Microbiome and Metabolites


A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.                              Dodd, D., Spitzer, M. H., Van Treuren, W., Merrill, B. D., Hryckowian, A. J., Higginbottom, S. K., Le, A., Cowan, T. M., Nolan, G. P., Fischbach, M. A., and Sonnenburg, J. L.                                                                                       Nature. 2017 551(7682): 648-652. [article link]

Modulation of a circulating uremic solute via rational genetic manipulation of the gut microbiota.                      Devlin, A. S., Marcobal, A., Dodd, D., Nayfach, S., Plummer, N., Meyer, T., Pollard, K. S., Sonnenburg, J. L., and Fischbach, M. A.                                                                                                                                                Cell Host & Microbe. 2016 S1931-3128(16): 30447-30454. [article link]

Your gut microbiome, deconstructed.                                                                                                                           Dodd, D., Tropini, C., and Sonnenburg, J. I.                                                                                                                  Nature Biotechnology 2015 33(12): 1238-1240. [article link]

 

Energy capture from polysaccharides


Enzymatic mechanism for arabinan degradation and transport in the thermophilic bacterium Caldanaerobius polysaccharolyticus.                                                                                                                                                       Wefers, D., Dong, J., Abdel-Hamid, A. M., Paul, H. M., Pereira, G. V., Han, Y., Dodd, D., Baskaran, R., Mayer, B., Mackie, R. I., Cann, I.                                                                                                                                                       Applied and Environmental Microbiology 2017 83(18): e00794-17. [article link]

Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17.                                                                                                                                                               Chekan, J. R., Kwon, I. H., Agarwal, V., Dodd, D., Revindran, V., Mackie, R. I., Cann, I., and Nair, S. K.                  Journal of Biological Chemistry 2014 289(50): 34965-34977. [article link]

Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.                                                                                                                 Zhang, M., Chekan, J. R., Dodd, D., Hong, P. Y., Radlinski, L., Revindran, V., Nair, S. K., Mackie, R. I., and Cann, I.                                                                                                                                                        Proceedings of the National Academy of Science of the United States of America 2014 111(35): e3708-17. [article link]

Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.                                                                                                                                         Hong, P. Y., Iakiviak, M., Dodd, D., Zhang, M., Mackie, R. I., Cann, I.                                                             Applied and Environmental Microbiology 2014 80(7): 2084-2093. [article link]

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.                                                                                                    Oyama, T., Schmitz, G. E., Dodd, D., Han, Y., Burnett, A., Nagasawa, N., Mackie, R. I., Nakamura, H., Morikawa, K., and Cann, I.                                                                                                                                                        PLoS One 2013 8(11): e80448. [article link]

Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii.                                                                                                                                                                          Su, X., Han, Y., Dodd, D., Moon, Y. H., Yoshida, S., Mackie, R. I., Cann, I. K.                                                 Applied and Environmental Microbiology 2013 79(5): 1481-1490. [article link]

Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.                                                                                                                                               Han, Y., Agarwal, V., Dodd, D., Kim, J., Bae, B., Mackie, R. I., Nair, S. K., Cann, I. K.                                   Journal of Biological Chemistry 2012 287(42): 34946-34960. [article link]

Biochemical characterization and relative expression levels of multiple carbohydrate esterases of the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate.                  Kabel, M. A., Yeoman, C. J., Han, Y., Dodd, D., Abbas, C. A., de Bont, J. A., Morrison, M., Cann, I. K., and Mackie, R. I.                                                                                                                                                         Applied and Environmental Microbiology 2011 77(16): 5671-5681. [article link]

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes.                  Dodd, D., Mackie, R. I., and Cann, I. K.                                                                                                          Molecular Microbiology 2011 79(2): 292-304. [article link]

Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules.                                                                                                                                Su, X., Agarwal, V., Dodd, D., Bae, B., Mackie, R. I., Nair, S. K., and Cann, I. K.                                           Journal of Biological Chemistry 2010 285(45): 34665-34676. [article link]

Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic Bacteroidetes.                                                                                                                                    Dodd, D., Moon, Y., Swaminathan, K., Mackie, R. I., and Cann, I. K.                                                              Journal of Biological Chemistry 2010 285(39): 30261-30273. [article link]

Comparative analysis of two thermostable enzymes exhibiting both beta-1,4-mannosidic and beta-1,4-glucosidic cleavage activities from Caldanaerobius polysaccharolyticus.                                                       Han, Y., Dodd, D., Schroeder, C. M., Mackie, R. I., and Cann, I. K.                                                                 Journal of Bacteriology 2010 192(16): 4111-4121. [article link]

Thermostable enzymes as biocatalysts in the biofuels industry.                                                                Yeoman, C., Han, Y., Dodd, D., Hespen, C. W., Ohene-Adjei, S., Schroeder, C. M., Mackie, R. I., and Cann, I. Advances in Applied Microbiology 2010 70: 1-55. [article link]

Functional diversity of four glycoside hydrolase family 3 enzymes from the rumen bacterium, Prevotella bryantii B14.                                                                                                                                                           Dodd, D., Kiyonari, S., Mackie, R. I., and Cann, I. K.                                                                                        Journal of Bacteriology 2010 192(9): 2335-2345. [article link]

Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23.                                                                                        Dodd, D., Kocherginskaya, S., Spies, M. A., Abbas, C. A., Beery, K. E., Mackie, R. I., and Cann, I. K.       Journal of Bacteriology 2009 191(10): 3328-3338. [article link]

Enzymatic deconstruction of xylan for biofuel production.                                                                              Dodd, D. and I. K. Cann.                                                                                                                                       Global Change Biology Bioenergy. 2009 1(1): 2-17. [article link]

 

Clinical Assay Development


Clinical utility of an ultrasensitive late night salivary cortisol assay by tandem mass spectrometry.          Sturmer, L. R., Dodd, D., Chao, C. S., and Shi, R. Z.                                                                                           Steroids 2018 129: 35-40. [article link]

 

Microbial Pathogenesis


Determinants of catalytic power and ligand binding in glutamate racemase.                                                     Spies, M. A., Reese, J. G., Dodd, D., Pankow, K. L., Blanke, S. R., and Baudry, J. Y.                                        Journal of the American Chemical Society 2009 131(14): 5274-5284. [article link]

Functional comparison of the Bacillus anthracis glutamate racemases.                                                             Dodd, D. Reese, J. G., Louer, C. R., Ballard, J. D., Spies, M. A., and Blanke, S. R.                                           Journal of Bacteriology 2007 189(14): 5265-5275. [article link]