Research Interests

Anaerobic Microbiology, Microbial Ecology and Evolution, Genomics, Bioinformatics

Microbiome research is among the most exciting and promising areas of science today due to many technological advances, particular in high throughput DNA and RNA sequencing, that allow us to determine in complex environments which microbes are present and their metabolism. A prominent component of our research is using genomic and computational methods to understand the ecology and evolution of gut and forest soil microbiomes. Our laboratory is set up for standard molecular biology and microbial physiology research and contains specialized equipment for isolating and culturing anaerobic bacteria. The research we do has led to the discovery of new bacterial species and metabolic processes that have have far ranging impacts from developing probiotics to understanding climate change. See our laboratory web site for a description of current projects.

Representative Publications

Sun, Z., Blanchard, J.L. 2014. Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PLOS ONE, Mar 3;9(3): e88837.

Mukherjee, S., Thompson, L.K., Godin, S., Schackwitz, W., Lipzen, A., Martin, J., Blanchard, J.L. 2014. Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans. PLOS ONE, 9(1): e86731.

Biddle, A.S., Black, S.J., Blanchard, J.L. 2013. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLOS ONE, PLoS ONE 8(10): e77599

Abdul-Rahman, F., Petit, E., Blanchard, J.L. 2013. The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly. J. Phylogen. Evolution. Biol., 1: e118.

Biddle, A.S., Stewart, L., Blanchard, J.L., Leschine, S.B. 2013. Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities. Diversity, 5(3), 627-640.

Tolonen, A.C., Petit, E., Blanchard, J.L., Warnick, T., Leschine, S.B. 2013. "Technologies to Study Plant Biomass Fermentation using the Model Bacterium Clostridium phytofermentans." Chapt 7 (pp 114-139) in "Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems". Edited by Jianzhong Sun, Shi-You Ding and Joy Peterson. The Royal Society of Chemistry.

Petit, E., Latouf, W., Coppi, M., Currie, D., Rhomasko, I., Desphande, S., Haas, K., Alvelo-Maurosa, J.G., Wardman, C., Schnell, D., Leschine, L., Blanchard, J. 2013. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS One, 8(1): e54337.

Damery, D., Hayes, J., Blanchard, J.L. 2010. The potential for production of ethanol from woody biomass by the microbe Clostridium phytofermentans. Wood Structures and Properties '10. Edited by Kúdela and Lagaňa. Arbora Publishers. p21-25.

Hu, J., Blanchard, J.L. 2009. Environmental sequence data from the Sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus are not a harbinger for an escalation in genetic drift. Molecular Biology and Evolution, Jan;26(1): 5-13.

Lu, S., Becker, K.A., Hagen, M.J., Yan, H., Roberts, A.L., Mathews, L.A., Schneider, S.S., Siegelmann, H.T., Macbeth, K.J., Tirrell, S.M., Blanchard, J.L., Jerry, D.J. 2008. Transcriptional Responses to Estrogen and Progesterone in Mammary Gland Identify Networks Regulating p53 Activity. Endocrinology, Oct;149(10): 4809-20. Epub 2008 Jun 12.

Blanchard, J.L., Chen, W., Conlon, E.M., Pomposiello, P.J. 2007. Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE, 2(11): e1186.

Conlon, E.M., Alpargu, G., Blanchard, J.L. 2006. Comparative genomics approaches for identifying genetic regulatory networks. Chance, 19:45-48.

Richards, T.A., Dacks, J.B., Campbell, S.A., Blanchard, J.L., Foster, P.G., McLeod, R., Roberts, C.W. 2006. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot Cell, 5: 1517-31.

Blanchard, J.L. 2004. Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change. Field Crops Research, 90: 117-131.

de Visser, A.J.M., Hermisson, J., Wagner, G.P., Ancel, L.W., Bagheri-Chaichian, H., Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G,, Hansen, T.F., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A., Whitlock, M.C. 2003. Evolution and detection of genetic robustness. Evolution, 57: 1959-1972.

Kuffner, R.M., Gonzales, M, Steadman P, Wlodek, D.K., Jankowitz, R.J., Boinoff, J.R., Montoya, A.L., Peterson, T.F., Bulmore, D.L., Blanchard. J.L. 2002. PathDB. Nucleic Acids Research Database Issue.

Brinkman, F.S.L., Blanchard, J.L., Greberg, H., Wan, I., De Koning, A., Av-Gay, Y., Brunham, R.C., Fernandez, R.C., Finlay, B.B., Otto, S.P., Ouellette, B.F., Keeling, P., Hancock, R.E.W., Rose, A.M., S.J.M. Jones. 2002. Plant-like genes in Chlamydia species reflect Chlamydia’s ancestral relationship with cyanobacteria and the chloroplast. Genome Research, 12: 1159-67.

Blanchard, J.L., Lynch, M. 2000. Organelle Genes: why do organellar genes end up in the nucleus? Trends in Genetics, 16: 315-320.

de Visser, A.J.M., Zeyl, C.W., Gerrish, P.J., Blanchard, J.L., Lenski, R.E. 1999. Diminishing returns from mutation supply rate in asexual populations. Science, 283: 404-406.

Lynch, M., Blanchard, J.L., Houle, D., Kibota, T., Schultz, S., Vassileva, L., Willis, J. 1999. Spontaneous deleterious mutation. Evolution, 53: 645-663.

Blanchard, J.L., Hicks, J.S. 1999. The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. Journal of Eukaryotic Microbiology, 46: 367-375.

Lynch, M., Blanchard, J.L. 1998. Deleterious mutation accumulation in organelle genomes. Genetica, 102/103: 29-39.

Bruns, B.U., Blanchard, J.L., Schmidt, G.W. 1998. On the modulation of thylakoid structure and function upon adaptation to prolonged nitrogen-deficiency. Pp. 3081-3086 in Photosynthesis: Mechanisms and Effects (IV), G. Garab (ed), Kluwer Acad. Publ., Dordrecht.

Blanchard, J.L., Schmidt, G.W. 1996. Mitochondrial DNA migration events in yeast and mammals: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Molecular Biology and Evolution, 13: 537-548.

Blanchard, J.L., Schmidt, G.W. 1995. Pervasive migration of organellar DNAto the nucleus in plants. Journal of Molecular Evolution, 41: 397-406.