller, M. and Elkins, J. G. 2010. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl. Environ. Microbiol. 76(4):1014-20.
  • Yang, S.J., Kataeva, I., Hamilton-Brehm, S.D., Engle, N.L., Tschaplinski, T.J., Doeppke, C., Davis, M., Westpheling, J. and Adams, M.W.W. 2009. Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Appl. Environ. Microbiol. 75(14):4762-9.
  • Hamilton-Brehm, S.D., Schut, G.J. and Adams, M.W. 2009. Antimicrobial Activity of the Iron Sulfur Nitroso Compound Roussin’s Black Salt (Fe4S3(NO)7) on the Hyperthermophilic Archaeon Pyrococcus furiosus. Appl. Environ. Microbiol. 75(7):1820-5.
  • Adams, M.W.W., Jenney, F.E. Jr., Chou, C.J., Hamilton-Brehm, S., Poole, F.L., Shockley, K.R., Tachdjian, S. and Kelly R.M. 2007. Transcriptomics, Proteomics and Structural Genomics of Pyrococcus furiosus. Archaea: Evolution, Physiology, and Molecular Biology (Garrett, R. and Klenk, H. P., eds.), Blackwell, 239-246.
  • Lee, H.S., Shockley, K.R., Schut, G.J., Conners, S.B., Montero, C.I., Johnson, M.R., Chou, C.J., Bridger, S.L., Wigner, N., Brehm, S.D., Jenney, F.E. Jr., Comfort, D.A., Kelly, R.M. and Adams, M.W. 2006. Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol 188:2115-25.
  • Hamilton-Brehm, S.D., Schut, G.J. and Adams, M.W. 2005. Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment. J. Bacteriol 187:7492-9.
  • Weinberg, M.V., Schut, G.J., Brehm, S., Datta, S. and Adams M.W. 2005. Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins. J. Bacteriol 187:336-48.
  • Schut, G.J., Brehm, S.D., Datta, S. and Adams M. W. 2003. Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J. Bacteriol 185:3935-47.